[{"intvolume":"        37","volume":37,"issue":"4","_id":"19670","external_id":{"isi":["001482986200001"],"arxiv":["2501.00536"]},"isi":1,"author":[{"full_name":"Bartolucci, G.","last_name":"Bartolucci","first_name":"G."},{"full_name":"Busiello, D. M.","last_name":"Busiello","first_name":"D. M."},{"first_name":"M.","full_name":"Ciarchi, M.","last_name":"Ciarchi"},{"full_name":"Corticelli, A.","last_name":"Corticelli","first_name":"A."},{"first_name":"I.","last_name":"Di Terlizzi","full_name":"Di Terlizzi, I."},{"first_name":"Fabrizio","last_name":"Olmeda","full_name":"Olmeda, Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689"},{"last_name":"Revignas","full_name":"Revignas, D.","first_name":"D."},{"first_name":"V. M.","last_name":"Schimmenti","full_name":"Schimmenti, V. M."}],"ddc":["530"],"publisher":"AIP Publishing","year":"2025","article_number":"044122","date_published":"2025-04-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","publication":"Physics of Fluids","date_created":"2025-05-11T22:02:40Z","publication_identifier":{"eissn":["1089-7666"],"issn":["1070-6631"]},"abstract":[{"text":"“Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio e pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the “Mozzarella Phase” and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. We further analyze the effect of a less traditional stabilizer, trisodium citrate, and observe a sharp transition from the Mozzarella Phase to a completely smooth and stable sauce, in contrast to starch-stabilized mixtures, where the transition is more gradual. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish.","lang":"eng"}],"type":"journal_article","date_updated":"2026-04-28T13:24:53Z","file_date_updated":"2025-05-12T09:31:22Z","title":"Phase behavior of Cacio e Pepe sauce","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"hybrid","article_type":"original","OA_place":"publisher","has_accepted_license":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"relation":"main_file","checksum":"242d05898aa0a2348b9c108747adb5ce","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":4926853,"creator":"dernst","date_updated":"2025-05-12T09:31:22Z","file_name":"2025_PhysicsFluids_Bartolucci.pdf","date_created":"2025-05-12T09:31:22Z","file_id":"19681"}],"citation":{"apa":"Bartolucci, G., Busiello, D. M., Ciarchi, M., Corticelli, A., Di Terlizzi, I., Olmeda, F., … Schimmenti, V. M. (2025). Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>","ama":"Bartolucci G, Busiello DM, Ciarchi M, et al. Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>","ieee":"G. Bartolucci <i>et al.</i>, “Phase behavior of Cacio e Pepe sauce,” <i>Physics of Fluids</i>, vol. 37, no. 4. AIP Publishing, 2025.","ista":"Bartolucci G, Busiello DM, Ciarchi M, Corticelli A, Di Terlizzi I, Olmeda F, Revignas D, Schimmenti VM. 2025. Phase behavior of Cacio e Pepe sauce. Physics of Fluids. 37(4), 044122.","mla":"Bartolucci, G., et al. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>, vol. 37, no. 4, 044122, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>.","chicago":"Bartolucci, G., D. M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, Fabrizio Olmeda, D. Revignas, and V. M. Schimmenti. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>.","short":"G. Bartolucci, D.M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, F. Olmeda, D. Revignas, V.M. Schimmenti, Physics of Fluids 37 (2025)."},"status":"public","acknowledgement":"he authors thank Frank Jülicher, for supporting the initiative and stimulating discussions. We thank Tetsuya Spippayashi for enlightening clarifications on the historical origins of Cacio e pepe and Giuseppe Ricchitelli for helping with the construction of the experimental apparatus. We further thank Martina Gaiba, Alessandro Gaiba, John D. Treado, Virginia Lepore, Eleonora Nanu, Julia Kirsch, Lara Koehler, Burak Budanur, Irina Pi-Jaumà, Elizabeth Brückner, M.J. Franco Oñate, Giorgio Nicoletti, and Marco Salvalaglio for their support and for eating up the sample leftovers. Finally, we thank Simone Frau for taking the photograph in Fig. 1(a).","scopus_import":"1","publication_status":"published","department":[{"_id":"EdHa"}],"doi":"10.1063/5.0255841","day":"01","related_material":{"link":[{"description":"News on ISTA","url":"https://ista.ac.at/en/news/2025-ig-nobel-prize-for-perfect-pasta-sauce/","relation":"press_release"}]},"month":"04","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1},{"volume":50,"intvolume":"        50","author":[{"first_name":"Daniela","full_name":"Arpigiani, Daniela","last_name":"Arpigiani"},{"full_name":"Aschero, Valeria","last_name":"Aschero","first_name":"Valeria"},{"first_name":"Rosina Matilde","full_name":"Soler Schaller, Rosina Matilde","id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803","last_name":"Soler Schaller"},{"full_name":"Amoroso, Mariano M.","last_name":"Amoroso","first_name":"Mariano M."}],"isi":1,"_id":"19671","issue":"4","external_id":{"isi":["001476761500001"]},"year":"2025","article_number":"e70058","publisher":"Wiley","article_processing_charge":"No","date_published":"2025-04-01T00:00:00Z","type":"journal_article","date_updated":"2025-09-30T12:31:04Z","publication":"Austral Ecology","date_created":"2025-05-11T22:02:41Z","publication_identifier":{"issn":["1442-9985"],"eissn":["1442-9993"]},"abstract":[{"lang":"eng","text":"Silvopastoral use in native forests could impact population dynamics of key tree species, with contrasting effects at different life cycle stages. Prior studies in South American temperate forests have mainly focused on initial stages, lacking a comprehensive understanding of the entire life cycle within productive systems. We assessed the population dynamics of two key species of mixed forests in northern Patagonia (Austrocedrus chilensis and Nothofagus dombeyi) under two silvopastoral use intensities (high vs. low), using demographic techniques and population projection models. Over 3 years, we quantified vital rates (survival, fertility, growth, reversion and stasis) and used matrix models to calculate deterministic population growth rates (λ). High-intensity silvopastoral use had predominantly negative effects on the elements of the projection matrices of A. chilensis, whereas N. dombeyi exhibited mostly positive or no changes. As a result, projections indicated slight population decreases for A. chilensis (mostly λ < 1) at high silvopastoral use levels compared to low levels, while N. dombeyi showed similar projections (λ ≅ 1) between use levels. Decreased λ for A. chilensis resulted mainly from lower adult tree survival, while early life stages had limited influence on λ for these long-lived species. In summary, silvopastoral use affects population dynamics of key tree species of these mixed forests of northern Patagonia, with implications for sustainable management. Our findings highlight the importance of considering the entire life cycle and suggest targeted practices to enhance A. chilensis populations."}],"title":"A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"closed access","article_type":"original","acknowledgement":"We would like to express our sincere gratitude to the owners of the estates, Lisandro and Oscar Lanfré, Roberto Criado and Yayo Tillería, for allowing us to conduct our research on their properties and for generously sharing their time and knowledge throughout these years. We are also deeply thankful to our field assistants, Matías Scotti, Clara Pissolito, Noel Szudruk, Mariano Varela, Ian Mott, Brisa Guenuleo, Nicolás Bistolfi, Facundo Gómez and Belén Vallerga, who tirelessly collaborated in the arduous tasks of monitoring and data collection, even in challenging weather conditions. We are grateful to CONICET for providing the doctoral scholarship to D. Arpigiani. This study received partial financial support from the Agencia MINCyT (PICT 2015-1692) and the Universidad Nacional de Río Negro (PI 40-B-478), Argentina.","scopus_import":"1","citation":{"ista":"Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. 2025. A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. Austral Ecology. 50(4), e70058.","short":"D. Arpigiani, V. Aschero, R.M. Soler Schaller, M.M. Amoroso, Austral Ecology 50 (2025).","mla":"Arpigiani, Daniela, et al. “A Life-Cycle Approach to Understand Consequences of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” <i>Austral Ecology</i>, vol. 50, no. 4, e70058, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/aec.70058\">10.1111/aec.70058</a>.","chicago":"Arpigiani, Daniela, Valeria Aschero, Rosina Matilde Soler Schaller, and Mariano M. Amoroso. “A Life-Cycle Approach to Understand Consequences of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” <i>Austral Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/aec.70058\">https://doi.org/10.1111/aec.70058</a>.","ama":"Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. <i>Austral Ecology</i>. 2025;50(4). doi:<a href=\"https://doi.org/10.1111/aec.70058\">10.1111/aec.70058</a>","apa":"Arpigiani, D., Aschero, V., Soler Schaller, R. M., &#38; Amoroso, M. M. (2025). A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. <i>Austral Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/aec.70058\">https://doi.org/10.1111/aec.70058</a>","ieee":"D. Arpigiani, V. Aschero, R. M. Soler Schaller, and M. M. Amoroso, “A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia,” <i>Austral Ecology</i>, vol. 50, no. 4. Wiley, 2025."},"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"None","department":[{"_id":"NiBa"}],"publication_status":"published","day":"01","doi":"10.1111/aec.70058","month":"04"},{"_id":"19672","issue":"4","external_id":{"isi":["001472439600001"]},"author":[{"id":"74c777f4-32da-11ee-b498-874db0835561","full_name":"Polesello, Andrea","last_name":"Polesello","first_name":"Andrea"},{"first_name":"Giousef Alexandros","last_name":"Charinti","id":"7f7cc04c-074c-11ed-af92-eb16afd85c75","full_name":"Charinti, Giousef Alexandros"},{"full_name":"Meroni, Agostino Niyonkuru","last_name":"Meroni","first_name":"Agostino Niyonkuru"},{"orcid":"0000-0001-5836-5350","first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"},{"first_name":"Claudia","full_name":"Pasquero, Claudia","last_name":"Pasquero"}],"isi":1,"intvolume":"        17","volume":17,"date_published":"2025-04-01T00:00:00Z","article_processing_charge":"Yes","ddc":["550"],"publisher":"Wiley","project":[{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041"}],"article_number":"e2024MS004613","year":"2025","OA_type":"gold","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes","OA_place":"publisher","article_type":"original","has_accepted_license":"1","oa":1,"publication_identifier":{"eissn":["1942-2466"]},"publication":"Journal of Advances in Modeling Earth Systems","date_created":"2025-05-11T22:02:41Z","abstract":[{"text":"Some of the classical models of tropical cyclone intensification predict tropical cyclones to intensify up to a steady intensity, which depends on surface fluxes only, without any relevant role played by convective motions in the troposphere, typically assumed to have a moist adiabatic lapse rate. Simulations performed using the non-hydrostatic, high-resolution model System for Atmosphere Modeling in idealized settings (rotating radiative-convective equilibrium on a doubly periodic domain) show early intensification consistent with these theoretical expectations, but different intensity evolution, with the cyclone undergoing an oscillation in wind speed. This oscillation can be linked to feedbacks between the cyclone intensity and air buoyancy: convective heating, radiative heating, and mixing with warm low stratospheric air warm the mid and upper troposphere of the cyclone stabilizing the air column and thus reducing its intensity. After the intensity decay phase, mid and upper tropospheric cooling, mostly through cold advection from the surroundings, cooled by radiation, rebuilds Convective Available Potential Energy, that peaks just before a new intensification phase. These idealized simulations thus highlight the potentially important interactions between a tropical cyclone, its environment and radiation.","lang":"eng"}],"date_updated":"2025-09-30T12:30:29Z","type":"journal_article","DOAJ_listed":"1","file_date_updated":"2025-05-12T12:17:08Z","day":"01","ec_funded":1,"doi":"10.1029/2024MS004613","publication_status":"published","department":[{"_id":"CaMu"}],"corr_author":"1","month":"04","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ama":"Polesello A, Charinti GA, Meroni AN, Muller CJ, Pasquero C. Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes. <i>Journal of Advances in Modeling Earth Systems</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1029/2024MS004613\">10.1029/2024MS004613</a>","apa":"Polesello, A., Charinti, G. A., Meroni, A. N., Muller, C. J., &#38; Pasquero, C. (2025). Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2024MS004613\">https://doi.org/10.1029/2024MS004613</a>","ieee":"A. Polesello, G. A. Charinti, A. N. Meroni, C. J. Muller, and C. Pasquero, “Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 4. Wiley, 2025.","ista":"Polesello A, Charinti GA, Meroni AN, Muller CJ, Pasquero C. 2025. Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes. Journal of Advances in Modeling Earth Systems. 17(4), e2024MS004613.","chicago":"Polesello, Andrea, Giousef Alexandros Charinti, Agostino Niyonkuru Meroni, Caroline J Muller, and Claudia Pasquero. “Intensity Oscillations of Tropical Cyclones: Surface versus Mid and Upper Tropospheric Processes.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2025. <a href=\"https://doi.org/10.1029/2024MS004613\">https://doi.org/10.1029/2024MS004613</a>.","mla":"Polesello, Andrea, et al. “Intensity Oscillations of Tropical Cyclones: Surface versus Mid and Upper Tropospheric Processes.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 4, e2024MS004613, Wiley, 2025, doi:<a href=\"https://doi.org/10.1029/2024MS004613\">10.1029/2024MS004613</a>.","short":"A. Polesello, G.A. Charinti, A.N. Meroni, C.J. Muller, C. Pasquero, Journal of Advances in Modeling Earth Systems 17 (2025)."},"file":[{"success":1,"access_level":"open_access","relation":"main_file","checksum":"2f7c74aceaeea4be1fff4de300791319","content_type":"application/pdf","file_name":"2025_JAMES_Polesello.pdf","date_created":"2025-05-12T12:17:08Z","file_id":"19683","file_size":942325,"creator":"dernst","date_updated":"2025-05-12T12:17:08Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","acknowledgement":"The authors acknowledge two anonymous reviewers and the editor who provided insightful remarks and comments that helped to significantly improve the manuscript. AP and CJM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). Part of this work is an outcome of the project MIUR—Dipartimenti di Eccellenza 2023–2027. ANM is supported by HPC-TRES Grant 2023-04.","scopus_import":"1"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"file":[{"content_type":"application/pdf","checksum":"f9a1057d146632890466a7dc33bf625e","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2025-05-12T10:23:26Z","creator":"dernst","file_size":1094167,"file_id":"19682","date_created":"2025-05-12T10:23:26Z","file_name":"2025_JAMR_Wang.pdf"}],"citation":{"ista":"Wang V. 2025. Prime Hasse principles via diophantine second moments. Journal of the Association for Mathematical Research. 3(1), 1–26.","chicago":"Wang, Victor. “Prime Hasse Principles via Diophantine Second Moments.” <i>Journal of the Association for Mathematical Research</i>. Association for Mathematical Research, 2025. <a href=\"https://doi.org/10.56994/JAMR.003.001.001\">https://doi.org/10.56994/JAMR.003.001.001</a>.","short":"V. Wang, Journal of the Association for Mathematical Research 3 (2025) 1–26.","mla":"Wang, Victor. “Prime Hasse Principles via Diophantine Second Moments.” <i>Journal of the Association for Mathematical Research</i>, vol. 3, no. 1, Association for Mathematical Research, 2025, pp. 1–26, doi:<a href=\"https://doi.org/10.56994/JAMR.003.001.001\">10.56994/JAMR.003.001.001</a>.","apa":"Wang, V. (2025). Prime Hasse principles via diophantine second moments. <i>Journal of the Association for Mathematical Research</i>. Association for Mathematical Research. <a href=\"https://doi.org/10.56994/JAMR.003.001.001\">https://doi.org/10.56994/JAMR.003.001.001</a>","ama":"Wang V. Prime Hasse principles via diophantine second moments. <i>Journal of the Association for Mathematical Research</i>. 2025;3(1):1-26. doi:<a href=\"https://doi.org/10.56994/JAMR.003.001.001\">10.56994/JAMR.003.001.001</a>","ieee":"V. Wang, “Prime Hasse principles via diophantine second moments,” <i>Journal of the Association for Mathematical Research</i>, vol. 3, no. 1. Association for Mathematical Research, pp. 1–26, 2025."},"status":"public","scopus_import":"1","acknowledgement":"This work was partially supported by the European Union’s Horizon 2020 research and innovation program under the MarieSkłodowska-Curie Grant Agreement No. 101034413","department":[{"_id":"TiBr"}],"publication_status":"published","ec_funded":1,"day":"23","doi":"10.56994/JAMR.003.001.001","month":"01","corr_author":"1","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","arxiv":1,"date_created":"2025-05-11T22:02:41Z","publication":"Journal of the Association for Mathematical Research","publication_identifier":{"eissn":["2998-4114"]},"abstract":[{"lang":"eng","text":"We show that almost all primes p =\\= ± 4 mod9 are sums of three cubes, assuming a conjecture due to Hooley, Manin, et al. on cubic fourfolds. This conjecture is approachable under standard statistical hypotheses on geometric families of L-functions."}],"type":"journal_article","date_updated":"2025-05-12T10:26:00Z","file_date_updated":"2025-05-12T10:23:26Z","title":"Prime Hasse principles via diophantine second moments","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"diamond","article_type":"original","OA_place":"publisher","has_accepted_license":"1","oa":1,"ddc":["510"],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"publisher":"Association for Mathematical Research","year":"2025","date_published":"2025-01-23T00:00:00Z","page":"1-26","article_processing_charge":"No","intvolume":"         3","volume":3,"issue":"1","_id":"19673","external_id":{"arxiv":["2304.08674"]},"author":[{"first_name":"Victor","orcid":"0000-0002-0704-7026","last_name":"Wang","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","full_name":"Wang, Victor"}]},{"article_processing_charge":"No","arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","date_published":"2025-04-14T00:00:00Z","month":"04","doi":"10.48550/arXiv.2411.00246","day":"14","publication_status":"submitted","department":[{"_id":"FrLo"}],"article_number":"2411.00246","year":"2025","acknowledgement":"The authors gratefully acknowledge Volkan Cevher for an insightful discussion about sparse recovery algorithms, Alex Smola for valuable feedback on the experiments, and Marco Baroni for an engaging conversation on the phenomenon of head specialization in NLP.\r\n","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2411.00246"}],"citation":{"ieee":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, and F. Locatello, “ResiDual transformer alignment with spectral decomposition,” <i>arXiv</i>. .","ama":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>","apa":"Basile, L., Maiorca, V., Bortolussi, L., Rodolà, E., &#38; Locatello, F. (n.d.). ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>","chicago":"Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>.","mla":"Basile, Lorenzo, et al. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, 2411.00246, doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>.","short":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.).","ista":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv, 2411.00246."},"author":[{"first_name":"Lorenzo","last_name":"Basile","full_name":"Basile, Lorenzo"},{"full_name":"Maiorca, Valentino","last_name":"Maiorca","first_name":"Valentino"},{"last_name":"Bortolussi","full_name":"Bortolussi, Luca","first_name":"Luca"},{"first_name":"Emanuele","last_name":"Rodolà","full_name":"Rodolà, Emanuele"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"}],"oa":1,"OA_place":"repository","_id":"19674","OA_type":"green","external_id":{"arxiv":["2411.00246"]},"title":"ResiDual transformer alignment with spectral decomposition","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-19T07:03:16Z","type":"preprint","abstract":[{"text":"When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets).","lang":"eng"}],"publication":"arXiv","date_created":"2025-05-11T22:02:41Z"},{"supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"date_created":"2025-05-12T15:12:28Z","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate.","lang":"eng"}],"type":"dissertation","date_updated":"2026-06-18T19:23:35Z","file_date_updated":"2025-05-12T15:43:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Transition to turbulence : Data-, solution-, and pattern-driven approaches","OA_place":"publisher","has_accepted_license":"1","oa":1,"citation":{"ama":"Yalniz G. Transition to turbulence : Data-, solution-, and pattern-driven approaches. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>","apa":"Yalniz, G. (2025). <i>Transition to turbulence : Data-, solution-, and pattern-driven approaches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>","ieee":"G. Yalniz, “Transition to turbulence : Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.","ista":"Yalniz G. 2025. Transition to turbulence : Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","chicago":"Yalniz, Gökhan. “Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>.","mla":"Yalniz, Gökhan. <i>Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>.","short":"G. Yalniz, Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025."