[{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1186/s12915-024-01956-4","has_accepted_license":"1","publication_identifier":{"eissn":["1741-7007"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-08-12T08:14:44Z","citation":{"short":"H. NAGAI, Y. Adachi, T. Nakasugi, E. Takigawa, J. Ui, T. Makino, M. Miura, Y.I. Nakajima, BMC Biology 22 (2024).","ama":"NAGAI H, Adachi Y, Nakasugi T, et al. Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. BMC Biology. 2024;22. doi:10.1186/s12915-024-01956-4","chicago":"NAGAI, HIROKI, Yuya Adachi, Tenki Nakasugi, Ema Takigawa, Junichiro Ui, Takashi Makino, Masayuki Miura, and Yu Ichiro Nakajima. “Highly Regenerative Species-Specific Genes Improve Age-Associated Features in the Adult Drosophila Midgut.” BMC Biology. Springer Nature, 2024. https://doi.org/10.1186/s12915-024-01956-4.","ista":"NAGAI H, Adachi Y, Nakasugi T, Takigawa E, Ui J, Makino T, Miura M, Nakajima YI. 2024. Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. BMC Biology. 22, 157.","apa":"NAGAI, H., Adachi, Y., Nakasugi, T., Takigawa, E., Ui, J., Makino, T., … Nakajima, Y. I. (2024). Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-024-01956-4","mla":"NAGAI, HIROKI, et al. “Highly Regenerative Species-Specific Genes Improve Age-Associated Features in the Adult Drosophila Midgut.” BMC Biology, vol. 22, 157, Springer Nature, 2024, doi:10.1186/s12915-024-01956-4.","ieee":"H. NAGAI et al., “Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut,” BMC Biology, vol. 22. Springer Nature, 2024."},"article_number":"157","quality_controlled":"1","article_type":"original","month":"08","_id":"17408","abstract":[{"text":"Background: The remarkable regenerative abilities observed in planarians and cnidarians are closely linked to the active proliferation of adult stem cells and the precise differentiation of their progeny, both of which typically deteriorate during aging in low regenerative animals. While regeneration-specific genes conserved in highly regenerative organisms may confer regenerative abilities and long-term maintenance of tissue homeostasis, it remains unclear whether introducing these regenerative genes into low regenerative animals can improve their regeneration and aging processes.\r\n\r\nResults: Here, we ectopically express highly regenerative species-specific JmjC domain-encoding genes (HRJDs) in Drosophila, a widely used low regenerative model organism. Surprisingly, HRJD expression impedes tissue regeneration in the developing wing disc but extends organismal lifespan when expressed in the intestinal stem cell lineages of the adult midgut under non-regenerative conditions. Notably, HRJDs enhance the proliferative activity of intestinal stem cells while maintaining their differentiation fidelity, ameliorating age-related decline in gut barrier functions.\r\n\r\nConclusions: These findings together suggest that the introduction of highly regenerative species-specific genes can improve stem cell functions and promote a healthy lifespan when expressed in aging animals.","lang":"eng"}],"intvolume":" 22","file":[{"access_level":"open_access","date_updated":"2024-08-12T08:14:44Z","relation":"main_file","file_name":"2024_BMCBio_Nagai.pdf","checksum":"318759626ec83b13f909c82904393ef1","creator":"dernst","file_size":3345718,"date_created":"2024-08-12T08:14:44Z","success":1,"content_type":"application/pdf","file_id":"17417"}],"department":[{"_id":"XiFe"}],"publication":"BMC Biology","volume":22,"external_id":{"isi":["001282893200001"],"pmid":["39090637"]},"date_updated":"2025-09-08T08:51:29Z","oa":1,"publisher":"Springer Nature","publication_status":"published","status":"public","date_created":"2024-08-11T22:01:11Z","acknowledgement":"We thank I. Miguel-Aliaga, N. Shinoda, M. Furuse, Y. Izumi, BDSC, Kyoto Stock Center, Drosophila Genomics Resource Center (DGRC), and Developmental Studies Hybridoma Bank (DSHB) for fly stocks and reagents.\r\nThis work was supported by JSPS/MEXT KAKENHI (grant numbers JP22J01430 to H.N., JP21H04774, JP23H04766, JP24H00567 to M.M., and JP17H06332, JP22H02762, JP23K18134, JP23H04696 to Y.N.), AMED-Aging (JP21gm5010001 to M.M.), AMED-PRIME (JP22gm6110025 to Y.N.), and Sadako O. Hirai Ban Award for Young Researchers (H.N.)","year":"2024","author":[{"orcid":"0000-0003-1671-9434","first_name":"Hiroki","full_name":"Nagai, Hiroki","last_name":"Nagai","id":"608df3e6-e2ab-11ed-8890-c9318cec7da4"},{"last_name":"Adachi","first_name":"Yuya","full_name":"Adachi, Yuya"},{"full_name":"Nakasugi, Tenki","first_name":"Tenki","last_name":"Nakasugi"},{"last_name":"Takigawa","first_name":"Ema","full_name":"Takigawa, Ema"},{"last_name":"Ui","first_name":"Junichiro","full_name":"Ui, Junichiro"},{"full_name":"Makino, Takashi","first_name":"Takashi","last_name":"Makino"},{"full_name":"Miura, Masayuki","first_name":"Masayuki","last_name":"Miura"},{"last_name":"Nakajima","full_name":"Nakajima, Yu Ichiro","first_name":"Yu Ichiro"}],"oa_version":"Published Version","article_processing_charge":"Yes","title":"Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut","pmid":1,"type":"journal_article","day":"02","ddc":["570"],"scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"date_published":"2024-08-02T00:00:00Z"},{"year":"2024","author":[{"last_name":"Van Vliet","full_name":"Van Vliet, Sven","first_name":"Sven"},{"first_name":"Jinyu","full_name":"Sheng, Jinyu","id":"639f0526-27c9-11ee-95a6-966cd7f102d8","last_name":"Sheng"},{"last_name":"Stindt","first_name":"Charlotte N.","full_name":"Stindt, Charlotte N."},{"last_name":"Feringa","first_name":"Ben L.","full_name":"Feringa, Ben L."}],"oa_version":"Published Version","article_processing_charge":"Yes","title":"All-visible-light-driven salicylidene schiff-base-functionalized artificial molecular motors","pmid":1,"publisher":"Springer Nature","publication_status":"published","status":"public","date_created":"2024-08-11T22:01:11Z","acknowledgement":"Financial support from the Netherlands Organization for Scientific Research (NWO-CW), the Dutch Ministry of Education, Culture and Science (Gravitation program No.024.001.035), the China Scholarship Council (CSC PhD Fellowship No.201808330459 to J. S.). We thank Dr. Youxin Fu, Dr. Alexander Ryabchun, Dr. Wojciech Danowski, Dr. Jianyu Zhang and Yahan Shan from University of Groningen for their help to this project and fruitful discussions.","date_published":"2024-07-31T00:00:00Z","type":"journal_article","ddc":["540"],"day":"31","scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Van Vliet S, Sheng J, Stindt CN, Feringa BL. All-visible-light-driven salicylidene schiff-base-functionalized artificial molecular motors. Nature Communications. 2024;15. doi:10.1038/s41467-024-50587-4","short":"S. Van Vliet, J. Sheng, C.N. Stindt, B.L. Feringa, Nature Communications 15 (2024).","ieee":"S. Van Vliet, J. Sheng, C. N. Stindt, and B. L. Feringa, “All-visible-light-driven salicylidene schiff-base-functionalized artificial molecular motors,” Nature Communications, vol. 15. Springer Nature, 2024.","mla":"Van Vliet, Sven, et al. “All-Visible-Light-Driven Salicylidene Schiff-Base-Functionalized Artificial Molecular Motors.” Nature Communications, vol. 15, 6461, Springer Nature, 2024, doi:10.1038/s41467-024-50587-4.","apa":"Van Vliet, S., Sheng, J., Stindt, C. N., & Feringa, B. L. (2024). All-visible-light-driven salicylidene schiff-base-functionalized artificial molecular motors. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-50587-4","ista":"Van Vliet S, Sheng J, Stindt CN, Feringa BL. 2024. All-visible-light-driven salicylidene schiff-base-functionalized artificial molecular motors. Nature Communications. 15, 6461.","chicago":"Van Vliet, Sven, Jinyu Sheng, Charlotte N. Stindt, and Ben L. Feringa. “All-Visible-Light-Driven Salicylidene Schiff-Base-Functionalized Artificial Molecular Motors.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50587-4."},"file_date_updated":"2024-08-12T08:23:10Z","article_number":"6461","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1038/s41467-024-50587-4","has_accepted_license":"1","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["001282384300020"],"pmid":["39085193"]},"date_updated":"2025-09-08T08:52:15Z","oa":1,"article_type":"original","month":"07","abstract":[{"text":"Light-driven rotary molecular motors are among the most promising classes of responsive molecular machines and take advantage of their intrinsic chirality which governs unidirectional rotation. As a consequence of their dynamic function, they receive considerable interest in the areas of supramolecular chemistry, asymmetric catalysis and responsive materials. Among the emerging classes of responsive photochromic molecules, multistate first-generation molecular motors driven by benign visible light remain unexplored, which limits the exploitation of the full potential of these mechanical light-powered systems. Herein, we describe a series of all-visible-light-driven first-generation molecular motors based on the salicylidene Schiff base functionality. Remarkable redshifts up to 100 nm in absorption are achieved compared to conventional first-generation motor structures. Taking advantage of all-visible-light-driven multistate motor scaffolds, adaptive behaviour is found as well, and potential application in multistate photoluminescence is demonstrated. These functional visible-light-responsive motors will likely stimulate the design and synthesis of more sophisticated nanomachinery with a myriad of future applications in powering dynamic systems.","lang":"eng"}],"_id":"17409","intvolume":" 15","file":[{"checksum":"4aca2ea30fe529947cb2f4c7fc2af2df","creator":"dernst","content_type":"application/pdf","success":1,"file_size":1355696,"date_created":"2024-08-12T08:23:10Z","file_id":"17418","access_level":"open_access","date_updated":"2024-08-12T08:23:10Z","relation":"main_file","file_name":"2024_NatureComm_vanVliet.pdf"}],"department":[{"_id":"RaKl"}],"publication":"Nature Communications","volume":15,"DOAJ_listed":"1"},{"citation":{"ama":"Schmidt P, Claessen R, Higgins G, et al. Remote sensing of a levitated superconductor with a flux-tunable microwave cavity. Physical Review Applied. 