[{"_id":"20730","article_processing_charge":"Yes (in subscription journal)","status":"public","related_material":{"record":[{"id":"20750","relation":"research_data","status":"public"}]},"date_updated":"2025-12-09T14:49:35Z","department":[{"_id":"GeKa"}],"intvolume":"        24","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":24,"year":"2025","project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"}],"file":[{"relation":"main_file","access_level":"open_access","checksum":"9906b32c7e3c79ed13d05ef88ff15586","content_type":"application/pdf","file_id":"20748","file_name":"2025_PhysReviewApplied_vanStraaten.pdf","success":1,"file_size":5754118,"date_updated":"2025-12-09T13:34:38Z","date_created":"2025-12-09T13:34:38Z","creator":"dernst"}],"abstract":[{"text":"Radio-frequency measurements could satisfy DiVincenzo’s readout criterion in future large-scale solid-state quantum processors, as they allow for high bandwidths and frequency multiplexing. However, the scalability potential of this readout technique can only be leveraged if quantum device tuning is performed using exclusively radio-frequency measurements, that is, without resorting to current measurements. We demonstrate an algorithm that performs automatic coarse tuning of double quantum dots with only radio-frequency measurements by exploiting their bandwidth and impedance matching. The tuning was completed within a few minutes with minimal prior knowledge about the device. Our results show that it is possible to eliminate the need for transport measurements for quantum-dot tuning, paving the way for more scalable device architectures.","lang":"eng"}],"acknowledgement":"We thank Nicholas Sim for providing help with the rf cavities and David Craig for his feedback on the paper. This work was supported by the Royal Society (URF-R1-191150), the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant (EP/R029229/1), the European Research Council (Grant Agreement 948932), the Scientific Service Units of IST Austria through resources provided by the nanofabrication facility, the FWF-P 30207, and FWF-I 05060 projects, and Grant No. FQXi-IAF19-01 from the Foundational Questions Institute Fund, a donor-advised fund of Silicon Valley Community Foundation.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"oa":1,"has_accepted_license":"1","publisher":"American Physical Society","author":[{"last_name":"Van Straaten","first_name":"Barnaby","full_name":"Van Straaten, Barnaby"},{"first_name":"Federico","last_name":"Fedele","full_name":"Fedele, Federico"},{"full_name":"Vigneau, Florian","first_name":"Florian","last_name":"Vigneau"},{"full_name":"Hickie, Joseph","last_name":"Hickie","first_name":"Joseph"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios"},{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"}],"month":"11","article_number":"054030","date_created":"2025-12-07T23:02:01Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"acknowledged_ssus":[{"_id":"NanoFab"}],"PlanS_conform":"1","OA_place":"publisher","day":"01","OA_type":"hybrid","fulldoi":"https://doi.org/10.1103/v11m-dbhm","date_published":"2025-11-01T00:00:00Z","file_date_updated":"2025-12-09T13:34:38Z","article_type":"original","publication_status":"published","scopus_import":"1","issue":"5","quality_controlled":"1","title":"All-rf-based coarse-tuning algorithm for quantum devices using machine learning","publication":"Physical Review Applied","publication_identifier":{"eissn":["2331-7019"]},"citation":{"mla":"Van Straaten, Barnaby, et al. “All-Rf-Based Coarse-Tuning Algorithm for Quantum Devices Using Machine Learning.” <i>Physical Review Applied</i>, vol. 24, no. 5, 054030, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/v11m-dbhm\">10.1103/v11m-dbhm</a>.","apa":"Van Straaten, B., Fedele, F., Vigneau, F., Hickie, J., Jirovec, D., Ballabio, A., … Ares, N. (2025). All-rf-based coarse-tuning algorithm for quantum devices using machine learning. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/v11m-dbhm\">https://doi.org/10.1103/v11m-dbhm</a>","ista":"Van Straaten B, Fedele F, Vigneau F, Hickie J, Jirovec D, Ballabio A, Chrastina D, Isella G, Katsaros G, Ares N. 2025. All-rf-based coarse-tuning algorithm for quantum devices using machine learning. Physical Review Applied. 