},"file":[{"file_id":"19685","date_created":"2025-05-12T15:13:28Z","file_name":"Gökhan Yalnız - PhD thesis.pdf","date_updated":"2025-05-12T15:13:28Z","creator":"gyalniz","file_size":20058169,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"0e452642b79f13633f1595bde71a67e3","relation":"main_file"},{"description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","access_level":"open_access","title":"Chapter 2 - Movie 2A.1","checksum":"921099d76adab2df784ce12ce41cfb22","relation":"supplementary_material","content_type":"video/mp4","file_name":"Movie 2A.1.mp4","file_id":"19686","date_created":"2025-05-12T15:15:59Z","creator":"gyalniz","file_size":37763743,"date_updated":"2025-05-12T15:43:28Z"},{"date_created":"2025-05-12T15:16:09Z","file_id":"19687","file_name":"Movie 3A.1.mp4","date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","file_size":3902655,"description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","access_level":"open_access","title":"Chapter 3 - Movie 3A.1","content_type":"video/mp4","checksum":"0ae5ac7d9896003c0c4207dd746808dc","relation":"supplementary_material"},{"date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","file_size":7043169,"date_created":"2025-05-12T15:16:21Z","file_id":"19688","file_name":"Movie 3A.2.mp4","content_type":"video/mp4","checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","relation":"supplementary_material","access_level":"open_access","description":"Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.2"},{"relation":"supplementary_material","checksum":"7ed871f428100d6827ac9b0e8ca8e985","content_type":"video/mp4","title":"Chapter 3 - Movie 3A.3","access_level":"open_access","description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","file_size":7748659,"creator":"gyalniz","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 3A.3.mp4","date_created":"2025-05-12T15:16:36Z","file_id":"19689"},{"date_created":"2025-05-12T15:16:50Z","file_id":"19690","file_name":"Movie 3A.4.mp4","date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","file_size":5873052,"access_level":"open_access","description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","title":"Chapter 3 - Movie 3A.4","content_type":"video/mp4","checksum":"dd5a252e1da00c8f303588e22e2baeef","relation":"supplementary_material"},{"file_name":"Movie 4A.1.mp4","file_id":"19691","date_created":"2025-05-12T15:17:11Z","creator":"gyalniz","file_size":9209327,"date_updated":"2025-05-12T15:43:28Z","access_level":"open_access","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit.","title":"Chapter 4 - Movie 4A.1","checksum":"5ac58b86810698db28cbfc28f351ff70","relation":"supplementary_material","content_type":"video/mp4"},{"creator":"gyalniz","file_size":5893993,"date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 5A.1.mp4","file_id":"19692","date_created":"2025-05-12T15:17:43Z","checksum":"ac877f1e1ef39439911bf37cb1793b8e","relation":"supplementary_material","content_type":"video/mp4","access_level":"open_access","description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","title":"Chapter 5 - Movie 5A.1"},{"file_name":"Movie 5A.2.mp4","date_created":"2025-05-12T15:17:49Z","file_id":"19693","file_size":3990352,"creator":"gyalniz","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 5 - Movie 5A.2","access_level":"open_access","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","relation":"supplementary_material","checksum":"fd17eabb70129ceaa414e40924d1d2fe","content_type":"video/mp4"},{"date_created":"2025-05-12T15:17:58Z","file_id":"19694","file_name":"Movie 5A.3.mp4","date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","file_size":5171009,"access_level":"open_access","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in of the full (L_x = L_z) domain.","title":"Chapter 5 - Movie 5A.3","content_type":"video/mp4","checksum":"32f904497ab0bbee38f0788d96b91454","relation":"supplementary_material"},{"access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","checksum":"f313261b9bb12dfb943fead8318954c6","date_created":"2025-05-12T15:27:10Z","file_id":"19695","file_name":"Gökhan Yalnız - PhD thesis.zip","date_updated":"2025-05-12T15:43:28Z","file_size":18991996,"creator":"gyalniz"}],"status":"public","acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"day":"13","doi":"10.15479/AT-ISTA-19684","related_material":{"record":[{"status":"public","id":"9558","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"12105"},{"status":"public","id":"13274","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14466"},{"status":"public","relation":"part_of_dissertation","id":"7563"}]},"corr_author":"1","month":"05","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"_id":"19684","author":[{"last_name":"Yalniz","full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","first_name":"Gökhan"}],"ddc":["514","519","532","004"],"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"publisher":"Institute of Science and Technology Austria","year":"2025","degree_awarded":"PhD","date_published":"2025-05-13T00:00:00Z","page":"155","article_processing_charge":"No"},{"file_date_updated":"2025-07-31T08:14:40Z","type":"research_data","date_updated":"2026-06-10T08:33:41Z","date_created":"2025-05-14T10:46:07Z","author":[{"first_name":"Benjamin","last_name":"Tatman","id":"71cda2f3-e604-11ee-a1df-da10587eda3f","full_name":"Tatman, Benjamin"}],"oa":1,"has_accepted_license":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","title":"Dataset for \"Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State\"","_id":"19696","year":"2025","status":"public","publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"citation":{"ista":"Tatman B. 2025. Dataset for ‘Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-19696\">10.15479/AT-ISTA-19696</a>.","mla":"Tatman, Benjamin. <i>Dataset for “Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19696\">10.15479/AT-ISTA-19696</a>.","chicago":"Tatman, Benjamin. “Dataset for ‘Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19696\">https://doi.org/10.15479/AT-ISTA-19696</a>.","short":"B. Tatman, (2025).","apa":"Tatman, B. (2025). Dataset for “Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19696\">https://doi.org/10.15479/AT-ISTA-19696</a>","ama":"Tatman B. Dataset for “Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.” 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19696\">10.15479/AT-ISTA-19696</a>","ieee":"B. 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We present new grid-based hydrodynamics simulations, performed with the binary on the grid and a locally isothermal equation of state, in which the binary is seen to functionally \"stop accreting\" if the orbital Mach number in the disk exceeds a threshold value of about 40. Above this threshold, the disk continues to extract angular momentum from the binary orbit, but it delivers very little mass to the black holes and instead piles up mass in a ring surrounding the binary. This ring will eventually become viscously relaxed and deliver mass to the binary at the large-scale inflow rate. However, we show that the timescale for such relaxation can far exceed the implied binary lifetime. We demonstrate that the ability of a binary–disk system to equilibrate is dependent on the efficiency at which accretion streams deposit mass onto the binary, which, in turn is highly sensitive to the thermodynamic conditions of the inner disk. If disks around massive black hole binaries do operate in such nonaccreting regimes, it suggests these systems may be dimmer than their single black hole counterparts but could exhibit dramatic rebrightening after the black holes inspiral and merge. This dimming begins in the UV/optical and could completely choke high-energy emission, such that these systems would likely be intrinsically X-ray weak with reddened continua, potentially resembling the spectra of \"little red dots\" recently identified in JWST observations.","lang":"eng"}],"has_accepted_license":"1","oa":1,"OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Suppressed accretion onto massive black hole binaries surrounded by thin disks","OA_place":"publisher","article_type":"original","acknowledgement":"C.T. sincerely thanks Daniel J. D'Orazio for useful and illuminating discussions. This work was supported by the European Union's Horizon 2023 research and innovation program under Marie Sklodowska-Curie grant agreement No. 101148364, by Sapere Aude Starting grant No. 121587 through the Danish Independent Research Fund, by the LISA Preparatory Science Program (LPS) through NASA grant 80NSSC24K0440, and by NASA Astrophysics Theory Program (ATP) grant 80NSSC22K0822. Computation time for this work was supported through the NYU IT High Performance Computing resources as well as the Tycho supercomputer hosted at the SCIENCE HPC center at the University of Copenhagen.","scopus_import":"1","file":[{"relation":"main_file","checksum":"0d4c57ee944599c0789f3db467c5ca2f","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":1058601,"creator":"dernst","date_updated":"2025-05-19T07:20:30Z","file_name":"2025_AstrophysicalJour_Tiede.pdf","file_id":"19708","date_created":"2025-05-19T07:20:30Z"}],"citation":{"ieee":"C. Tiede, J. Zrake, A. Macfadyen, and Z. Haiman, “Suppressed accretion onto massive black hole binaries surrounded by thin disks,” <i>The Astrophysical Journal</i>, vol. 984, no. 2. IOP Publishing, 2025.","apa":"Tiede, C., Zrake, J., Macfadyen, A., &#38; Haiman, Z. (2025). Suppressed accretion onto massive black hole binaries surrounded by thin disks. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/adc727\">https://doi.org/10.3847/1538-4357/adc727</a>","ama":"Tiede C, Zrake J, Macfadyen A, Haiman Z. Suppressed accretion onto massive black hole binaries surrounded by thin disks. <i>The Astrophysical Journal</i>. 2025;984(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/adc727\">10.3847/1538-4357/adc727</a>","mla":"Tiede, Christopher, et al. “Suppressed Accretion onto Massive Black Hole Binaries Surrounded by Thin Disks.” <i>The Astrophysical Journal</i>, vol. 984, no. 2, 144, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4357/adc727\">10.3847/1538-4357/adc727</a>.","chicago":"Tiede, Christopher, Jonathan Zrake, Andrew Macfadyen, and Zoltán Haiman. “Suppressed Accretion onto Massive Black Hole Binaries Surrounded by Thin Disks.” <i>The Astrophysical Journal</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4357/adc727\">https://doi.org/10.3847/1538-4357/adc727</a>.","short":"C. Tiede, J. Zrake, A. Macfadyen, Z. Haiman, The Astrophysical Journal 984 (2025).","ista":"Tiede C, Zrake J, Macfadyen A, Haiman Z. 2025. Suppressed accretion onto massive black hole binaries surrounded by thin disks. The Astrophysical Journal. 984(2), 144."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","arxiv":1,"doi":"10.3847/1538-4357/adc727","day":"09","department":[{"_id":"ZoHa"}],"publication_status":"published","month":"05"},{"acknowledgement":"B.W. and J.L. acknowledge support from JWST-GO-04233.009-A. R.L.D. is supported by the Australian Research Council through the Discovery Early Career Researcher Award (DECRA) Fellowship DE240100136 funded by the Australian Government. T.B.M. was supported by a CIERA postdoctoral fellowship. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project #562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). The JWST data presented in this article were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed here can be accessed via DOI:10.17909/c3t4-9p39. Computations for this research were performed on the Pennsylvania State University's Institute for Computational and Data Sciences' Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information.","scopus_import":"1","status":"public","citation":{"ieee":"B. Wang <i>et al.</i>, “RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow,” <i>The Astrophysical Journal</i>, vol. 984, no. 2. IOP Publishing, 2025.","apa":"Wang, B., De Graaff, A., Davies, R. L., Greene, J. E., Leja, J., Brammer, G. B., … Whitaker, K. E. (2025). RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">https://doi.org/10.3847/1538-4357/adc1ca</a>","ama":"Wang B, De Graaff A, Davies RL, et al. RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow. <i>The Astrophysical Journal</i>. 2025;984(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">10.3847/1538-4357/adc1ca</a>","mla":"Wang, Bingjie, et al. “RUBIES: JWST/NIRSpec Confirmation of an Infrared-Luminous, Broad-Line Little Red Dot with an Ionized Outflow.” <i>The Astrophysical Journal</i>, vol. 984, no. 2, 121, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">10.3847/1538-4357/adc1ca</a>.","short":"B. Wang, A. De Graaff, R.L. Davies, J.E. Greene, J. Leja, G.B. Brammer, A.D. Goulding, T.B. Miller, K.A. Suess, A. Weibel, C.C. Williams, R. Bezanson, L.A. Boogaard, N.J. Cleri, M. Hirschmann, H. Katz, I. Labbé, M.V. Maseda, J.J. Matthee, I. Mcconachie, R.P. Naidu, P.A. Oesch, H.W. Rix, D.J. Setton, K.E. Whitaker, The Astrophysical Journal 984 (2025).","chicago":"Wang, Bingjie, Anna De Graaff, Rebecca L. Davies, Jenny E. Greene, Joel Leja, Gabriel B. Brammer, Andy D. Goulding, et al. “RUBIES: JWST/NIRSpec Confirmation of an Infrared-Luminous, Broad-Line Little Red Dot with an Ionized Outflow.” <i>The Astrophysical Journal</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">https://doi.org/10.3847/1538-4357/adc1ca</a>.","ista":"Wang B, De Graaff A, Davies RL, Greene JE, Leja J, Brammer GB, Goulding AD, Miller TB, Suess KA, Weibel A, Williams CC, Bezanson R, Boogaard LA, Cleri NJ, Hirschmann M, Katz H, Labbé I, Maseda MV, Matthee JJ, Mcconachie I, Naidu RP, Oesch PA, Rix HW, Setton DJ, Whitaker KE. 2025. RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow. The Astrophysical Journal. 984(2), 121."},"file":[{"content_type":"application/pdf","checksum":"1a9ff4516d11808bc6947744473c9fc2","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2025-05-19T07:08:39Z","creator":"dernst","file_size":3522072,"file_id":"19707","date_created":"2025-05-19T07:08:39Z","file_name":"2025_AstrophysicalJour_Wang.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"arxiv":1,"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"month":"05","day":"09","doi":"10.3847/1538-4357/adc1ca","publication_status":"published","department":[{"_id":"JoMa"}],"file_date_updated":"2025-05-19T07:08:39Z","date_updated":"2026-02-16T12:42:43Z","DOAJ_listed":"1","type":"journal_article","abstract":[{"lang":"eng","text":"The JWST discovery of \"little red dots\" (LRDs) is reshaping our picture of the early Universe, yet the physical mechanisms driving their compact size and UV-optical colors remain elusive. Here, we report an unusually bright LRD (zspec = 3.1) observed as part of the RUBIES program. This LRD exhibits broad emission lines (FWHM ∼ 4000 km s−1), a blue UV continuum, a clear Balmer break, and a red continuum sampled out to rest-frame 4 μm with MIRI. We develop a new joint galaxy and active galactic nucleus (AGN) model within the Prospector Bayesian inference framework and perform spectrophotometric modeling using NIRCam, MIRI, and NIRSpec/Prism observations. Our fiducial model reveals a M* ∼ 109 M⊙ galaxy alongside a dust-reddened AGN driving the optical emission. Explaining the rest-frame optical color as a reddened AGN requires AV ≳ 3, suggesting that a great majority of the accretion disk energy is reradiated as dust emission. Yet, despite clear AGN signatures, we find a surprising lack of hot torus emission, which implies that either the dust emission in this object must be cold, or the red continuum must instead be driven by a massive, evolved stellar population of the host galaxy—seemingly inconsistent with the high-EW broad lines (Hα rest-frame EW ∼ 800 Å). The widths and luminosities of Pa-β, Pa-δ, Pa-γ, and Hα imply a modest black hole mass of MBH ∼ 108 M⊙. Additionally, we identify a narrow blueshifted He i λ 1.083 μm absorption feature in NIRSpec/G395M spectra, signaling an ionized outflow with kinetic energy up to ∼1% the luminosity of the AGN. The low redshift of RUBIES-BLAGN-1, combined with the depth and richness of the JWST imaging and spectroscopic observations, provides a unique opportunity to build a physical model for these so-far mysterious LRDs, which may prove to be a crucial phase in the early formation of massive galaxies and their supermassive black holes."}],"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"publication":"The Astrophysical Journal","date_created":"2025-05-18T22:02:49Z","has_accepted_license":"1","oa":1,"OA_place":"publisher","article_type":"original","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow","article_number":"121","year":"2025","publisher":"IOP Publishing","ddc":["520"],"article_processing_charge":"Yes","date_published":"2025-05-09T00:00:00Z","volume":984,"intvolume":"       984","author":[{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"last_name":"De Graaff","full_name":"De Graaff, Anna","first_name":"Anna"},{"full_name":"Davies, Rebecca L.","last_name":"Davies","first_name":"Rebecca L."},{"last_name":"Greene","full_name":"Greene, Jenny E.","first_name":"Jenny E."},{"first_name":"Joel","last_name":"Leja","full_name":"Leja, Joel"},{"full_name":"Brammer, Gabriel B.","last_name":"Brammer","first_name":"Gabriel B."},{"first_name":"Andy D.","full_name":"Goulding, Andy D.","last_name":"Goulding"},{"full_name":"Miller, Tim B.","last_name":"Miller","first_name":"Tim B."},{"first_name":"Katherine A.","last_name":"Suess","full_name":"Suess, Katherine A."},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"},{"first_name":"Rachel","last_name":"Bezanson","full_name":"Bezanson, Rachel"},{"last_name":"Boogaard","full_name":"Boogaard, Leindert A.","first_name":"Leindert A."},{"first_name":"Nikko J.","last_name":"Cleri","full_name":"Cleri, Nikko J."},{"first_name":"Michaela","last_name":"Hirschmann","full_name":"Hirschmann, Michaela"},{"first_name":"Harley","full_name":"Katz, Harley","last_name":"Katz"},{"full_name":"Labbé, Ivo","last_name":"Labbé","first_name":"Ivo"},{"first_name":"Michael V.","full_name":"Maseda, Michael V.","last_name":"Maseda"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"full_name":"Mcconachie, Ian","last_name":"Mcconachie","first_name":"Ian"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"last_name":"Oesch","full_name":"Oesch, Pascal A.","first_name":"Pascal A."},{"last_name":"Rix","full_name":"Rix, Hans Walter","first_name":"Hans Walter"},{"full_name":"Setton, David J.","last_name":"Setton","first_name":"David J."},{"full_name":"Whitaker, Katherine E.","last_name":"Whitaker","first_name":"Katherine E."}],"isi":1,"_id":"19700","issue":"2","external_id":{"arxiv":["2403.02304"],"isi":["001481589300001"]}},{"date_published":"2025-05-01T00:00:00Z","pmid":1,"page":"249-274","article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"project":[{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"}],"publisher":"Annual Reviews","year":"2025","_id":"19701","external_id":{"pmid":["39929539"],"isi":["001488641500013"]},"isi":1,"author":[{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper"},{"first_name":"Pieter Rein Ten","last_name":"Wolde","full_name":"Wolde, Pieter Rein Ten"}],"intvolume":"        54","volume":54,"department":[{"_id":"GaTk"}],"publication_status":"published","doi":"10.1146/annurev-biophys-060524-102720","day":"01","corr_author":"1","month":"05","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual review of biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual review of biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025.","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual review of biophysics. 54, 249–274.","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>.","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>.","short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274."},"file":[{"access_level":"open_access","success":1,"checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","relation":"main_file","content_type":"application/pdf","file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","date_created":"2025-05-19T07:55:51Z","file_id":"19710","creator":"dernst","file_size":317925,"date_updated":"2025-05-19T07:55:51Z"}],"status":"public","scopus_import":"1","acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","title":"Information processing in biochemical networks","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid","article_type":"original","OA_place":"publisher","has_accepted_license":"1","oa":1,"date_created":"2025-05-18T22:02:50Z","publication":"Annual review of biophysics","publication_identifier":{"eissn":["1936-1238"]},"abstract":[{"text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.","lang":"eng"}],"type":"journal_article","date_updated":"2025-09-30T12:33:33Z","file_date_updated":"2025-05-19T07:55:51Z"},{"citation":{"ista":"Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs. PLoS computational biology. 21(5), e1012868.","short":"L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.","mla":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>, vol. 21, no. 5, Public Library of Science, 2025, p. e1012868, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>.","chicago":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>. Public Library of Science, 2025. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>.","apa":"Kopfová, L., &#38; Tkadlec, J. (2025). Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>","ama":"Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. <i>PLoS computational biology</i>. 2025;21(5):e1012868. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>","ieee":"L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,” <i>PLoS computational biology</i>, vol. 21, no. 5. Public Library of Science, p. e1012868, 2025."