2024;22. doi:10.1103/PhysRevApplied.22.014078","short":"P. Schmidt, R. Claessen, G. Higgins, J. Hofer, J.J. Hansen, P. Asenbaum, M. Zemlicka, K. Uhl, R. Kleiner, R. Gross, H. Huebl, M. Trupke, M. Aspelmeyer, Physical Review Applied 22 (2024).","ieee":"P. Schmidt et al., “Remote sensing of a levitated superconductor with a flux-tunable microwave cavity,” Physical Review Applied, vol. 22. American Physical Society, 2024.","chicago":"Schmidt, Philip, Remi Claessen, Gerard Higgins, Joachim Hofer, Jannek J. Hansen, Peter Asenbaum, Martin Zemlicka, et al. “Remote Sensing of a Levitated Superconductor with a Flux-Tunable Microwave Cavity.” Physical Review Applied. American Physical Society, 2024. https://doi.org/10.1103/PhysRevApplied.22.014078.","mla":"Schmidt, Philip, et al. “Remote Sensing of a Levitated Superconductor with a Flux-Tunable Microwave Cavity.” Physical Review Applied, vol. 22, 014078, American Physical Society, 2024, doi:10.1103/PhysRevApplied.22.014078.","apa":"Schmidt, P., Claessen, R., Higgins, G., Hofer, J., Hansen, J. J., Asenbaum, P., … Aspelmeyer, M. (2024). Remote sensing of a levitated superconductor with a flux-tunable microwave cavity. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.22.014078","ista":"Schmidt P, Claessen R, Higgins G, Hofer J, Hansen JJ, Asenbaum P, Zemlicka M, Uhl K, Kleiner R, Gross R, Huebl H, Trupke M, Aspelmeyer M. 2024. Remote sensing of a levitated superconductor with a flux-tunable microwave cavity. Physical Review Applied. 22, 014078."},"article_number":"014078","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2401.08854","open_access":"1"}],"quality_controlled":"1","doi":"10.1103/PhysRevApplied.22.014078","publication_identifier":{"eissn":["2331-7019"]},"external_id":{"isi":["001284571700002"],"arxiv":["2401.08854"]},"date_updated":"2025-09-08T08:50:31Z","oa":1,"_id":"17410","abstract":[{"text":"We present a cavity-electromechanical system comprising a superconducting quantum interference device which is embedded in a microwave resonator and coupled via a pickup loop to a 6-μ⁢g magnetically levitated superconducting sphere. The motion of the sphere in the magnetic trap induces a frequency shift in the SQUID-cavity system. We use microwave spectroscopy to characterize the system, and we demonstrate that the electromechanical interaction is tunable. The measured displacement sensitivity of 10−7m/√Hz defines a path towards ground-state cooling of levitated particles with Planck-scale masses at millikelvin environment temperatures.","lang":"eng"}],"intvolume":" 22","article_type":"original","month":"07","volume":22,"department":[{"_id":"JoFi"}],"publication":"Physical Review Applied","year":"2024","author":[{"full_name":"Schmidt, Philip","first_name":"Philip","last_name":"Schmidt"},{"full_name":"Claessen, Remi","first_name":"Remi","last_name":"Claessen"},{"last_name":"Higgins","full_name":"Higgins, Gerard","first_name":"Gerard"},{"last_name":"Hofer","first_name":"Joachim","full_name":"Hofer, Joachim"},{"last_name":"Hansen","full_name":"Hansen, Jannek J.","first_name":"Jannek J."},{"first_name":"Peter","full_name":"Asenbaum, Peter","last_name":"Asenbaum"},{"first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Uhl","full_name":"Uhl, Kevin","first_name":"Kevin"},{"last_name":"Kleiner","full_name":"Kleiner, Reinhold","first_name":"Reinhold"},{"full_name":"Gross, Rudolf","first_name":"Rudolf","last_name":"Gross"},{"first_name":"Hans","full_name":"Huebl, Hans","last_name":"Huebl"},{"last_name":"Trupke","first_name":"Michael","full_name":"Trupke, Michael"},{"first_name":"Markus","full_name":"Aspelmeyer, Markus","last_name":"Aspelmeyer"}],"arxiv":1,"oa_version":"Preprint","title":"Remote sensing of a levitated superconductor with a flux-tunable microwave cavity","article_processing_charge":"No","publication_status":"published","publisher":"American Physical Society","date_created":"2024-08-11T22:01:12Z","status":"public","acknowledgement":"We gratefully acknowledge valuable discussions with Uros Delic, Lorenzo Magrini, and Corentin Gut. This work was supported by the European Union’s Horizon 2020 research and innovation program under Grant No. 863132 (iQLev) and No. 101080143 (SuperMeQ), the European Research Council under Grant No. 951234 (ERC Synergy QXtreme), the Austrian and Bavarian Academy of Sciences (Topical Team SGQ), the Alexander von Humboldt Foundation through a Feodor Lynen Fellowship (P.S.), the Swedish Research Council under Grant No. 2020-00381 (G.H.), and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Germany’s Excellence Strategy EXC-2111-390814868 (H.H., R.G.).","date_published":"2024-07-30T00:00:00Z","type":"journal_article","day":"30","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1"},{"publication_identifier":{"eissn":["2753-1457"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)"},"has_accepted_license":"1","doi":"10.1039/d4ya00334a","quality_controlled":"1","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-01-09T12:29:09Z","citation":{"ama":"Gong L, Zhao S, Yu J, et al. Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin. Energy Advances. 2024;3(9):2287-2294. doi:10.1039/d4ya00334a","short":"L. Gong, S. Zhao, J. Yu, J. Li, J. Arbiol, T. Kallio, M. Calcabrini, P.R. Martínez-Alanis, M. Ibáñez, A. Cabot, Energy Advances 3 (2024) 2287–2294.","ieee":"L. Gong et al., “Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin,” Energy Advances, vol. 3, no. 9. Royal Society of Chemistry, pp. 2287–2294, 2024.","ista":"Gong L, Zhao S, Yu J, Li J, Arbiol J, Kallio T, Calcabrini M, Martínez-Alanis PR, Ibáñez M, Cabot A. 2024. Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin. Energy Advances. 3(9), 2287–2294.","apa":"Gong, L., Zhao, S., Yu, J., Li, J., Arbiol, J., Kallio, T., … Cabot, A. (2024). Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin. Energy Advances. Royal Society of Chemistry. https://doi.org/10.1039/d4ya00334a","mla":"Gong, Li, et al. “Influence of the Catalyst Surface Chemistry on the Electrochemical Self-Coupling of Biomass-Derived Benzaldehyde into Hydrobenzoin.” Energy Advances, vol. 3, no. 9, Royal Society of Chemistry, 2024, pp. 2287–94, doi:10.1039/d4ya00334a.","chicago":"Gong, Li, Shiling Zhao, Jing Yu, Junshan Li, Jordi Arbiol, Tanja Kallio, Mariano Calcabrini, Paulina R. Martínez-Alanis, Maria Ibáñez, and Andreu Cabot. “Influence of the Catalyst Surface Chemistry on the Electrochemical Self-Coupling of Biomass-Derived Benzaldehyde into Hydrobenzoin.” Energy Advances. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4ya00334a."},"publication":"Energy Advances","department":[{"_id":"MaIb"}],"DOAJ_listed":"1","volume":3,"month":"09","article_type":"original","file":[{"file_name":"2024_EnergyAdvances_Gong.pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-01-09T12:29:09Z","file_id":"18812","date_created":"2025-01-09T12:29:09Z","file_size":1448762,"success":1,"content_type":"application/pdf","creator":"dernst","checksum":"4a49515ec90354d005852e741bff1d29"}],"intvolume":" 3","_id":"17412","abstract":[{"lang":"eng","text":"The electroreduction of biomass-derived benzaldehyde (BZH) provides a potentially cost-effective route to produce benzyl alcohol (BA). This reaction competes with the electrochemical self-coupling of BZH to hydrobenzoin (HDB), which holds significance as a biofuel. Herein, we demonstrate the selectivity towards one or the other product strongly depends on the surface chemistry of the catalyst, specifically on its ability to adsorb hydrogen, as showcased with Cu2S electrocatalysts. We particularly analyze the effect of surface ligands, oleylamine (OAm), on the selective conversion of BZH to BA or HDB. The effect of the electrode potential, electrolyte pH, and temperature are studied. Results indicate that bare Cu2S exhibits higher selectivity towards BA, while OAm-capped Cu2S promotes HDB formation. This difference is explained by the competing adsorption of protons and BZH. During the BZH electrochemical conversion, electrons first transfer to the C in the C[double bond, length as m-dash]O group to form a ketyl radical. Then the radical either couples with surrounding H+ to form BA or self-couple to produce HDB, depending on the H+ availability that is affected by the electrocatalyst surface properties. The presence of OAm inhibits the H adsorption on the electrode surface therefore reducing the formation of high-energy state Had and its combination with ketyl radicals to form BA. Instead, the presence of OAm promotes the outer sphere reaction for obtaining HDB."}],"oa":1,"date_updated":"2025-01-09T12:30:16Z","acknowledgement":"L. Gong and J. Yu thank the China Scholarship Council for the scholarship support. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya. The authors thank support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/AEI/10.13039/501100011033/and by “ERDF A way of making Europe”, by the “European Union”. ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. Authors acknowledge the use of instrumentation as well as the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is founding member of e-DREAM.","date_created":"2024-08-11T22:01:12Z","status":"public","publisher":"Royal Society of Chemistry","publication_status":"published","article_processing_charge":"Yes","title":"Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin","oa_version":"Published Version","OA_place":"publisher","author":[{"last_name":"Gong","first_name":"Li","full_name":"Gong, Li"},{"last_name":"Zhao","first_name":"Shiling","full_name":"Zhao, Shiling"},{"first_name":"Jing","full_name":"Yu, Jing","last_name":"Yu"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Kallio","first_name":"Tanja","full_name":"Kallio, Tanja"},{"orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini"},{"last_name":"Martínez-Alanis","first_name":"Paulina R.","full_name":"Martínez-Alanis, Paulina R."