24(5), 054030.","ama":"Van Straaten B, Fedele F, Vigneau F, et al. All-rf-based coarse-tuning algorithm for quantum devices using machine learning. <i>Physical Review Applied</i>. 2025;24(5). doi:<a href=\"https://doi.org/10.1103/v11m-dbhm\">10.1103/v11m-dbhm</a>","ieee":"B. Van Straaten <i>et al.</i>, “All-rf-based coarse-tuning algorithm for quantum devices using machine learning,” <i>Physical Review Applied</i>, vol. 24, no. 5. American Physical Society, 2025.","chicago":"Van Straaten, Barnaby, Federico Fedele, Florian Vigneau, Joseph Hickie, Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, Giovanni Isella, Georgios Katsaros, and Natalia Ares. “All-Rf-Based Coarse-Tuning Algorithm for Quantum Devices Using Machine Learning.” <i>Physical Review Applied</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/v11m-dbhm\">https://doi.org/10.1103/v11m-dbhm</a>.","short":"B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, G. Katsaros, N. Ares, Physical Review Applied 24 (2025)."},"doi":"10.1103/v11m-dbhm"},{"acknowledgement":"Funding provided by the European Union (grant 101057429) to G.N.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa":1,"has_accepted_license":"1","publisher":"Annual Reviews","page":"415-434","_id":"20731","article_processing_charge":"Yes (in subscription journal)","date_updated":"2025-12-09T12:55:11Z","status":"public","department":[{"_id":"GaNo"}],"intvolume":"        59","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":59,"year":"2025","external_id":{"pmid":["40902207"]},"project":[{"_id":"349d1832-11ca-11ed-8bc3-d79b574010e0","grant_number":"101057429","name":"Reducing the impact of major environmental challenges on mental health"}],"file":[{"file_size":3629986,"file_name":"2025_AnnualRevGenetics_Marano.pdf","success":1,"creator":"dernst","date_updated":"2025-12-09T12:53:09Z","date_created":"2025-12-09T12:53:09Z","access_level":"open_access","relation":"main_file","file_id":"20745","content_type":"application/pdf","checksum":"1000228dc9aca3d48e92605607a99c41"}],"abstract":[{"lang":"eng","text":"The adult human brain, under resting conditions, consumes approximately 20% of total body glucose, a demand that is even higher during the first decade of life. The brain metabolic landscape is intricately regulated throughout development, and each cell type exhibits distinct metabolic signatures at each specific stage. This picture becomes even more intricate when considering that metabolism is dynamically modulated to sustain critical biological processes, such as cell proliferation and differentiation and synaptic activity–dependent processes. The orchestration between metabolic regulation and the aforementioned physiological processes often relies on metabolism-dependent changes in the epigenetic landscape, which shape gene expression patterns to trigger selected downstream biological responses. Perturbations of brain metabolic pathways are frequently the cause of severe neurodevelopmental disorders. This review explores the latest insights into the regulation of brain metabolism in health and disease."}],"corr_author":"1","pmid":1,"quality_controlled":"1","title":"Fueling the mind: Brain metabolism in health and neurodevelopmental disorders","publication":"Annual Review of Genetics","citation":{"mla":"Marano, Domenico, et al. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” <i>Annual Review of Genetics</i>, vol. 59, Annual Reviews, 2025, pp. 415–34, doi:<a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">10.1146/annurev-genet-111523-102424</a>.","ista":"Marano D, Mariano V, Novarino G. 2025. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 59, 415–434.","apa":"Marano, D., Mariano, V., &#38; Novarino, G. (2025). Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. <i>Annual Review of Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">https://doi.org/10.1146/annurev-genet-111523-102424</a>","ama":"Marano D, Mariano V, Novarino G. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. <i>Annual Review of Genetics</i>. 2025;59:415-434. doi:<a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">10.1146/annurev-genet-111523-102424</a>","ieee":"D. Marano, V. Mariano, and G. Novarino, “Fueling the mind: Brain metabolism in health and neurodevelopmental disorders,” <i>Annual Review of Genetics</i>, vol. 59. Annual Reviews, pp. 415–434, 2025.","chicago":"Marano, Domenico, Vittoria Mariano, and Gaia Novarino. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” <i>Annual Review of Genetics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">https://doi.org/10.1146/annurev-genet-111523-102424</a>.","short":"D. Marano, V. Mariano, G. Novarino, Annual Review of Genetics 59 (2025) 415–434."},"publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"doi":"10.1146/annurev-genet-111523-102424","author":[{"full_name":"Marano, Domenico","last_name":"Marano","id":"3b004c42-803f-11ed-ab7e-ecee8f08bd58","first_name":"Domenico"},{"full_name":"Mariano, Vittoria","first_name":"Vittoria","id":"ee829c33-edb3-11ed-b4fb-c020aaca4b01","last_name":"Mariano"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"month":"11","date_created":"2025-12-07T23:02:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","PlanS_conform":"1","OA_place":"publisher","day":"03","OA_type":"hybrid","fulldoi":"https://doi.org/10.1146/annurev-genet-111523-102424","file_date_updated":"2025-12-09T12:53:09Z","date_published":"2025-11-03T00:00:00Z","article_type":"review","publication_status":"published","scopus_import":"1"},{"publisher":"American Physical Society","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994. G.K.M. has received funding from the Austrian Science Fund (FWF) [DOI: 10.55776/F1004].","oa":1,"ddc":["530"],"project":[{"name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403","_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3"}],"corr_author":"1","abstract":[{"lang":"eng","text":"We investigate the real-time dynamics of a quenched quantum impurity immersed in a one-dimensional ultracold Fermi gas, focusing on the breakdown of the adiabatic Born-Oppenheimer approximation due to nonadiabatic effects. Despite a sizable impurity-bath mass imbalance, increasing interactions induce strong nonadiabatic couplings, disrupting adiabatic motion and enabling population transfer between the adiabatic potential energy curves. These transitions are governed by conical intersections arising from the pseudo Jahn-Teller effect, dynamically shaping the impurity's motion through the bath. Using ab initio simulations via the multilayer multiconfiguration time-dependent Hartree method and a multichannel Born-Oppenheimer framework, we track the impurity's evolution and directly prove the dynamical manifestation of the pseudo Jahn-Teller effect. We analyze two key scenarios: (i) a small initial shift, where a single avoided crossing drives transitions, and (ii) a large shift, where multiple avoided crossings lead to enhanced nonadiabaticity, self-trapping, and energy redistribution. Our findings establish ultracold fermionic few-body systems as tunable platforms for studying nonadiabatic quantum dynamics, opening new avenues for controlled impurity transport in strongly correlated environments."}],"file":[{"relation":"main_file","access_level":"open_access","checksum":"b9f5ccd6957759b0e578bc817a050532","file_id":"20754","content_type":"application/pdf","file_name":"2025_PhysReviewResearch_Becker.pdf","success":1,"file_size":2878032,"date_updated":"2025-12-09T14:14:46Z","date_created":"2025-12-09T14:14:46Z","creator":"dernst"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"arxiv":["2503.09835"]},"year":"2025","volume":7,"department":[{"_id":"MiLe"}],"intvolume":"         7","_id":"20732","date_updated":"2025-12-09T14:16:15Z","status":"public","article_processing_charge":"Yes","arxiv":1,"publication_identifier":{"issn":["2643-1564"]},"citation":{"ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions,” <i>Physical Review Research</i>, vol. 7, no. 3. American Physical Society, 2025.","mla":"Becker, A., et al. “Dynamical Probe of the Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” <i>Physical Review Research</i>, vol. 7, no. 3, 033088, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/2fr6-b59y\">10.1103/2fr6-b59y</a>.","apa":"Becker, A., Koutentakis, G., &#38; Schmelcher, P. (2025). Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/2fr6-b59y\">https://doi.org/10.1103/2fr6-b59y</a>","ista":"Becker A, Koutentakis G, Schmelcher P. 2025. Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 7(3), 033088.","ama":"Becker A, Koutentakis G, Schmelcher P. Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions. <i>Physical Review Research</i>. 2025;7(3). doi:<a href=\"https://doi.org/10.1103/2fr6-b59y\">10.1103/2fr6-b59y</a>","short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 7 (2025).","chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Dynamical Probe of the Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” <i>Physical Review Research</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/2fr6-b59y\">https://doi.org/10.1103/2fr6-b59y</a>."},"doi":"10.1103/2fr6-b59y","title":"Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions","DOAJ_listed":"1","publication":"Physical Review Research","issue":"3","quality_controlled":"1","fulldoi":"https://doi.org/10.1103/2fr6-b59y","day":"01","OA_type":"gold","scopus_import":"1","article_type":"original","file_date_updated":"2025-12-09T14:14:46Z","date_published":"2025-07-01T00:00:00Z","publication_status":"published","OA_place":"publisher","PlanS_conform":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","article_number":"033088","month":"07","author":[{"full_name":"Becker, A.","first_name":"A.","last_name":"Becker"},{"full_name":"Koutentakis, Georgios","first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis"},{"full_name":"Schmelcher, P.","first_name":"P.","last_name":"Schmelcher"}],"date_created":"2025-12-07T23:02:02Z"},{"fulldoi":"https://doi.org/10.1103/q3dx-kyqj","day":"01","OA_type":"gold","scopus_import":"1","article_type":"letter_note","date_published":"2025-07-01T00:00:00Z","file_date_updated":"2025-12-09T14:05:56Z","publication_status":"published","OA_place":"publisher","PlanS_conform":"1","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"month":"07","article_number":"L032017","author":[{"first_name":"Kushagra","last_name":"Aggarwal","full_name":"Aggarwal, Kushagra"},{"full_name":"Rolandi, Alberto","last_name":"Rolandi","first_name":"Alberto"},{"full_name":"Yang, Yikai","last_name":"Yang","first_name":"Yikai"},{"full_name":"Hickie, Joseph","last_name":"Hickie","first_name":"Joseph"},{"first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"last_name":"Ballabio","first_name":"Andrea","full_name":"Ballabio, Andrea"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"full_name":"Mitchison, Mark T.","last_name":"Mitchison","first_name":"Mark T."},{"first_name":"Martí","last_name":"Perarnau-Llobet","full_name":"Perarnau-Llobet, Martí"},{"full_name":"Ares, Natalia","first_name":"Natalia","last_name":"Ares"}],"date_created":"2025-12-07T23:02:02Z","arxiv":1,"publication_identifier":{"eissn":["2643-1564"]},"citation":{"short":"K. Aggarwal, A. Rolandi, Y. Yang, J. Hickie, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M.T. Mitchison, M. Perarnau-Llobet, N. Ares, Physical Review Research 7 (2025).","chicago":"Aggarwal, Kushagra, Alberto Rolandi, Yikai Yang, Joseph Hickie, Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, et al. “Rapid Optimal Work Extraction from a Quantum-Dot Information Engine.” <i>Physical Review Research</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/q3dx-kyqj\">https://doi.org/10.1103/q3dx-kyqj</a>.","ieee":"K. Aggarwal <i>et al.</i>, “Rapid optimal work extraction from a quantum-dot information engine,” <i>Physical Review Research</i>, vol. 7, no. 3. American Physical Society, 2025.","mla":"Aggarwal, Kushagra, et al. “Rapid Optimal Work Extraction from a Quantum-Dot Information Engine.” <i>Physical Review Research</i>, vol. 7, no. 3, L032017, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/q3dx-kyqj\">10.1103/q3dx-kyqj</a>.","ista":"Aggarwal K, Rolandi A, Yang Y, Hickie J, Jirovec D, Ballabio A, Chrastina D, Isella G, Mitchison MT, Perarnau-Llobet M, Ares N. 2025. Rapid optimal work extraction from a quantum-dot information engine. Physical Review Research. 7(3), L032017.","apa":"Aggarwal, K., Rolandi, A., Yang, Y., Hickie, J., Jirovec, D., Ballabio, A., … Ares, N. (2025). Rapid optimal work extraction from a quantum-dot information engine. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/q3dx-kyqj\">https://doi.org/10.1103/q3dx-kyqj</a>","ama":"Aggarwal K, Rolandi A, Yang Y, et al. Rapid optimal work extraction from a quantum-dot information engine. <i>Physical Review Research</i>. 