},"file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"73e35151eebd5064972c5a07ffdf2b69","relation":"main_file","date_created":"2025-05-19T07:45:31Z","file_id":"19709","file_name":"2025_PloSCompBio_Kopfova.pdf","date_updated":"2025-05-19T07:45:31Z","creator":"dernst","file_size":6805943}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","scopus_import":"1","day":"01","doi":"10.1371/journal.pcbi.1012868","department":[{"_id":"GradSch"}],"publication_status":"published","month":"05","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","arxiv":1,"publication_identifier":{"eissn":["1553-7358"]},"date_created":"2025-05-18T22:02:50Z","publication":"PLoS computational biology","abstract":[{"text":"Moran Birth-death process is a standard stochastic process that is used to model natural selection in spatially structured populations. A newly occurring mutation that invades a population of residents can either fixate on the whole population or it can go extinct due to random drift. The duration of the process depends not only on the total population size n, but also on the spatial structure of the population. In this work, we consider the Moran process with a single type of individuals who invade and colonize an otherwise empty environment. Mathematically, this corresponds to the setting where the residents have zero reproduction rate, thus they never reproduce. The spatial structure is represented by a graph. We present two main contributions. First, in contrast to the Moran process in which residents do reproduce, we show that the colonization time is always at most a polynomial function of the population size n. Namely, we show that colonization always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify the slowest graph where it takes exactly that many steps. Moreover, we establish a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various complications that one faces when attempting to measure fixation times and colonization times in spatially structured populations, and we propose to measure the real duration of the process, rather than counting the steps of the classic Moran process.","lang":"eng"}],"date_updated":"2025-09-30T12:34:03Z","DOAJ_listed":"1","type":"journal_article","file_date_updated":"2025-05-19T07:45:31Z","OA_type":"gold","title":"Colonization times in Moran process on graphs","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","article_type":"original","has_accepted_license":"1","oa":1,"ddc":["000"],"publisher":"Public Library of Science","year":"2025","date_published":"2025-05-01T00:00:00Z","page":"e1012868","article_processing_charge":"Yes","intvolume":"        21","volume":21,"external_id":{"isi":["001481670600002"],"arxiv":["2410.09476"]},"_id":"19702","issue":"5","isi":1,"author":[{"id":"17691681-50b9-11ef-ad56-edf4cacb21b0","full_name":"Kopfová, Lenka","last_name":"Kopfová","first_name":"Lenka"},{"first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","last_name":"Tkadlec"}]},{"publisher":"Elsevier","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288"}],"ddc":["570"],"year":"2025","date_published":"2025-09-08T00:00:00Z","pmid":1,"article_processing_charge":"Yes (in subscription journal)","page":"2237-2247.e4","intvolume":"        60","volume":60,"_id":"19703","issue":"17","external_id":{"isi":["001570502100005"],"pmid":["40347948"]},"author":[{"full_name":"Mclaren, Susannah B.P.","last_name":"Mclaren","first_name":"Susannah B.P."},{"first_name":"Shi-lei","last_name":"Xue","full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Siyuan","full_name":"Ding, Siyuan","last_name":"Ding"},{"first_name":"Alexander K.","last_name":"Winkel","full_name":"Winkel, Alexander K."},{"first_name":"Oscar","last_name":"Baldwin","full_name":"Baldwin, Oscar"},{"last_name":"Dwarakacherla","full_name":"Dwarakacherla, Shreya","first_name":"Shreya"},{"first_name":"Kristian","full_name":"Franze, Kristian","last_name":"Franze"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Xiong","full_name":"Xiong, Fengzhu","first_name":"Fengzhu"}],"isi":1,"status":"public","citation":{"ieee":"S. B. P. Mclaren <i>et al.</i>, “Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord,” <i>Developmental Cell</i>, vol. 60, no. 17. Elsevier, p. 2237–2247.e4, 2025.","apa":"Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla, S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>","ama":"Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. 2025;60(17):2237-2247.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>","mla":"Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>, vol. 60, no. 17, Elsevier, 2025, p. 2237–2247.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>.","short":"S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla, K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4.","chicago":"Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel, Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>.","ista":"Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. Developmental Cell. 60(17), 2237–2247.e4."},"file":[{"success":1,"access_level":"open_access","relation":"main_file","checksum":"1ca6f0822c1cbd430686d5e2a4f96401","content_type":"application/pdf","file_name":"2025_DevelopmentalCell_McLaren.pdf","file_id":"20872","date_created":"2025-12-29T13:45:05Z","file_size":12564806,"creator":"dernst","date_updated":"2025-12-29T13:45:05Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"scopus_import":"1","acknowledgement":"We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum, I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi, and Xiong labs for technical assistance and constructive feedback. We thank Ryan Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.; an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an ERC Starting Grant (851288) to E.H.","month":"09","doi":"10.1016/j.devcel.2025.04.010","ec_funded":1,"day":"08","publication_status":"published","department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"An enlarged brain underlies the complex central nervous system of vertebrates. The dramatic expansion of the brain that diverges its shape from the spinal cord follows neural tube closure during embryonic development. Here, we show that this differential deformation is encoded by a pre-pattern of tissue material properties in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting in a thinning versus a resisting response to increasing lumen pressure, respectively. The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain cells to the spinal cord can locally create an expanded brain-like morphology in some cases. Our findings raise questions in vertebrate head evolution and suggest a general role of mechanical pre-patterning in sculpting epithelial tubes.","lang":"eng"}],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"date_created":"2025-05-18T22:02:50Z","publication":"Developmental Cell","file_date_updated":"2025-12-29T13:45:05Z","PlanS_conform":"1","date_updated":"2025-12-29T14:58:14Z","type":"journal_article","OA_place":"publisher","article_type":"original","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord","oa":1,"has_accepted_license":"1"},{"page":"398-410","article_processing_charge":"Yes (via OA deal)","date_published":"2025-06-12T00:00:00Z","pmid":1,"year":"2025","ddc":["570"],"publisher":"Springer Nature","project":[{"grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba"},{"first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"first_name":"Michał","full_name":"Januszewski, Michał","last_name":"Januszewski"},{"full_name":"Vistunou, Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","first_name":"Vitali"},{"first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas"},{"first_name":"Jakob","orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline"},{"first_name":"Bárbara","last_name":"Oliveira","full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Viren","last_name":"Jain","full_name":"Jain, Viren"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G"}],"isi":1,"_id":"19704","external_id":{"isi":["001483477000001"],"pmid":["40335689"]},"volume":642,"intvolume":"       642","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"ec_funded":1,"doi":"10.1038/s41586-025-08985-1","day":"12","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"GaNo"}],"publication_status":"published","month":"06","corr_author":"1","related_material":{"record":[{"relation":"earlier_version","id":"18677","status":"public"},{"id":"18697","relation":"research_data","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/","relation":"press_release","description":"News on ISTA website"}]},"scopus_import":"1","acknowledgement":"We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).","file":[{"file_id":"19959","date_created":"2025-07-03T06:55:20Z","file_name":"2025_Nature_Tavakoli.pdf","date_updated":"2025-07-03T06:55:20Z","creator":"dernst","file_size":133201290,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"ebc99d7108e728f46db0a009292675ef","relation":"main_file"}],"citation":{"mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp. 398–410, doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>.","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410.","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410, 2025.","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","oa":1,"has_accepted_license":"1","OA_type":"hybrid","title":"Light-microscopy-based connectomic reconstruction of mammalian brain tissue","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","article_type":"original","date_updated":"2026-04-28T13:33:34Z","type":"journal_article","PlanS_conform":"1","file_date_updated":"2025-07-03T06:55:20Z","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","date_created":"2025-05-18T22:02:51Z","abstract":[{"text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner.","lang":"eng"}]},{"oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Virtual bound states of the Pauli operator with an Aharonov–Bohm potential","OA_type":"hybrid","APC_amount":"2320,48 EUR","article_type":"original","OA_place":"publisher","type":"journal_article","date_updated":"2026-05-06T13:03:25Z","PlanS_conform":"1","file_date_updated":"2025-12-30T08:23:12Z","date_created":"2025-05-18T22:02:51Z","publication":"Reviews in Mathematical Physics","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"abstract":[{"text":"A maximal realization of the two-dimensional Pauli operator, subject to Aharonov–Bohm magnetic field, is investigated. Contrary to the case of the Pauli operator with regular magnetic potentials, it is shown that both components of the Pauli operator are critical. Asymptotics of the weakly coupled eigenvalues, generated by electric (not necessarily self-adjoint) perturbations, are derived.","lang":"eng"}],"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","arxiv":1,"department":[{"_id":"RoSe"}],"publication_status":"published","ec_funded":1,"day":"01","doi":"10.1142/S0129055X25500114","month":"07","scopus_import":"1","acknowledgement":"Thanks belong to Johannes Ageskov and Matˇej Tuˇsek for helpful discussions on some technical details. M. F. would further like to acknowledge support for research on this paper from the European Unions Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413 as well as support by funding from Villum Fonden through the QMATH Centreof Excellence Grant No. 10059. D. K. was supported by the EXPRO Grant No.20-17749X of the Czech Science Foundation (GACR).