},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"year":"2024","scopus_import":"1","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/3.0/","page":"2287-2294","ddc":["540"],"day":"01","type":"journal_article","issue":"9","date_published":"2024-09-01T00:00:00Z"},{"isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","page":"284-303","day":"01","ddc":["000"],"type":"conference","date_published":"2024-07-01T00:00:00Z","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, the Academy of Finland under the project 336092 and by a gift from Intel Corporation.","status":"public","date_created":"2024-08-11T22:01:13Z","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"publication_status":"published","publisher":"Springer Nature","arxiv":1,"article_processing_charge":"Yes (in subscription journal)","title":"Certifying phase abstraction","oa_version":"Published Version","ec_funded":1,"author":[{"last_name":"Froleyks","full_name":"Froleyks, Nils","first_name":"Nils"},{"id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342","last_name":"Yu","full_name":"Yu, Zhengqi","first_name":"Zhengqi"},{"full_name":"Biere, Armin","first_name":"Armin","last_name":"Biere"},{"full_name":"Heljanko, Keijo","first_name":"Keijo","last_name":"Heljanko"}],"year":"2024","volume":14739,"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","department":[{"_id":"ToHe"}],"file":[{"relation":"main_file","date_updated":"2024-08-12T06:53:39Z","access_level":"open_access","file_name":"2024_LNCS_Froleyks.pdf","creator":"dernst","checksum":"7d7839fc8c5c680ea3ac09f40a66e55d","file_id":"17414","date_created":"2024-08-12T06:53:39Z","success":1,"file_size":556902,"content_type":"application/pdf"}],"_id":"17413","intvolume":" 14739","abstract":[{"text":"Certification helps to increase trust in formal verification of safety-critical systems which require assurance on their correctness. In hardware model checking, a widely used formal verification technique, phase abstraction is considered one of the most commonly used preprocessing techniques. We present an approach to certify an extended form of phase abstraction using a generic certificate format. As in earlier works our approach involves constructing a witness circuit with an inductive invariant property that certifies the correctness of the entire model checking process, which is then validated by an independent certificate checker. We have implemented and evaluated the proposed approach including certification for various preprocessing configurations on hardware model checking competition benchmarks. As an improvement on previous work in this area, the proposed method is able to efficiently complete certification with an overhead of a fraction of model checking time.","lang":"eng"}],"month":"07","oa":1,"alternative_title":["LNCS"],"date_updated":"2025-09-08T08:49:53Z","external_id":{"isi":["001273489700017"],"arxiv":["2405.04297"]},"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031634970"],"issn":["0302-9743"]},"has_accepted_license":"1","doi":"10.1007/978-3-031-63498-7_17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"start_date":"2024-07-03","name":"IJCAR: International Joint Conference on Automated Reasoning","end_date":"2024-07-06","location":"Nancy, France"},"quality_controlled":"1","file_date_updated":"2024-08-12T06:53:39Z","citation":{"ieee":"N. Froleyks, E. Yu, A. Biere, and K. Heljanko, “Certifying phase abstraction,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Nancy, France, 2024, vol. 14739, pp. 284–303.","chicago":"Froleyks, Nils, Emily Yu, Armin Biere, and Keijo Heljanko. “Certifying Phase Abstraction.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 14739:284–303. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-63498-7_17.","ista":"Froleyks N, Yu E, Biere A, Heljanko K. 2024. Certifying phase abstraction. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 14739, 284–303.","apa":"Froleyks, N., Yu, E., Biere, A., & Heljanko, K. (2024). Certifying phase abstraction. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 14739, pp. 284–303). Nancy, France: Springer Nature. https://doi.org/10.1007/978-3-031-63498-7_17","mla":"Froleyks, Nils, et al. “Certifying Phase Abstraction.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 14739, Springer Nature, 2024, pp. 284–303, doi:10.1007/978-3-031-63498-7_17.","ama":"Froleyks N, Yu E, Biere A, Heljanko K. Certifying phase abstraction. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 14739. Springer Nature; 2024:284-303. doi:10.1007/978-3-031-63498-7_17","short":"N. Froleyks, E. Yu, A. Biere, K. Heljanko, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2024, pp. 284–303."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_updated":"2024-08-12T10:11:19Z","date_published":"2024-07-13T00:00:00Z","extern":"1","day":"13","_id":"17423","type":"conference","abstract":[{"text":"We introduce an algorithm to reconstruct a mesh from discrete samples of a shape’s Signed Distance Function (SDF). A simple geometric reinterpretation of the SDF lets us formulate the problem through a point cloud, from which a surface can be extracted with existing techniques. We extract all possible information from the SDF data, outperforming commonly used algorithms and imposing no topological or geometric restrictions.","lang":"eng"}],"month":"07","language":[{"iso":"eng"}],"publication":"SIGGRAPH '24: Special Interest Group on Computer Graphics and Interactive Techniques Conference","scopus_import":"1","article_number":"23","author":[{"last_name":"Sellán","full_name":"Sellán, Silvia","first_name":"Silvia"},{"first_name":"Yingying","full_name":"Ren, Yingying","last_name":"Ren","id":"93d68d10-3540-11ef-a265-f748a50dba3d"},{"full_name":"Batty, Christopher","first_name":"Christopher","last_name":"Batty"},{"last_name":"Stein","first_name":"Oded","full_name":"Stein, Oded"}],"citation":{"chicago":"Sellán, Silvia, Yingying Ren, Christopher Batty, and Oded Stein. “Reach for the Arcs: Reconstructing Surfaces from SDFs via Tangent Points.” In SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657419.","ista":"Sellán S, Ren Y, Batty C, Stein O. 2024. Reach for the arcs: Reconstructing surfaces from SDFs via tangent points. SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 23.","mla":"Sellán, Silvia, et al. “Reach for the Arcs: Reconstructing Surfaces from SDFs via Tangent Points.” SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference, 23, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657419.","apa":"Sellán, S., Ren, Y., Batty, C., & Stein, O. (2024). Reach for the arcs: Reconstructing surfaces from SDFs via tangent points. In SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference. Denver, CO, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657419","ieee":"S. Sellán, Y. Ren, C. Batty, and O. Stein, “Reach for the arcs: Reconstructing surfaces from SDFs via tangent points,” in SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference, Denver, CO, United States, 2024.","short":"S. Sellán, Y. Ren, C. Batty, O. Stein, in:, SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference, Association for Computing Machinery, 2024.","ama":"Sellán S, Ren Y, Batty C, Stein O. Reach for the arcs: Reconstructing surfaces from SDFs via tangent points. In: SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657419"},"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2024-08-01","start_date":"2024-07-27","location":"Denver, CO, United States"},"quality_controlled":"1","title":"Reach for the arcs: Reconstructing surfaces from SDFs via tangent points","article_processing_charge":"No","oa_version":"None","doi":"10.1145/3641519.3657419","publication_status":"published","publisher":"Association for Computing Machinery","publication_identifier":{"isbn":["9798400705250"]},"date_created":"2024-08-12T10:02:58Z","status":"public"},{"year":"2024","citation":{"ama":"Ren Y, Panetta J, Suzuki S, Kusupati U, Isvoranu F, Pauly M. Computational homogenization for inverse design of surface-based inflatables. ACM Transactions on Graphics. 2024;43(4). doi:10.1145/3658125","short":"Y. Ren, J. Panetta, S. Suzuki, U. Kusupati, F. Isvoranu, M. Pauly, ACM Transactions on Graphics 43 (2024).","ieee":"Y. Ren, J. Panetta, S. Suzuki, U. Kusupati, F. Isvoranu, and M. Pauly, “Computational homogenization for inverse design of surface-based inflatables,” ACM Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.","ista":"Ren Y, Panetta J, Suzuki S, Kusupati U, Isvoranu F, Pauly M. 2024. Computational homogenization for inverse design of surface-based inflatables. ACM Transactions on Graphics. 43(4), 87.","mla":"Ren, Yingying, et al. “Computational Homogenization for Inverse Design of Surface-Based Inflatables.” ACM Transactions on Graphics, vol. 43, no. 4, 87, Association for Computing Machinery, 2024, doi:10.1145/3658125.","apa":"Ren, Y., Panetta, J., Suzuki, S., Kusupati, U., Isvoranu, F., & Pauly, M. (2024). Computational homogenization for inverse design of surface-based inflatables. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658125","chicago":"Ren, Yingying, Julian Panetta, Seiichi Suzuki, Uday Kusupati, Florin Isvoranu, and Mark Pauly. “Computational Homogenization for Inverse Design of Surface-Based Inflatables.” ACM Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658125."},"author":[{"last_name":"Ren","id":"93d68d10-3540-11ef-a265-f748a50dba3d","full_name":"Ren, Yingying","first_name":"Yingying"},{"last_name":"Panetta","first_name":"Julian","full_name":"Panetta, Julian"},{"last_name":"Suzuki","first_name":"Seiichi","full_name":"Suzuki, Seiichi"},{"last_name":"Kusupati","full_name":"Kusupati, Uday","first_name":"Uday"},{"first_name":"Florin","full_name":"Isvoranu, Florin","last_name":"Isvoranu"},{"first_name":"Mark","full_name":"Pauly, Mark","last_name":"Pauly"}],"article_number":"87","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","quality_controlled":"1","title":"Computational homogenization for inverse design of surface-based inflatables","article_processing_charge":"No","doi":"10.1145/3658125","publication_status":"published","publisher":"Association for Computing Machinery","status":"public","date_created":"2024-08-12T10:03:38Z","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"date_updated":"2024-08-12T10:08:13Z","date_published":"2024-07-19T00:00:00Z","extern":"1","issue":"4","intvolume":" 43","_id":"17424","type":"journal_article","abstract":[{"lang":"eng","text":"Surface-based inflatables are composed of two thin layers of nearly inextensible sheet material joined together along carefully selected fusing curves. During inflation, pressure forces separate the two sheets to maximize the enclosed volume. The fusing curves restrict this expansion, leading to a spatially varying in-plane contraction and hence metric frustration. The inflated structure settles into a 3D equilibrium that balances pressure forces with the internal elastic forces of the sheets.\r\nWe present a computational framework for analyzing and designing surface-based inflatable structures with arbitrary fusing patterns. Our approach employs numerical homogenization to characterize the behavior of parametric families of periodic inflatable patch geometries, which can then be combined to tessellate the sheet with smoothly varying patterns. We propose a novel parametrization of the underlying deformation space that allows accurate, efficient, and systematical analysis of the stretching and bending behavior of inflated patches with potentially open boundaries.\r\nWe apply our homogenization algorithm to create a database of geometrically diverse fusing patterns spanning a wide range of material properties and deformation characteristics. This database is employed in an inverse design algorithm that solves for fusing curves to best approximate a given input target surface. Local patches are selected and blended to form a global network of curves based on a geometric flattening algorithm. These fusing curves are then further optimized to minimize the distance of the deployed structure to target surface. We show that this approach offers greater flexibility to approximate given target geometries compared to previous work while significantly improving structural performance."}],"day":"19","article_type":"original","month":"07","language":[{"iso":"eng"}],"volume":43,"publication":"ACM Transactions on Graphics","scopus_import":"1"},{"issue":"15","date_published":"2024-08-16T00:00:00Z","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","ddc":["550"],"day":"16","type":"journal_article","title":"Regimes of precipitation change over Europe and the Mediterranean","article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"oa_version":"Published Version","author":[{"last_name":"André","full_name":"André, Julie","first_name":"Julie"},{"last_name":"D'Andrea","full_name":"D'Andrea, Fabio","first_name":"Fabio"},{"last_name":"Drobinski","full_name":"Drobinski, Philippe","first_name":"Philippe"},{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"year":"2024","project":[{"name":"Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020"}],"acknowledgement":"CJM gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No 805041). The authors also thank Samuel Somot (Centre National de Recherches Météorologiques, Toulouse) and Juliette Blanchet (Institut des Géosciences de l’Environnement, Grenoble) for their fruitful discussions on the project.","date_created":"2024-08-18T22:01:04Z","status":"public","publisher":"Wiley","publication_status":"published","oa":1,"date_updated":"2025-09-08T08:56:53Z","external_id":{"isi":["001285897600001"]},"publication":"Journal of Geophysical Research: Atmospheres","department":[{"_id":"CaMu"}],"volume":129,"month":"08","article_type":"original","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2024-08-19T06:32:21Z","file_name":"2024_JGRAtmospheres_Andre.pdf","creator":"dernst","checksum":"71d7f966318e11ce474737f4e37405ef","file_id":"17438","file_size":8126046,"date_created":"2024-08-19T06:32:21Z","success":1,"content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"The Mediterranean region is experiencing pronounced aridification and in certain areas higher occurrence of intense precipitation. In this work, we analyze the evolution of the precipitation probability distribution in terms of precipitating days (or “wet-days”) and all-days quantile trends, in Europe and the Mediterranean, using the ERA5 reanalysis. Looking at the form of wet-days quantile trends curves, we identify four regimes. Two are predominant: in most of northern Europe the precipitation quantiles all intensify, while in the Mediterranean the low-medium quantiles are mostly decreasing as extremes intensify or decrease. The wet-days distribution is then modeled by a Weibull law with two parameters, whose changes capture the four regimes. Assessing the significance of the parameters' changes over 1950–2020 shows that a signal on wet-days distribution has already emerged in northern Europe (where the distribution shifts to more intense precipitation), but not yet in the Mediterranean, where the natural variability is stronger. We extend the results by describing the all-days distribution change as the wet-days’ change plus a contribution from the dry-days frequency change, and study their relative contribution. In northern Europe, the wet-days distribution change is the dominant driver, and the contribution of dry-days frequency change can be neglected for wet-days percentiles above about 50%. In the Mediterranean, however, the change of precipitation distribution comes from the significant increase of dry-days frequency instead of an intensity change during wet-days. Therefore, in the Mediterranean the increase of dry-days frequency is crucial for all-days trends, even for heavy precipitation."}],"_id":"17435","intvolume":" 129","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"e2023JD040413","file_date_updated":"2024-08-19T06:32:21Z","citation":{"ista":"André J, D’Andrea F, Drobinski P, Muller CJ. 2024. Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. 129(15), e2023JD040413.","mla":"André, Julie, et al. “Regimes of Precipitation Change over Europe and the Mediterranean.” Journal of Geophysical Research: Atmospheres, vol. 129, no. 15, e2023JD040413, Wiley, 2024, doi:10.1029/2023JD040413.","apa":"André, J., D’Andrea, F., Drobinski, P., & Muller, C. J. (2024). Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. Wiley. https://doi.org/10.1029/2023JD040413","chicago":"André, Julie, Fabio D’Andrea, Philippe Drobinski, and Caroline J Muller. “Regimes of Precipitation Change over Europe and the Mediterranean.” Journal of Geophysical Research: Atmospheres. Wiley, 2024. https://doi.org/10.1029/2023JD040413.","ieee":"J. André, F. D’Andrea, P. Drobinski, and C. J. Muller, “Regimes of precipitation change over Europe and the Mediterranean,” Journal of Geophysical Research: Atmospheres, vol. 129, no. 15. Wiley, 2024.","short":"J. André, F. D’Andrea, P. Drobinski, C.J. Muller, Journal of Geophysical Research: Atmospheres 129 (2024).","ama":"André J, D’Andrea F, Drobinski P, Muller CJ. Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. 2024;129(15). doi:10.1029/2023JD040413"},"publication_identifier":{"issn":["2169-897X"],"eissn":["2169-8996"]},"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"has_accepted_license":"1","doi":"10.1029/2023JD040413"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-01-09T12:25:32Z","citation":{"ama":"Das S, De Roij M, Bellows S, et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 2024;5(11). doi:10.1016/j.xplc.2024.101039","short":"S. Das, M. De Roij, S. Bellows, M.D. Alvarez, S. Mutte, W. Kohlen, E. Farcot, D. Weijers, J.W. Borst, Plant Communications 5 (2024).","ieee":"S. Das et al., “Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination,” Plant Communications, vol. 5, no. 11. Elsevier, 2024.","chicago":"Das, Shubhajit, Martijn De Roij, Simon Bellows, Melissa Dipp Alvarez, Sumanth Mutte, Wouter Kohlen, Etienne Farcot, Dolf Weijers, and Jan Willem Borst. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” Plant Communications. Elsevier, 2024. https://doi.org/10.1016/j.xplc.2024.101039.","ista":"Das S, De Roij M, Bellows S, Alvarez MD, Mutte S, Kohlen W, Farcot E, Weijers D, Borst JW. 2024. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 5(11), 101039.","mla":"Das, Shubhajit, et al. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” Plant Communications, vol. 5, no. 11, 101039, Elsevier, 2024, doi:10.1016/j.xplc.2024.101039.","apa":"Das, S., De Roij, M., Bellows, S., Alvarez, M. D., Mutte, S., Kohlen, W., … Borst, J. W. (2024). Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2024.101039"},"article_number":"101039","quality_controlled":"1","OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.xplc.2024.101039","has_accepted_license":"1","publication_identifier":{"eissn":["2590-3462"]},"external_id":{"pmid":["38988072"]},"date_updated":"2025-01-09T12:26:55Z","oa":1,"article_type":"original","month":"11","abstract":[{"lang":"eng","text":"The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination."}],"_id":"17436","intvolume":" 5","file":[{"checksum":"38cabc1042ac7fb70e6c4c510eba88fc","creator":"dernst","content_type":"application/pdf","file_size":4970540,"date_created":"2025-01-09T12:25:32Z","success":1,"file_id":"18811","access_level":"open_access","date_updated":"2025-01-09T12:25:32Z","relation":"main_file","file_name":"2024_PlantCommunications_Das.pdf"}],"department":[{"_id":"JiFr"}],"publication":"Plant Communications","volume":5,"DOAJ_listed":"1","OA_place":"publisher","year":"2024","author":[{"first_name":"Shubhajit","full_name":"Das, Shubhajit","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be","last_name":"Das"},{"last_name":"De Roij","full_name":"De Roij, Martijn","first_name":"Martijn"},{"first_name":"Simon","full_name":"Bellows, Simon","last_name":"Bellows"},{"last_name":"Alvarez","first_name":"Melissa Dipp","full_name":"Alvarez, Melissa Dipp"},{"last_name":"Mutte","first_name":"Sumanth","full_name":"Mutte, Sumanth"},{"full_name":"Kohlen, Wouter","first_name":"Wouter","last_name":"Kohlen"},{"last_name":"Farcot","full_name":"Farcot, Etienne","first_name":"Etienne"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Borst, Jan Willem","first_name":"Jan Willem","last_name":"Borst"}],"oa_version":"Published Version","title":"Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination","article_processing_charge":"Yes","pmid":1,"publisher":"Elsevier","publication_status":"published","date_created":"2024-08-18T22:01:04Z","status":"public","acknowledgement":"We are grateful to Iris Nieuwland and Neri van Laar for experimental support. No conflict of interest declared.