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_created":"2025-12-30T08:23:12Z","file_id":"20893","file_name":"2025_ReviewsMathPhysics_Fialova.pdf","date_updated":"2025-12-30T08:23:12Z","creator":"dernst","file_size":484646,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"559d97ee2da28bf0bd2c6af507f3a914","relation":"main_file"}],"citation":{"ieee":"M. Fialova and D. Krejčiřík, “Virtual bound states of the Pauli operator with an Aharonov–Bohm potential,” <i>Reviews in Mathematical Physics</i>, vol. 37, no. 6. World Scientific Publishing, 2025.","ama":"Fialova M, Krejčiřík D. Virtual bound states of the Pauli operator with an Aharonov–Bohm potential. <i>Reviews in Mathematical Physics</i>. 2025;37(6). doi:<a href=\"https://doi.org/10.1142/S0129055X25500114\">10.1142/S0129055X25500114</a>","apa":"Fialova, M., &#38; Krejčiřík, D. (2025). Virtual bound states of the Pauli operator with an Aharonov–Bohm potential. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X25500114\">https://doi.org/10.1142/S0129055X25500114</a>","mla":"Fialova, Marie, and David Krejčiřík. “Virtual Bound States of the Pauli Operator with an Aharonov–Bohm Potential.” <i>Reviews in Mathematical Physics</i>, vol. 37, no. 6, 2550011, World Scientific Publishing, 2025, doi:<a href=\"https://doi.org/10.1142/S0129055X25500114\">10.1142/S0129055X25500114</a>.","chicago":"Fialova, Marie, and David Krejčiřík. “Virtual Bound States of the Pauli Operator with an Aharonov–Bohm Potential.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2025. <a href=\"https://doi.org/10.1142/S0129055X25500114\">https://doi.org/10.1142/S0129055X25500114</a>.","short":"M. Fialova, D. Krejčiřík, Reviews in Mathematical Physics 37 (2025).","ista":"Fialova M, Krejčiřík D. 2025. Virtual bound states of the Pauli operator with an Aharonov–Bohm potential. Reviews in Mathematical Physics. 37(6), 2550011."},"status":"public","author":[{"full_name":"Fialova, Marie","id":"e9c9844d-9e21-11ec-b482-f96fc09f7c4d","last_name":"Fialova","first_name":"Marie"},{"last_name":"Krejčiřík","full_name":"Krejčiřík, David","first_name":"David"}],"isi":1,"issue":"6","_id":"19705","external_id":{"isi":["001481012500001"],"arxiv":["2501.17029"]},"volume":37,"intvolume":"        37","article_processing_charge":"Yes (in subscription journal)","date_published":"2025-07-01T00:00:00Z","year":"2025","article_number":"2550011","ddc":["530","510"],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413"}],"publisher":"World Scientific Publishing"},{"article_processing_charge":"No","page":"385-415","date_published":"2025-04-28T00:00:00Z","year":"2025","publisher":"Springer Nature","author":[{"orcid":"0000-0002-2505-4246","first_name":"Miguel","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"first_name":"Simon-Philipp","full_name":"Merz, Simon-Philipp","last_name":"Merz"},{"full_name":"Stählin, Patrick","last_name":"Stählin","first_name":"Patrick"},{"first_name":"Akin","orcid":"0000-0002-8929-0221","last_name":"Ünal","id":"f6b56fb6-dc63-11ee-9dbf-f6780863a85a","full_name":"Ünal, Akin"}],"_id":"19712","alternative_title":["LNCS"],"volume":15606,"intvolume":"     15606","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Submitted Version","corr_author":"1","month":"04","doi":"10.1007/978-3-031-91095-1_14","day":"28","publication_status":"published","department":[{"_id":"KrPi"}],"acknowledgement":"We thank Pierre Briaud and Morten Øygarden for helpful discussions on algebraic attacks on RSD, and the EC reviewers for helpful comments.","scopus_import":"1","main_file_link":[{"url":"https://www.research-collection.ethz.ch/handle/20.500.11850/732894","open_access":"1"}],"status":"public","citation":{"short":"M. Cueto Noval, S.-P. Merz, P. Stählin, A. Ünal, in:, 44th Annual International Conference on the Theory and Applications of Cryptographic Techniques, Springer Nature, 2025, pp. 385–415.","chicago":"Cueto Noval, Miguel, Simon-Philipp Merz, Patrick Stählin, and Akin Ünal. “On the Soundness of Algebraic Attacks against Code-Based Assumptions.” In <i>44th Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>, 15606:385–415. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-031-91095-1_14\">https://doi.org/10.1007/978-3-031-91095-1_14</a>.","mla":"Cueto Noval, Miguel, et al. “On the Soundness of Algebraic Attacks against Code-Based Assumptions.” <i>44th Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>, vol. 15606, Springer Nature, 2025, pp. 385–415, doi:<a href=\"https://doi.org/10.1007/978-3-031-91095-1_14\">10.1007/978-3-031-91095-1_14</a>.","ista":"Cueto Noval M, Merz S-P, Stählin P, Ünal A. 2025. On the soundness of algebraic attacks against code-based assumptions. 44th Annual International Conference on the Theory and Applications of Cryptographic Techniques. EUROCRYPT: International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 15606, 385–415.","ieee":"M. Cueto Noval, S.-P. Merz, P. Stählin, and A. Ünal, “On the soundness of algebraic attacks against code-based assumptions,” in <i>44th Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>, Madrid, Spain, 2025, vol. 15606, pp. 385–415.","apa":"Cueto Noval, M., Merz, S.-P., Stählin, P., &#38; Ünal, A. (2025). On the soundness of algebraic attacks against code-based assumptions. In <i>44th Annual International Conference on the Theory and Applications of Cryptographic Techniques</i> (Vol. 15606, pp. 385–415). Madrid, Spain: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-91095-1_14\">https://doi.org/10.1007/978-3-031-91095-1_14</a>","ama":"Cueto Noval M, Merz S-P, Stählin P, Ünal A. On the soundness of algebraic attacks against code-based assumptions. In: <i>44th Annual International Conference on the Theory and Applications of Cryptographic Techniques</i>. Vol 15606. Springer Nature; 2025:385-415. doi:<a href=\"https://doi.org/10.1007/978-3-031-91095-1_14\">10.1007/978-3-031-91095-1_14</a>"},"conference":{"location":"Madrid, Spain","end_date":"2025-05-08","name":"EUROCRYPT: International Conference on the Theory and Applications of Cryptographic Techniques","start_date":"2025-05-04"},"oa":1,"OA_place":"repository","OA_type":"green","title":"On the soundness of algebraic attacks against code-based assumptions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-28T06:12:39Z","type":"conference","abstract":[{"lang":"eng","text":"We study recent algebraic attacks (Briaud-Øygarden EC’23) on the Regular Syndrome Decoding (RSD) problem and the assumptions underlying the correctness of their attacks’ complexity estimates. By relating these assumptions to interesting algebraic-combinatorial problems, we prove that they do not hold in full generality. However, we show that they are (asymptotically) true for most parameter sets, supporting the soundness of algebraic attacks on RSD. Further, we prove—without any heuristics or assumptions—that RSD can be broken in polynomial time whenever the number of error blocks times the square of the size of error blocks is larger than 2 times the square of the dimension of the code.\r\nAdditionally, we use our methodology to attack a variant of the Learning With Errors problem where each error term lies in a fixed set of constant size. We prove that this problem can be broken in polynomial time, given a sufficient number of samples. This result improves on the seminal work by Arora and Ge (ICALP’11), as the attack’s time complexity is independent of the LWE modulus."}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031910951"],"eissn":["1611-3349"],"isbn":["9783031910944"]},"date_created":"2025-05-19T14:15:01Z","publication":"44th Annual International Conference on the Theory and Applications of Cryptographic Techniques"},{"volume":39,"intvolume":"        39","author":[{"first_name":"Shayan","last_name":"Talaei","full_name":"Talaei, Shayan"},{"first_name":"Matin","last_name":"Ansaripour","full_name":"Ansaripour, Matin"},{"orcid":"0000-0001-5634-0731","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"_id":"19713","external_id":{"arxiv":["2210.07703"]},"issue":"19","year":"2025","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publisher":"Association for the Advancement of Artificial Intelligence","page":"20778-20786","article_processing_charge":"No","date_published":"2025-04-11T00:00:00Z","type":"journal_article","date_updated":"2026-02-16T12:34:44Z","date_created":"2025-05-19T14:15:35Z","publication":"Proceedings of the 39th AAAI Conference on Artificial Intelligence","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"abstract":[{"text":"Distributed optimization is the standard way of speeding up machine learning training, and most of the research in the area focuses on distributed first-order, gradient-based methods. Yet, there are settings where some computationally-bounded nodes may not be able to implement first-order, gradient-based optimization, while they could still contribute to joint optimization tasks. In this paper, we initiate the study of hybrid decentralized optimization, studying settings where nodes with zeroth-order and first-order optimization capabilities co-exist in a distributed system, and attempt to jointly solve an optimization task over some data distribution. We essentially show that, under reasonable parameter settings, such a system can not only withstand noisier zeroth-order agents but can even benefit from integrating such agents into the optimization process, rather than ignoring their information. At the core of our approach is a new analysis of distributed optimization with noisy and possibly-biased gradient estimators, which may be of independent interest. Our results hold for both convex and non-convex objectives. Experimental results on standard optimization tasks confirm our analysis, showing that hybrid first-zeroth order optimization can be practical, even when training deep neural networks.","lang":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Hybrid decentralized optimization: Leveraging both first- and zeroth-order optimizers for faster convergence","OA_type":"free access","article_type":"original","OA_place":"publisher","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement\r\nNo 805223 ScaleML). The authors would like to acknowledge Eugenia Iofinova for useful discussions during the inception of this project.","scopus_import":"1","citation":{"apa":"Talaei, S., Ansaripour, M., Nadiradze, G., &#38; Alistarh, D.-A. (2025). Hybrid decentralized optimization: Leveraging both first- and zeroth-order optimizers for faster convergence. <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v39i19.34290\">https://doi.org/10.1609/aaai.v39i19.34290</a>","ama":"Talaei S, Ansaripour M, Nadiradze G, Alistarh D-A. Hybrid decentralized optimization: Leveraging both first- and zeroth-order optimizers for faster convergence. <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. 2025;39(19):20778-20786. doi:<a href=\"https://doi.org/10.1609/aaai.v39i19.34290\">10.1609/aaai.v39i19.34290</a>","ieee":"S. Talaei, M. Ansaripour, G. Nadiradze, and D.