\r\nThis work was supported by the Netherlands Organisation for Scientific Research, the Netherlands (grants ALWOP.402 and OCENW.M20.031 to J.W.B.) and the Human Frontiers Research Program (grant RGP0015/2022 to D.W.).","date_published":"2024-11-11T00:00:00Z","issue":"11","type":"journal_article","day":"11","ddc":["580"],"scopus_import":"1","language":[{"iso":"eng"}]},{"author":[{"full_name":"Vernet, Tanguy","first_name":"Tanguy","id":"19f1e3bf-c59a-11ee-a1af-ed269948817b","last_name":"Vernet"}],"year":"2024","title":"Rational singularities for moment maps of totally negative quivers","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","ec_funded":1,"publication_status":"epub_ahead","publisher":"Springer Nature","acknowledgement":"I would like to warmly thank Dimitri Wyss for his guidance and supervision and Nero Budur for helpful discussions and answering all my questions on his previous works. I would also like to thank Francesca Carocci, Ben Davison, Lucien Hennecart and Olivier Schiffmann for helpful remarks and discussions during the writing of this paper. Finally, I would like to thank the anonymous referees for their careful reading and suggesting improvements in the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This work was supported by the Swiss National Science Foundation [No. 196960]. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","date_created":"2024-08-18T22:01:04Z","status":"public","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"date_published":"2024-09-09T00:00:00Z","day":"09","ddc":["510"],"type":"journal_article","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","citation":{"ista":"Vernet T. 2024. Rational singularities for moment maps of totally negative quivers. Transformation Groups.","mla":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” Transformation Groups, Springer Nature, 2024, doi:10.1007/s00031-024-09873-0.","apa":"Vernet, T. (2024). Rational singularities for moment maps of totally negative quivers. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-024-09873-0","chicago":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” Transformation Groups. Springer Nature, 2024. https://doi.org/10.1007/s00031-024-09873-0.","ieee":"T. Vernet, “Rational singularities for moment maps of totally negative quivers,” Transformation Groups. Springer Nature, 2024.","short":"T. Vernet, Transformation Groups (2024).","ama":"Vernet T. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 2024. doi:10.1007/s00031-024-09873-0"},"main_file_link":[{"url":"https://doi.org/10.1007/s00031-024-09873-0","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","has_accepted_license":"1","doi":"10.1007/s00031-024-09873-0","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["1083-4362"],"eissn":["1531-586X"]},"date_updated":"2025-09-08T08:56:08Z","external_id":{"isi":["001287455300001"]},"corr_author":"1","oa":1,"abstract":[{"text":"We prove that the zero-fiber of the moment map of a totally negative quiver has rational singularities. Our proof consists in generalizing dimension bounds on jet spaces of this fiber, which were introduced by Budur. We also transfer the rational singularities property to other moduli spaces of objects in 2-Calabi-Yau categories, based on recent work of Davison. This has interesting arithmetic applications on quiver moment maps and moduli spaces of objects in 2-Calabi-Yau categories. First, we generalize results of Wyss on the asymptotic behaviour of counts of jets of quiver moment maps over finite fields. Moreover, we interpret the limit of counts of jets on a given moduli space as its p-adic volume under a canonical measure analogous to the measure built by Carocci, Orecchia and Wyss on certain moduli spaces of coherent sheaves.","lang":"eng"}],"_id":"17437","month":"09","article_type":"original","publication":"Transformation Groups","department":[{"_id":"TaHa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11649018/","open_access":"1"}],"citation":{"chicago":"Bravo, Jack Peter Kelly, Delisa A. Ramos, Rodrigo Fregoso Ocampo, Caiden Ingram, and David W. Taylor. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07515-9.","ista":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. 2024. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. 630(8018), 961–967.","mla":"Bravo, Jack Peter Kelly, et al. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” Nature, vol. 630, no. 8018, Springer Nature, 2024, pp. 961–67, doi:10.1038/s41586-024-07515-9.","apa":"Bravo, J. P. K., Ramos, D. A., Fregoso Ocampo, R., Ingram, C., & Taylor, D. W. (2024). Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07515-9","ieee":"J. P. K. Bravo, D. A. Ramos, R. Fregoso Ocampo, C. Ingram, and D. W. Taylor, “Plasmid targeting and destruction by the DdmDE bacterial defence system,” Nature, vol. 630, no. 8018. Springer Nature, pp. 961–967, 2024.","short":"J.P.K. Bravo, D.A. Ramos, R. Fregoso Ocampo, C. Ingram, D.W. Taylor, Nature 630 (2024) 961–967.","ama":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. 2024;630(8018):961-967. doi:10.1038/s41586-024-07515-9"},"quality_controlled":"1","OA_type":"green","doi":"10.1038/s41586-024-07515-9","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"external_id":{"pmid":["38740055"]},"date_updated":"2025-06-24T12:47:21Z","corr_author":"1","oa":1,"article_type":"original","month":"06","_id":"17442","abstract":[{"lang":"eng","text":"Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE–guide–target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.\r\n\r\n"}],"intvolume":" 630","department":[{"_id":"JaBr"}],"publication":"Nature","volume":630,"OA_place":"repository","year":"2024","author":[{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753"},{"last_name":"Ramos","full_name":"Ramos, Delisa A.","first_name":"Delisa A."},{"last_name":"Fregoso Ocampo","first_name":"Rodrigo","full_name":"Fregoso Ocampo, Rodrigo"},{"full_name":"Ingram, Caiden","first_name":"Caiden","last_name":"Ingram"},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"oa_version":"Submitted Version","title":"Plasmid targeting and destruction by the DdmDE bacterial defence system","article_processing_charge":"No","pmid":1,"publisher":"Springer Nature","publication_status":"published","status":"public","date_created":"2024-08-19T09:41:18Z","acknowledgement":"We thank K. Kiernan, G. Hibshman and I. Strohkendl for insightful discussions and comments on the manuscript, and R. Lin for assistance with the ATPase assay. Data were collected at the Sauer Structural Biology Laboratory at the University of Texas at Austin. This work was supported in part by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) R35GM138348 (to D.W.T.) and Welch Foundation research grant F-1938 (to D.W.T.).","date_published":"2024-06-27T00:00:00Z","issue":"8018","type":"journal_article","page":"961-967","day":"27","scopus_import":"1","language":[{"iso":"eng"}]},{"acknowledgement":"This paper is an important component of the thesis work described in [25]; many of my acknowledgements there apply here as well. I also thank my advisor, Peter Sarnak, for many helpful suggestions and questions on the exposition, references, assumptions, and scope of (various drafts of) the present work. I am also grateful to Trevor Wooley for providing some helpful general comments on special subvarieties and the reference [24]. I thank Tim Browning for inspiring part of the current title of the paper. Finally, thanks are due to the referee for providing many helpful suggestions. This work was partially supported by NSF grant DMS-1802211, and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant AgreementNo. 101034413.","status":"public","date_created":"2024-08-20T08:41:40Z","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"publication_status":"published","publisher":"Wiley","arxiv":1,"title":"Special cubic zeros and the dual variety","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","ec_funded":1,"author":[{"first_name":"Victor","full_name":"Wang, Victor","last_name":"Wang","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","orcid":"0000-0002-0704-7026"}],"year":"2024","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","day":"14","ddc":["512"],"type":"journal_article","issue":"3","date_published":"2024-08-14T00:00:00Z","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"has_accepted_license":"1","doi":"10.1112/jlms.12975","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","article_number":"e12975","citation":{"ama":"Wang V. Special cubic zeros and the dual variety. Journal of the London Mathematical Society. 2024;110(3). doi:10.1112/jlms.12975","short":"V. Wang, Journal of the London Mathematical Society 110 (2024).","ieee":"V. Wang, “Special cubic zeros and the dual variety,” Journal of the London Mathematical Society, vol. 110, no. 3. Wiley, 2024.","ista":"Wang V. 2024. Special cubic zeros and the dual variety. Journal of the London Mathematical Society. 110(3), e12975.","apa":"Wang, V. (2024). Special cubic zeros and the dual variety. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12975","mla":"Wang, Victor. “Special Cubic Zeros and the Dual Variety.” Journal of the London Mathematical Society, vol. 110, no. 3, e12975, Wiley, 2024, doi:10.1112/jlms.12975.","chicago":"Wang, Victor. “Special Cubic Zeros and the Dual Variety.” Journal of the London Mathematical Society. Wiley, 2024. https://doi.org/10.1112/jlms.12975."},"file_date_updated":"2024-08-21T06:36:40Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":110,"publication":"Journal of the London Mathematical Society","department":[{"_id":"TiBr"}],"file":[{"file_id":"17454","content_type":"application/pdf","file_size":438751,"success":1,"date_created":"2024-08-21T06:36:40Z","creator":"dernst","checksum":"90437e19f57520b4d66ca62408f6c81e","file_name":"2024_JourLondonMathSoc_Wang.pdf","relation":"main_file","access_level":"open_access","date_updated":"2024-08-21T06:36:40Z"}],"_id":"17447","intvolume":" 110","abstract":[{"lang":"eng","text":"Let F be a diagonal cubic form over Z in six variables. From the dual variety in the delta method of Duke–Friedlander–Iwaniec and Heath‐Brown, we unconditionally extract a weighted count of certain special integral zeros of F in regions of diameter X - 8 . Heath‐Brown did the same in four variables, but our analysis differs and captures some novel features. We also put forth an axiomatic framework for more general F."}],"article_type":"original","month":"08","corr_author":"1","oa":1,"date_updated":"2025-09-08T08:58:20Z","external_id":{"isi":["001310529600001"],"arxiv":["2108.03396"]}},{"publication":"Algebra & Number Theory","volume":18,"month":"02","article_type":"original","file":[{"date_updated":"2024-08-21T06:46:56Z","access_level":"open_access","relation":"main_file","file_name":"2024_AlgebraNumberTheory_Pandey.pdf","checksum":"1e3467a14de754bf8d3bff03a015e1ce","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2024-08-21T06:46:56Z","file_size":1401725,"file_id":"17455"}],"intvolume":" 18","_id":"17449","abstract":[{"lang":"eng","text":"We prove that the $k$-th positive integer moment of partial sums of Steinhaus random multiplicative functions over the interval $(x, x+H]$ matches the corresponding Gaussian moment, as long as $H\\ll x/(\\log x)^{2k^2+2+o(1)}$ and $H$ tends to infinity with $x$. We show that properly normalized partial sums of typical multiplicative functions arising from realizations of random multiplicative functions have Gaussian limiting distribution in short moving intervals $(x, x+H]$ with $H\\ll X/(\\log X)^{W(X)}$ tending to infinity with $X$, where $x$ is uniformly chosen from $\\{1,2,\\dots, X\\}$, and $W(X)$ tends to infinity with $X$ arbitrarily slowly. This makes some initial progress on a recent question of Harper."}],"extern":"1","oa":1,"date_updated":"2024-08-21T06:58:43Z","external_id":{"arxiv":["2207.11758"]},"publication_identifier":{"eissn":["1944-7833"],"issn":["1937-0652"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.2140/ant.2024.18.389","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.11758","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pandey, Mayank, Victor Wang, and Max Wenqiang Xu. “Partial Sums of Typical Multiplicative Functions over Short Moving Intervals.” Algebra & Number Theory. Mathematical Sciences Publishers, 2024. https://doi.org/10.2140/ant.2024.18.389.","apa":"Pandey, M., Wang, V., & Xu, M. W. (2024). Partial sums of typical multiplicative functions over short moving intervals. Algebra & Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2024.18.389","ista":"Pandey M, Wang V, Xu MW. 2024. Partial sums of typical multiplicative functions over short moving intervals. Algebra & Number Theory. 18(2), 389–408.","mla":"Pandey, Mayank, et al. “Partial Sums of Typical Multiplicative Functions over Short Moving Intervals.” Algebra & Number Theory, vol. 18, no. 2, Mathematical Sciences Publishers, 2024, pp. 389–408, doi:10.2140/ant.2024.18.389.","ieee":"M. Pandey, V. Wang, and M. W. Xu, “Partial sums of typical multiplicative functions over short moving intervals,” Algebra & Number Theory, vol. 18, no. 2. Mathematical Sciences Publishers, pp. 389–408, 2024.","short":"M. Pandey, V. Wang, M.W. Xu, Algebra & Number Theory 18 (2024) 389–408.","ama":"Pandey M, Wang V, Xu MW. Partial sums of typical multiplicative functions over short moving intervals. Algebra & Number Theory. 2024;18(2):389-408. doi:10.2140/ant.2024.18.389"},"file_date_updated":"2024-08-21T06:46:56Z","scopus_import":"1","language":[{"iso":"eng"}],"day":"06","ddc":["510"],"page":"389-408","type":"journal_article","issue":"2","date_published":"2024-02-06T00:00:00Z","acknowledgement":"We thank Andrew Granville and the anonymous referee for many detailed comments that led us to significantly improve the results and presentation of our work. We thank and Adam Harper for helpful discussions and useful comments and corrections on earlier versions. We also thank Yuqiu Fu, Larry Guth, Kannan Soundararajan, Katharine Woo, and Liyang Yang for helpful discussions. Finally, we thank Peter Sarnak for introducing us (the authors) to each other during the “50 Years of Number Theory and Random Matrix Theory” Conference at IAS and making the collaboration possible. \r\nOpen Access made possible by participating institutions via Subscribe to Open.","status":"public","date_created":"2024-08-20T08:48:26Z","publisher":"Mathematical Sciences Publishers","publication_status":"published","title":"Partial sums of typical multiplicative functions over short moving intervals","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","arxiv":1,"author":[{"last_name":"Pandey","first_name":"Mayank","full_name":"Pandey, Mayank"},{"full_name":"Wang, Victor","first_name":"Victor","last_name":"Wang","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","orcid":"0000-0002-0704-7026"},{"full_name":"Xu, Max Wenqiang","first_name":"Max Wenqiang","last_name":"Xu"}],"year":"2024"},{"related_material":{"link":[{"url":"https://doi.org/10.1101/2023.10.04.560631","relation":"earlier_version"}]},"date_updated":"2025-09-08T08:59:37Z","external_id":{"pmid":["39141878"],"isi":["001291908600001"]},"oa":1,"article_type":"original","month":"09","file":[{"file_id":"18815","content_type":"application/pdf","file_size":855818,"date_created":"2025-01-09T13:42:42Z","success":1,"creator":"dernst","checksum":"1e6d1230e0387f72752e3268f5330c9e","file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-01-09T13:42:42Z"}],"_id":"17457","abstract":[{"lang":"eng","text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening."}],"intvolume":" 11","publication":"Neurology, Neuroimmunology and Neuroinflammation","department":[{"_id":"RySh"}],"DOAJ_listed":"1","volume":11,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"A. Ritzau-Jost et al., “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” Neurology, Neuroimmunology and Neuroinflammation, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024.","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” Neurology, Neuroimmunology and Neuroinflammation. Wolters Kluwer, 2024. https://doi.org/10.1212/NXI.0000000000200284.","ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. 11(5), e200284.","mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” Neurology, Neuroimmunology and Neuroinflammation, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:10.1212/NXI.0000000000200284.","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. Wolters Kluwer. https://doi.org/10.1212/NXI.0000000000200284","ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. 2024;11(5):e200284. doi:10.1212/NXI.0000000000200284","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology and Neuroinflammation 11 (2024) e200284."},"file_date_updated":"2025-01-09T13:42:42Z","quality_controlled":"1","OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1212/NXI.0000000000200284","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["2332-7812"]},"date_published":"2024-09-01T00:00:00Z","issue":"5","ddc":["570"],"page":"e200284","day":"01","type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"OA_place":"publisher","author":[{"last_name":"Ritzau-Jost","full_name":"Ritzau-Jost, Andreas","first_name":"Andreas"},{"full_name":"Gsell, Felix","first_name":"Felix","last_name":"Gsell"},{"last_name":"Sell","first_name":"Josefine","full_name":"Sell, Josefine"},{"first_name":"Stefan","full_name":"Sachs, Stefan","last_name":"Sachs"},{"first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Toni","full_name":"Kirmann, Toni","last_name":"Kirmann"},{"last_name":"Maaß","first_name":"Sebastian","full_name":"Maaß, Sebastian"},{"full_name":"Irani, Sarosh R.","first_name":"Sarosh R.","last_name":"Irani"},{"full_name":"Werner, Christian","first_name":"Christian","last_name":"Werner"},{"last_name":"Geis","full_name":"Geis, Christian","first_name":"Christian"},{"first_name":"Markus","full_name":"Sauer, Markus","last_name":"Sauer"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hallermann","full_name":"Hallermann, Stefan","first_name":"Stefan"}],"year":"2024","article_processing_charge":"Yes","title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","oa_version":"Published Version","pmid":1,"publisher":"Wolters Kluwer","publication_status":"published","project":[{"name":"LGI1 antibody-induced pathophysiology in synapses","grant_number":"I04638","_id":"05970B30-7A3F-11EA-A408-12923DDC885E"}],"acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","date_created":"2024-08-25T22:01:07Z","status":"public"},{"author":[{"full_name":"Cecalev, Daniela","first_name":"Daniela","last_name":"Cecalev"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"},{"last_name":"Galupa","full_name":"Galupa, Rafael","first_name":"Rafael"}],"year":"2024","title":"Compensation of gene dosage on the mammalian X","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","pmid":1,"publisher":"The Company of Biologists","publication_status":"published","acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","status":"public","date_created":"2024-08-25T22:01:07Z","date_published":"2024-08-14T00:00:00Z","issue":"15","day":"14","ddc":["599"],"type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"dev202891","file_date_updated":"2024-08-28T10:32:16Z","citation":{"ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891.","apa":"Cecalev, D., Vicoso, B., & Galupa, R. (2024). Compensation of gene dosage on the mammalian X. Development. The Company of Biologists. https://doi.org/10.1242/dev.202891","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” Development, vol. 151, no. 15, dev202891, The Company of Biologists, 2024, doi:10.1242/dev.202891.","chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202891.","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” Development, vol. 151, no. 15. The Company of Biologists, 2024.","short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development. 