-A. Alistarh, “Hybrid decentralized optimization: Leveraging both first- and zeroth-order optimizers for faster convergence,” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 19. Association for the Advancement of Artificial Intelligence, pp. 20778–20786, 2025.","ista":"Talaei S, Ansaripour M, Nadiradze G, Alistarh D-A. 2025. Hybrid decentralized optimization: Leveraging both first- and zeroth-order optimizers for faster convergence. Proceedings of the 39th AAAI Conference on Artificial Intelligence. 39(19), 20778–20786.","short":"S. Talaei, M. Ansaripour, G. Nadiradze, D.-A. Alistarh, Proceedings of the 39th AAAI Conference on Artificial Intelligence 39 (2025) 20778–20786.","chicago":"Talaei, Shayan, Matin Ansaripour, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Hybrid Decentralized Optimization: Leveraging Both First- and Zeroth-Order Optimizers for Faster Convergence.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Association for the Advancement of Artificial Intelligence, 2025. <a href=\"https://doi.org/10.1609/aaai.v39i19.34290\">https://doi.org/10.1609/aaai.v39i19.34290</a>.","mla":"Talaei, Shayan, et al. “Hybrid Decentralized Optimization: Leveraging Both First- and Zeroth-Order Optimizers for Faster Convergence.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 19, Association for the Advancement of Artificial Intelligence, 2025, pp. 20778–86, doi:<a href=\"https://doi.org/10.1609/aaai.v39i19.34290\">10.1609/aaai.v39i19.34290</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1609/aaai.v39i19.34290"}],"status":"public","oa_version":"Preprint","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"publication_status":"published","department":[{"_id":"DaAl"}],"day":"11","ec_funded":1,"doi":"10.1609/aaai.v39i19.34290","related_material":{"link":[{"relation":"software","url":"https://github.com/ShayanTalaei/HDO"}]},"corr_author":"1","month":"04"},{"_id":"19717","OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis","OA_place":"repository","oa":1,"author":[{"first_name":"I","last_name":"Varela-Martínez","full_name":"Varela-Martínez, I"},{"orcid":"0000-0002-5615-5277","first_name":"Ana","full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","last_name":"Villalba Requena"},{"full_name":"Garcia-Marqués, J.","last_name":"Garcia-Marqués","first_name":"J."},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"first_name":"M.","full_name":"Nieto, M.","last_name":"Nieto"}],"publication":"bioRxiv","date_created":"2025-05-20T10:19:29Z","abstract":[{"text":"Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.","lang":"eng"}],"date_updated":"2025-05-28T06:37:46Z","type":"preprint","doi":"10.1101/2025.05.07.652665","day":"07","department":[{"_id":"SiHi"}],"publication_status":"published","month":"05","date_published":"2025-05-07T00:00:00Z","oa_version":"Preprint","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"ama":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. 2025. doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>","apa":"Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., &#38; Nieto, M. (2025). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>","ieee":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis,” <i>bioRxiv</i>. 2025.","ista":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. 2025. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","chicago":"Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer, and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, 2025. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>.","short":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (2025).","mla":"Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, 2025, doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>."},"main_file_link":[{"url":"https://doi.org/10.1101/2025.05.07.652665","open_access":"1"}],"status":"public","acknowledgement":"We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression; C. Varela747 Martínez for help with the code for graphical analysis; all members from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU (PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI /10.13039/501100011033.\r\n","year":"2025"},{"title":"How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","article_type":"original","OA_place":"publisher","oa":1,"has_accepted_license":"1","publication":"Current Opinion in Neurobiology","date_created":"2025-05-20T10:20:09Z","publication_identifier":{"issn":["0959-4388"]},"abstract":[{"text":"The cerebral cortex is arguably the most complex organ in humans. The cortical architecture is characterized by a remarkable diversity of neuronal and glial cell types that make up its neuronal circuits. Following a precise temporally ordered program, radial glia progenitor (RGP) cells generate all cortical excitatory projection neurons and glial cell-types. Cortical excitatory projection neurons are produced either directly or via intermediate progenitors, through indirect neurogenesis. How the extensive cortical cell-type diversity is generated during cortex development remains, however, a fundamental open question. How do RGPs quantitatively and qualitatively generate all the neocortical neurons? How does direct and indirect neurogenesis contribute to the establishment of neuronal and lineage heterogeneity? Whether RGPs represent a homogeneous and/or multipotent progenitor population, or if RGPs consist of heterogeneous groups is currently also not known. In this review, we will summarize the latest findings that contributed to a deeper insight into the above key questions.","lang":"eng"}],"type":"journal_article","date_updated":"2025-12-30T10:54:14Z","PlanS_conform":"1","file_date_updated":"2025-12-30T08:25:49Z","department":[{"_id":"SiHi"}],"publication_status":"published","day":"01","doi":"10.1016/j.conb.2025.103046","month":"08","corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Pipicelli F, Villalba Requena A, Hippenmeyer S. 2025. How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. Current Opinion in Neurobiology. 93, 103046.","mla":"Pipicelli, Fabrizia, et al. “How Radial Glia Progenitor Lineages Generate Cell-Type Diversity in the Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>, vol. 93, 103046, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.conb.2025.103046\">10.1016/j.conb.2025.103046</a>.","chicago":"Pipicelli, Fabrizia, Ana Villalba Requena, and Simon Hippenmeyer. “How Radial Glia Progenitor Lineages Generate Cell-Type Diversity in the Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.conb.2025.103046\">https://doi.org/10.1016/j.conb.2025.103046</a>.","short":"F. Pipicelli, A. Villalba Requena, S. Hippenmeyer, Current Opinion in Neurobiology 93 (2025).","ama":"Pipicelli F, Villalba Requena A, Hippenmeyer S. How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. 2025;93. doi:<a href=\"https://doi.org/10.1016/j.conb.2025.103046\">10.1016/j.conb.2025.103046</a>","apa":"Pipicelli, F., Villalba Requena, A., &#38; Hippenmeyer, S. (2025). How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2025.103046\">https://doi.org/10.1016/j.conb.2025.103046</a>","ieee":"F. Pipicelli, A. Villalba Requena, and S. Hippenmeyer, “How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex,” <i>Current Opinion in Neurobiology</i>, vol. 93. Elsevier, 2025."},"file":[{"file_name":"2025_CurrentOpNeurobiology_Pipicelli.pdf","date_created":"2025-12-30T08:25:49Z","file_id":"20894","file_size":1592649,"creator":"dernst","date_updated":"2025-12-30T08:25:49Z","success":1,"access_level":"open_access","relation":"main_file","checksum":"05bacb4acbe6275d43e873dec9ba1d52","content_type":"application/pdf"}],"status":"public","scopus_import":"1","acknowledgement":"We wish to thank all members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. We apologize to colleagues whose work we could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the discussed topic is supported by ISTA institutional funds, an EMBO LTF (ALTF 994–2023) to F.P, and FWF SFB F78 to S.H.","external_id":{"pmid":["40383049"],"isi":["001496227000001"]},"_id":"19718","isi":1,"author":[{"last_name":"Pipicelli","full_name":"Pipicelli, Fabrizia","id":"649134fd-d012-11ed-8f82-db1e5050f9ba","first_name":"Fabrizia"},{"last_name":"Villalba Requena","full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","first_name":"Ana"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"intvolume":"        93","volume":93,"pmid":1,"date_published":"2025-08-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"project":[{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"name":"Role of cell lineage in generating cell-type diversity in developing neocortex’","grant_number":"ALTF 994-2023","_id":"7c084566-9f16-11ee-852c-c88a1dbbf1cf"}],"publisher":"Elsevier","year":"2025","article_number":"103046"},{"intvolume":"       437","volume":437,"_id":"19725","issue":"17","external_id":{"isi":["001494762800001"],"pmid":["40324743"]},"author":[{"first_name":"James","full_name":"Antoney, James","last_name":"Antoney"},{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6709-2195","first_name":"Stephanie"},{"full_name":"Dubowsky, Joshua G.","last_name":"Dubowsky","first_name":"Joshua G."},{"first_name":"F. Hafna","last_name":"Ahmed","full_name":"Ahmed, F. Hafna"},{"full_name":"Kang, Suk Woo","last_name":"Kang","first_name":"Suk Woo"},{"last_name":"Mackie","full_name":"Mackie, Emily R.R.","first_name":"Emily R.R."},{"last_name":"Bracho Granado","full_name":"Bracho Granado, Gustavo","first_name":"Gustavo"},{"full_name":"Soares Da Costa, Tatiana P.","last_name":"Soares Da Costa","first_name":"Tatiana P."},{"first_name":"Colin J.","full_name":"Jackson, Colin J.","last_name":"Jackson"},{"first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"isi":1,"project":[{"_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24"}],"publisher":"Elsevier","ddc":["570"],"year":"2025","article_number":"169184","pmid":1,"date_published":"2025-09-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Protein-protein interactions (PPIs) mediate many fundamental cellular processes. Control of PPIs through optically or chemically responsive protein domains has had a profound impact on basic research and some clinical applications. Most chemogenetic methods induce the association, i.e., dimerization or oligomerization, of target proteins, whilst the few available dissociation approaches either break large oligomeric protein clusters or heteromeric complexes. Here, we have exploited the controlled dissociation of a homodimeric oxidoreductase from mycobacteria (MSMEG_2027) by its native cofactor, F420, which is not present in mammals, as a bioorthogonal monomerization switch. Using X-ray crystallography, we found that in the absence of F420 MSMEG_2027 forms a unique domain-swapped dimer that occludes the cofactor binding site. Rearrangement of the N-terminal helix upon F420 binding results in the dissolution of the dimer. We then showed that MSMEG_2027 can be fused to proteins of interest in human cells and applied it as a tool to induce and release MAPK/ERK signalling downstream of a chimeric fibroblast growth factor receptor 1 (FGFR1) tyrosine kinase. This F420-dependent chemogenetic de-homodimerization tool is stoichiometric and based on a single domain and thus represents a novel mechanism to investigate protein complexes in situ.","lang":"eng"}],"publication":"Journal of Molecular Biology","date_created":"2025-05-25T22:16:39Z","publication_identifier":{"issn":["0022-2836"],"eissn":["1089-8638"]},"file_date_updated":"2025-12-30T08:18:07Z","PlanS_conform":"1","type":"journal_article","date_updated":"2025-12-30T08:18:25Z","article_type":"original","OA_place":"publisher","title":"A F420-dependent single domain chemogenetic tool for protein de-dimerization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","has_accepted_license":"1","oa":1,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Antoney J, Kainrath S, Dubowsky JG, Ahmed FH, Kang SW, Mackie ERR, Bracho Granado G, Soares Da Costa TP, Jackson CJ, Janovjak HL. 2025. A F420-dependent single domain chemogenetic tool for protein de-dimerization. Journal of Molecular Biology. 