2024;151(15). doi:10.1242/dev.202891"},"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1242/dev.202891","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"date_updated":"2025-09-08T08:58:58Z","external_id":{"isi":["001292608800003"],"pmid":["39140247"]},"oa":1,"month":"08","article_type":"original","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2024-08-28T10:32:16Z","file_name":"2024_Development_Cecalev.pdf","creator":"cchlebak","checksum":"5e428bda0440d3f957c694b315a8f2a9","file_id":"17464","file_size":2085135,"success":1,"date_created":"2024-08-28T10:32:16Z","content_type":"application/pdf"}],"intvolume":" 151","_id":"17458","abstract":[{"lang":"eng","text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species."}],"publication":"Development","department":[{"_id":"BeVi"}],"volume":151},{"APC_amount":"12348 EUR","date_published":"2024-10-01T00:00:00Z","day":"01","ddc":["570"],"page":"1670-1678","type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"OA_place":"publisher","author":[{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo"},{"first_name":"Kevin D.","full_name":"Whitley, Kevin D.","last_name":"Whitley"},{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"last_name":"Holden","full_name":"Holden, Séamus","first_name":"Séamus"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"}],"year":"2024","title":"Self-organization of mortal filaments and its role in bacterial division ring formation","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","ec_funded":1,"pmid":1,"publisher":"Springer Nature","publication_status":"published","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division"},{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"acknowledgement":"We thank I. Palaia (ISTA) for useful discussions and K. Lim and R. W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266; C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.) and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z; S.H. and K.D.W.).","date_created":"2024-08-25T22:01:08Z","status":"public","date_updated":"2025-09-08T09:02:20Z","external_id":{"pmid":["39416851"],"isi":["001289394500005"]},"corr_author":"1","oa":1,"article_type":"original","month":"10","file":[{"checksum":"c4842152e2b90d67f48ea8c9ed7c473b","creator":"dernst","date_created":"2025-04-14T06:06:35Z","success":1,"file_size":8058249,"content_type":"application/pdf","file_id":"19556","access_level":"open_access","date_updated":"2025-04-14T06:06:35Z","relation":"main_file","file_name":"2024_NaturePhysics_VanhilleCampos.pdf"}],"abstract":[{"text":"Filaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the organization of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments.","lang":"eng"}],"_id":"17460","intvolume":" 20","publication":"Nature Physics","department":[{"_id":"AnSa"},{"_id":"MaLo"}],"volume":20,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and A. Šarić, “Self-organization of mortal filaments and its role in bacterial division ring formation,” Nature Physics, vol. 20. Springer Nature, pp. 1670–1678, 2024.","mla":"Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:10.1038/s41567-024-02597-8.","ista":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 20, 1670–1678.","apa":"Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., & Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02597-8","chicago":"Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02597-8.","ama":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 2024;20:1670-1678. doi:10.1038/s41567-024-02597-8","short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678."},"file_date_updated":"2025-04-14T06:06:35Z","quality_controlled":"1","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1038/s41567-024-02597-8","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]}},{"language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","day":"01","ddc":["570"],"page":"780-787","issue":"9","date_published":"2024-09-01T00:00:00Z","status":"public","date_created":"2024-08-25T22:01:08Z","acknowledgement":"We thank Koos Boomsma and two anonymous reviewers for their constructive comments on the manuscript.","publication_status":"published","publisher":"Elsevier","pmid":1,"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","title":"Unconditional versus condition-dependent social immunity","year":"2024","author":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"full_name":"Pull, Christopher","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982"}],"OA_place":"publisher","volume":40,"department":[{"_id":"SyCr"}],"publication":"Trends in Parasitology","intvolume":" 40","_id":"17461","abstract":[{"lang":"eng","text":"Socially living animals can counteract disease through cooperative defences, leading to social immunity that collectively exceeds the sum of individual defences. In superorganismal colonies of social insects with permanent caste separation between reproductive queen(s) and nonreproducing workers, workers are obligate altruists and thus engage in unconditional social immunity, including highly specialised and self-sacrificial hygiene behaviours. Contrastingly, cooperation is facultative in cooperatively breeding families, where all members are reproductively totipotent but offspring transiently forgo reproduction to help their parents rear more siblings. Here, helpers should either express condition-dependent social immunity or disperse to pursue independent reproduction. We advocate inclusive fitness theory as a framework to predict when and how indirect fitness gains may outweigh direct fitness costs, thus favouring conditional social immunity."}],"file":[{"file_size":1068464,"success":1,"date_created":"2025-01-09T13:46:05Z","content_type":"application/pdf","file_id":"18816","checksum":"362fc994e5df66caf3025b7dc437b647","creator":"dernst","file_name":"2024_TrendsParasitology_Cremer.pdf","date_updated":"2025-01-09T13:46:05Z","access_level":"open_access","relation":"main_file"}],"article_type":"original","month":"09","oa":1,"corr_author":"1","external_id":{"isi":["001307815700001"],"pmid":["39152078"]},"date_updated":"2025-09-08T09:01:42Z","publication_identifier":{"issn":["1471-4922"],"eissn":["1471-5007"]},"doi":"10.1016/j.pt.2024.07.014","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_type":"hybrid","quality_controlled":"1","citation":{"ama":"Cremer S, Pull C. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 2024;40(9):780-787. doi:10.1016/j.pt.2024.07.014","short":"S. Cremer, C. Pull, Trends in Parasitology 40 (2024) 780–787.","ieee":"S. Cremer and C. Pull, “Unconditional versus condition-dependent social immunity,” Trends in Parasitology, vol. 40, no. 9. Elsevier, pp. 780–787, 2024.","ista":"Cremer S, Pull C. 2024. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 40(9), 780–787.","apa":"Cremer, S., & Pull, C. (2024). Unconditional versus condition-dependent social immunity. Trends in Parasitology. Elsevier. https://doi.org/10.1016/j.pt.2024.07.014","mla":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” Trends in Parasitology, vol. 40, no. 9, Elsevier, 2024, pp. 780–87, doi:10.1016/j.pt.2024.07.014.","chicago":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” Trends in Parasitology. Elsevier, 2024. https://doi.org/10.1016/j.pt.2024.07.014."},"file_date_updated":"2025-01-09T13:46:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"publication_identifier":{"eissn":["1540-3467"],"issn":["1540-3459"]},"doi":"10.1137/23M1603819","quality_controlled":"1","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2309.06798"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"N. Clozeau, L. Wang, Multiscale Modeling and Simulation 22 (2024) 973–1029.","ama":"Clozeau N, Wang L. Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. 2024;22(3):973-1029. doi:10.1137/23M1603819","chicago":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” Multiscale Modeling and Simulation. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/23M1603819.","ista":"Clozeau N, Wang L. 2024. Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. 22(3), 973–1029.","mla":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” Multiscale Modeling and Simulation, vol. 22, no. 3, Society for Industrial and Applied Mathematics, 2024, pp. 973–1029, doi:10.1137/23M1603819.","apa":"Clozeau, N., & Wang, L. (2024). Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/23M1603819","ieee":"N. Clozeau and L. Wang, “Artificial boundary conditions for random elliptic systems with correlated coefficient field,” Multiscale Modeling and Simulation, vol. 22, no. 3. Society for Industrial and Applied Mathematics, pp. 973–1029, 2024."