437(17), 169184.","mla":"Antoney, James, et al. “A F420-Dependent Single Domain Chemogenetic Tool for Protein de-Dimerization.” <i>Journal of Molecular Biology</i>, vol. 437, no. 17, 169184, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">10.1016/j.jmb.2025.169184</a>.","chicago":"Antoney, James, Stephanie Kainrath, Joshua G. Dubowsky, F. Hafna Ahmed, Suk Woo Kang, Emily R.R. Mackie, Gustavo Bracho Granado, Tatiana P. Soares Da Costa, Colin J. Jackson, and Harald L Janovjak. “A F420-Dependent Single Domain Chemogenetic Tool for Protein de-Dimerization.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">https://doi.org/10.1016/j.jmb.2025.169184</a>.","short":"J. Antoney, S. Kainrath, J.G. Dubowsky, F.H. Ahmed, S.W. Kang, E.R.R. Mackie, G. Bracho Granado, T.P. Soares Da Costa, C.J. Jackson, H.L. Janovjak, Journal of Molecular Biology 437 (2025).","apa":"Antoney, J., Kainrath, S., Dubowsky, J. G., Ahmed, F. H., Kang, S. W., Mackie, E. R. R., … Janovjak, H. L. (2025). A F420-dependent single domain chemogenetic tool for protein de-dimerization. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">https://doi.org/10.1016/j.jmb.2025.169184</a>","ama":"Antoney J, Kainrath S, Dubowsky JG, et al. A F420-dependent single domain chemogenetic tool for protein de-dimerization. <i>Journal of Molecular Biology</i>. 2025;437(17). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">10.1016/j.jmb.2025.169184</a>","ieee":"J. Antoney <i>et al.</i>, “A F420-dependent single domain chemogenetic tool for protein de-dimerization,” <i>Journal of Molecular Biology</i>, vol. 437, no. 17. Elsevier, 2025."},"file":[{"checksum":"fb6e84ba7dc92faee97647fd2bc8cca8","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","file_size":1682721,"date_updated":"2025-12-30T08:18:07Z","file_name":"2025_JourMolecularBiology_Antoney.pdf","file_id":"20892","date_created":"2025-12-30T08:18:07Z"}],"scopus_import":"1","acknowledgement":"We thank J. Kaczmarski for advice on isothermal titration calorimetry and helpful comments, and Alexandra Tichy, Elliot Gerrard and Rahkesh T Sabapathy for assistance with experiments. This study was supported by grants of the Australian Research Council (FT200100519 and DP200102093, to H.J.; DE190100806, DP220101901, FT230100203, and DP250102939 to T.P.S.D.C; DP200102093, CE200100029 and CE200100012 to C.J.J.), the National Health and Medical Research Council (APP1187638, to H.J.). S.K. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund FWF W1232). The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. The EMBL Australia Partnership Laboratory (EMBL Australia) is supported by the National Collaborative Research Infrastructure Strategy (NCRIS) of the Australian Government. T.P.S.D.C. acknowledges the University of Adelaide for a Future Making Fellowship. E.R.R.M acknowledges the Grains Research and Development Corporation (9176977) for support through a PhD scholarship and operational funding. J.A. and E.R.R.M. were supported by Australian Research Training Program scholarship. MicroMon of Monash University provided Sanger sequencing services. Imaging was performed in the CellScreen SA screening center of Flinders University. C.J.J. thanks the ARC Centre of Excellence for Innovations in Peptide and Protein Science and the ARC Centre of Excellence in Synthetic Biology. We thank the staff of the MX2 beamline at the Australian Synchrotron, part of ANSTO, which made use of the Australian Cancer Research Foundation (ACRF) detector.","month":"09","publication_status":"published","department":[{"_id":"CaGu"}],"day":"01","doi":"10.1016/j.jmb.2025.169184","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1"},{"citation":{"apa":"Mejia-Centeno, K. V., Montaña-Mora, G., Chacón-Borrero, J., Xue, Q., Gong, L., Martí-Sánchez, S., … Cabot, A. (2025). Glucose electrooxidation with simultaneous H2 production on nickel-zinc electrocatalysts derived from an ethylenediamine-functionalized zeolitic imidazole framework. <i>Chemical Engineering Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cej.2025.163491\">https://doi.org/10.1016/j.cej.2025.163491</a>","ama":"Mejia-Centeno KV, Montaña-Mora G, Chacón-Borrero J, et al. Glucose electrooxidation with simultaneous H2 production on nickel-zinc electrocatalysts derived from an ethylenediamine-functionalized zeolitic imidazole framework. <i>Chemical Engineering Journal</i>. 2025;515. doi:<a href=\"https://doi.org/10.1016/j.cej.2025.163491\">10.1016/j.cej.2025.163491</a>","ieee":"K. V. Mejia-Centeno <i>et al.</i>, “Glucose electrooxidation with simultaneous H2 production on nickel-zinc electrocatalysts derived from an ethylenediamine-functionalized zeolitic imidazole framework,” <i>Chemical Engineering Journal</i>, vol. 515. Elsevier, 2025.","ista":"Mejia-Centeno KV, Montaña-Mora G, Chacón-Borrero J, Xue Q, Gong L, Martí-Sánchez S, Berlanga-Vázquez A, Llorca J, Ibáñez M, Arbiol J, Qi X, Martinez-Alanis PR, Cabot A. 2025. Glucose electrooxidation with simultaneous H2 production on nickel-zinc electrocatalysts derived from an ethylenediamine-functionalized zeolitic imidazole framework. Chemical Engineering Journal. 515, 163491.","chicago":"Mejia-Centeno, Karol V., Guillem Montaña-Mora, Jesús Chacón-Borrero, Qian Xue, Li Gong, Sara Martí-Sánchez, Armando Berlanga-Vázquez, et al. “Glucose Electrooxidation with Simultaneous H2 Production on Nickel-Zinc Electrocatalysts Derived from an Ethylenediamine-Functionalized Zeolitic Imidazole Framework.” <i>Chemical Engineering Journal</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cej.2025.163491\">https://doi.org/10.1016/j.cej.2025.163491</a>.","mla":"Mejia-Centeno, Karol V., et al. “Glucose Electrooxidation with Simultaneous H2 Production on Nickel-Zinc Electrocatalysts Derived from an Ethylenediamine-Functionalized Zeolitic Imidazole Framework.” <i>Chemical Engineering Journal</i>, vol. 515, 163491, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.cej.2025.163491\">10.1016/j.cej.2025.163491</a>.","short":"K.V. Mejia-Centeno, G. Montaña-Mora, J. Chacón-Borrero, Q. Xue, L. Gong, S. Martí-Sánchez, A. Berlanga-Vázquez, J. Llorca, M. Ibáñez, J. Arbiol, X. Qi, P.R. Martinez-Alanis, A. Cabot, Chemical Engineering Journal 515 (2025)."},"status":"public","scopus_import":"1","acknowledgement":"This work was financially supported by the SyDECat and AmaDE projects from the Spanish MCIN/AEI/FEDER (PID2022-136883OB-C22 & PID2023-149158OB-C43). The authors acknowledge funding from Generalitat de Catalunya 2021SGR01581, 2021SGR00457 and European Union Next Generation EU/PRTR. KVMC acknowledges the grant from Call 906 of 2021 for Doctorates Abroad from the Ministry of Science, Technology, and Innovation of Colombia. PRMA acknowledges support from the Ramón y Cajal grant RYC2023-042982-I, funded by MICIU/AEI (10.13039/501100011033) and co-financed by FSE+. 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 (In-CAEM Project). 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. ICN2 is founding member of e-DREAM. [76] J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and to projects PID2021-124572OB-C31 and CEX2023-001300-M funded by MCIN/AEI/10.13039/501100011033, EU and FEDER, and to the GC 2021 SGR 01061 grant.","doi":"10.1016/j.cej.2025.163491","day":"01","publication_status":"published","department":[{"_id":"MaIb"}],"month":"07","oa_version":"None","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1385-8947"]},"date_created":"2025-05-25T22:16:40Z","publication":"Chemical Engineering Journal","abstract":[{"lang":"eng","text":"The oxidation of biomass-derived compounds such as glucose within electrochemical cells enables both the energy-efficient production of hydrogen and the generation of additional added-value chemicals from biomass. However, for this biomass valorization approach to become commercially viable, selective, cost-effective, and highly active electrooxidation catalysts need to be developed. In this work, we detail the synthesis of a nickel (Ni) and zinc (Zn)-based electrocatalyst for the glucose oxidation reaction (GOR) to formic acid (FoA) via calcination of a Zn-based zeolitic imidazole framework (ZIF) functionalized with ethylenediamine and doped with Ni. The structure, morphology, and electrochemical performance of the catalysts towards the anodic GOR to FoA coupled with the cathodic hydrogen evolution reaction (HER) are subsequently studied. Chronopotentiometry tests with 0.1 M of glucose show a conversion of 94 % at 250 mA in only 70 min, with a Faradaic efficiency (FE) of 91 % toward the production of FoA. Meanwhile, at the cathode, the HER FE is close to 98 %."}],"date_updated":"2025-12-30T08:28:59Z","type":"journal_article","OA_type":"closed access","title":"Glucose electrooxidation with simultaneous H2 production on nickel-zinc electrocatalysts derived from an ethylenediamine-functionalized zeolitic imidazole framework","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publisher":"Elsevier","article_number":"163491","year":"2025","date_published":"2025-07-01T00:00:00Z","article_processing_charge":"No","intvolume":"       515","volume":515,"external_id":{"isi":["001501928300003"]},"_id":"19726","author":[{"first_name":"Karol V.","full_name":"Mejia-Centeno, Karol V.","last_name":"Mejia-Centeno"},{"full_name":"Montaña-Mora, Guillem","last_name":"Montaña-Mora","first_name":"Guillem"},{"last_name":"Chacón-Borrero","full_name":"Chacón-Borrero, Jesús","first_name":"Jesús"},{"first_name":"Qian","last_name":"Xue","full_name":"Xue, Qian"},{"first_name":"Li","full_name":"Gong, Li","last_name":"Gong"},{"first_name":"Sara","full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez"},{"first_name":"Armando","last_name":"Berlanga-Vázquez","full_name":"Berlanga-Vázquez, Armando"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Qi, Xueqiang","last_name":"Qi","first_name":"Xueqiang"},{"last_name":"Martinez-Alanis","full_name":"Martinez-Alanis, Paulina R.","first_name":"Paulina R."},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"isi":1}]