},"publication":"Multiscale Modeling and Simulation","department":[{"_id":"JuFi"}],"volume":22,"article_type":"original","month":"09","_id":"17462","intvolume":" 22","abstract":[{"text":"We are interested in numerical algorithms for computing the electrical field generated by a charge distribution localized on scale l in an infinite heterogeneous correlated random medium, in a situation where the medium is only known in a box of diameter L >>l around the support of the charge. We show that the algorithm in [J. Lu, F. Otto, and L. Wang, Optimal Artificial Boundary Conditions Based on Second-Order Correctors for Three Dimensional Random Ellilptic Media, preprint, arXiv:2109.01616, 2021], suggesting optimal Dirichlet boundary conditions motivated by the multipole expansion [P. Bella, A. Giunti, and F. Otto, Comm. Partial Differential Equations, 45 (2020), pp. 561–640], still performs well in correlated media. With overwhelming probability, we obtain a convergence rate in terms of l, L, and the size of the correlations for which optimality is supported with numerical simulations. These estimates are provided for ensembles which satisfy a multiscale logarithmic Sobolev inequality, where our main tool is an extension of the semigroup estimates in [N. Clozeau, Stoch. Partial Differ. Equ. Anal. Comput., 11 (2023), pp. 1254–1378]. As part of our strategy, we construct sublinear second-order correctors in this correlated setting, which is of independent interest.","lang":"eng"}],"corr_author":"1","oa":1,"date_updated":"2025-09-08T09:01:00Z","external_id":{"isi":["001285416500001"],"arxiv":["2309.06798"]},"project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}],"acknowledgement":"We would like to thank our affiliations, Institute of Science and Technology Austria and Max Planck Institute for Mathematics in the Sciences, for supporting the authors’ visits to each other, which greatly facilitated this work. We would like to thank Marc Josien and Quinn Winters for assistance in numerical implementation.","status":"public","date_created":"2024-08-25T22:01:08Z","publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","article_processing_charge":"No","title":"Artificial boundary conditions for random elliptic systems with correlated coefficient field","oa_version":"Preprint","ec_funded":1,"arxiv":1,"OA_place":"repository","author":[{"first_name":"Nicolas","full_name":"Clozeau, Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","last_name":"Clozeau"},{"full_name":"Wang, Lihan","first_name":"Lihan","last_name":"Wang"}],"year":"2024","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"page":"973-1029","day":"01","type":"journal_article","issue":"3","date_published":"2024-09-01T00:00:00Z"},{"status":"public","date_created":"2024-08-25T22:01:08Z","acknowledgement":"We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor for helpful discussions and K. VanWormer and L. Goldschmidt for technical support. We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504, A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no. DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design (A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute (D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D. and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract no. HR0011-21-2-0012, D.B.).","publication_status":"published","publisher":"Springer Nature","pmid":1,"oa_version":"Published Version","title":"De novo design of allosterically switchable protein assemblies","article_processing_charge":"Yes (in subscription journal)","year":"2024","author":[{"full_name":"Pillai, Arvind","first_name":"Arvind","last_name":"Pillai"},{"first_name":"Abbas","full_name":"Idris, Abbas","last_name":"Idris"},{"full_name":"Philomin, Annika","first_name":"Annika","last_name":"Philomin"},{"full_name":"Weidle, Connor","first_name":"Connor","last_name":"Weidle"},{"full_name":"Skotheim, Rebecca","first_name":"Rebecca","last_name":"Skotheim"},{"first_name":"Philip J.Y.","full_name":"Leung, Philip J.Y.","last_name":"Leung"},{"last_name":"Broerman","first_name":"Adam","full_name":"Broerman, Adam"},{"last_name":"Demakis","full_name":"Demakis, Cullen","first_name":"Cullen"},{"last_name":"Borst","full_name":"Borst, Andrew J.","first_name":"Andrew J."},{"last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","first_name":"Florian M"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","ddc":["570"],"day":"22","page":"911–920 ","date_published":"2024-08-22T00:00:00Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"doi":"10.1038/s41586-024-07813-2","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"quality_controlled":"1","file_date_updated":"2024-09-09T12:01:14Z","citation":{"mla":"Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” Nature, vol. 632, Springer Nature, 2024, pp. 911–920, doi:10.1038/s41586-024-07813-2.","apa":"Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J. Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07813-2","ista":"Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically switchable protein assemblies. Nature. 632, 911–920.","chicago":"Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07813-2.","ieee":"A. Pillai et al., “De novo design of allosterically switchable protein assemblies,” Nature, vol. 632. Springer Nature, pp. 911–920, 2024.","short":"A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A. Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024) 911–920.","ama":"Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable protein assemblies. Nature. 2024;632:911–920. doi:10.1038/s41586-024-07813-2"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":632,"department":[{"_id":"FlPr"}],"publication":"Nature","_id":"17463","abstract":[{"text":"Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1,2,3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such ‘action at a distance’ modulation and to create synthetic proteins whose functions can be regulated by effectors4,5,6,7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain–side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry.","lang":"eng"}],"intvolume":" 632","file":[{"date_updated":"2024-09-09T12:01:14Z","access_level":"open_access","relation":"main_file","file_name":"2024_Nature_Pillai.pdf","checksum":"39127601621a360ec0edc538627eb211","creator":"dernst","content_type":"application/pdf","date_created":"2024-09-09T12:01:14Z","success":1,"file_size":16572040,"file_id":"18005"}],"article_type":"original","month":"08","corr_author":"1","oa":1,"external_id":{"pmid":["39143214"],"isi":["001300534300019"]},"date_updated":"2025-09-08T09:00:16Z"},{"ec_funded":1,"oa_version":"None","article_processing_charge":"No","title":"Data for \"Enhanced many-body quantum scars from the non-Hermitian Fock skin effect\"","contributor":[{"contributor_type":"researcher","first_name":"Ruizhe","last_name":"Shen"},{"first_name":"Fang","last_name":"Qin","contributor_type":"researcher"},{"orcid":"0000-0002-3749-6375","contributor_type":"researcher","last_name":"Desaules","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","first_name":"Jean-Yves Marc"},{"first_name":"Zlatko","last_name":"Papić","contributor_type":"researcher"},{"last_name":"Lee","first_name":"Ching Hua","contributor_type":"researcher"}],"year":"2024","file_date_updated":"2024-08-30T13:19:57Z","citation":{"ieee":"J.-Y. M. Desaules, “Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.’” Institute of Science and Technology Austria, 2024.","chicago":"Desaules, Jean-Yves Marc. “Data for ‘Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17471.","ista":"Desaules J-YM. 2024. Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17471.","apa":"Desaules, J.-Y. M. (2024). Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17471","mla":"Desaules, Jean-Yves Marc. Data for “Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17471.","ama":"Desaules J-YM. Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” 2024. doi:10.15479/AT:ISTA:17471","short":"J.-Y.M. Desaules, (2024)."},"author":[{"last_name":"Desaules","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","first_name":"Jean-Yves Marc","full_name":"Desaules, Jean-Yves Marc","orcid":"0000-0002-3749-6375"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_created":"2024-08-30T12:59:43Z","status":"public","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"doi":"10.15479/AT:ISTA:17471","has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"publisher":"Institute of Science and Technology Austria","oa":1,"related_material":{"record":[{"relation":"used_in_publication","id":"18627","status":"public"}]},"date_updated":"2025-09-08T14:54:55Z","date_published":"2024-08-30T00:00:00Z","keyword":["quantum many-body scars","non-equilibrium physics","non-Hermitian physics"],"department":[{"_id":"MaSe"}],"_id":"17471","type":"research_data","abstract":[{"lang":"eng","text":"Mechanisms for suppressing thermalization in disorder-free many-body systems, such as Hilbert space fragmentation and quantum many-body scars, have recently attracted much interest in foundations of quantum statistical physics and potential quantum information processing applications. However, their sensitivity to realistic effects such as finite temperature remains largely unexplored. Here, we have utilized IBM's Kolkata quantum processor to demonstrate an unexpected robustness of quantum many-body scars at finite temperatures when the system is prepared in a thermal Gibbs ensemble. We identify such robustness in the PXP model, which describes quantum many-body scars in experimental systems of Rydberg atom arrays and ultracold atoms in tilted Bose--Hubbard optical lattices. By contrast, other theoretical models which host exact quantum many-body scars are found to lack such robustness, and their scarring properties quickly decay with temperature. Our study sheds light on the important differences between scarred models in terms of their algebraic structures, which impacts their resilience to finite temperature."}],"day":"30","file":[{"file_name":"FiguresData.zip","access_level":"open_access","date_updated":"2024-08-30T12:55:37Z","relation":"main_file","success":1,"file_size":322400,"date_created":"2024-08-30T12:55:37Z","content_type":"application/zip","file_id":"17472","checksum":"2bd49ce5a63f1951c1ed3d89cce4fe27","creator":"jdesaule"},{"content_type":"text/plain","file_size":1368,"success":1,"date_created":"2024-08-30T13:19:57Z","file_id":"17473","checksum":"c2ba113a241e98c394cc3ca21f3fa126","creator":"jdesaule","file_name":"readme.txt","date_updated":"2024-08-30T13:19:57Z","access_level":"open_access","relation":"main_file"}],"ddc":["530"],"month":"08"}]