2025;7(3). doi:<a href=\"https://doi.org/10.1103/q3dx-kyqj\">10.1103/q3dx-kyqj</a>"},"doi":"10.1103/q3dx-kyqj","title":"Rapid optimal work extraction from a quantum-dot information engine","publication":"Physical Review Research","issue":"3","quality_controlled":"1","abstract":[{"lang":"eng","text":"The conversion of thermal energy into work is usually more efficient in the slow-driving regime, where the power output is vanishingly small. Efficient work extraction for fast-driving protocols remains an outstanding challenge at the nanoscale, where fluctuations play a significant role. In this Letter, we use a quantum-dot Szilard engine to extract work from thermal fluctuations with maximum efficiency over two decades of driving speed. We design and implement a family of optimized protocols ranging from the slow- to the fast-driving regime, and we measure the engine's efficiency as well as the mean and variance of its power output in each case. These optimized protocols exhibit significant improvements in power and efficiency compared to the naive approach. Our results also show that, when optimizing for efficiency, boosting the power output of a Szilard engine inevitably comes at the cost of increased power fluctuations."}],"file":[{"creator":"dernst","date_updated":"2025-12-09T14:05:56Z","date_created":"2025-12-09T14:05:56Z","success":1,"file_name":"2025_PhysReviewResearch_Aggarwal.pdf","file_size":536624,"file_id":"20753","content_type":"application/pdf","checksum":"66f2b572a36a7b5fe611a7639a8b6f12","access_level":"open_access","relation":"main_file"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"arxiv":["2412.06916"]},"volume":7,"year":"2025","department":[{"_id":"GeKa"}],"intvolume":"         7","_id":"20733","status":"public","date_updated":"2025-12-09T14:07:49Z","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.14516009"}]},"article_processing_charge":"Yes","publisher":"American Physical Society","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Georgios Katsaros for providing the device for this experiment. K.A. and N.A. acknowledge the support provided by funding from the Engineering and Physical Sciences Research Council IAA (Grant No. EP/X525777/1). N.A. acknowledges support from the European Research Council (Grant Agreement No. 948932) and the Royal Society (URF-R1-191150). A.R. is supported by the Swiss National Science Foundation through a Postdoc. Mobility (Grant No. P500PT 225461). M.T.M. is supported by a Royal Society University Research Fellowship. M.P.-L. is supported by the Grant RYC2022-036958-I funded by the Spanish MICIU/AEI/10.13039/501100011033 and by ESF+. This project is cofunded by the European Union and UK Research & Innovation (Quantum Flagship project ASPECTS, Grant Agreement No. 101080167). However, views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union, Research Executive Agency, or UK Research & Innovation. Neither the European Union nor UK Research & Innovation can be held responsible for them.","oa":1,"ddc":["530"]},{"month":"09","author":[{"full_name":"Zhang, Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","orcid":"0000-0002-6465-6258","first_name":"Yihan"},{"last_name":"Ji","first_name":"Hong Chang","full_name":"Ji, Hong Chang"},{"first_name":"Ramji","last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji"},{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"date_created":"2025-12-07T23:02:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","OA_place":"publisher","PlanS_conform":"1","fulldoi":"https://doi.org/10.4171/MSL/52","OA_type":"diamond","day":"02","scopus_import":"1","file_date_updated":"2025-12-09T13:50:03Z","publication_status":"published","article_type":"original","date_published":"2025-09-02T00:00:00Z","issue":"3-4","quality_controlled":"1","title":"Spectral estimators for structured generalized linear models via approximate message passing","publication":"Mathematical Statistics and Learning","citation":{"chicago":"Zhang, Yihan, Hong Chang Ji, Ramji Venkataramanan, and Marco Mondelli. “Spectral Estimators for Structured Generalized Linear Models via Approximate Message Passing.” <i>Mathematical Statistics and Learning</i>. EMS Press, 2025. <a href=\"https://doi.org/10.4171/MSL/52\">https://doi.org/10.4171/MSL/52</a>.","short":"Y. Zhang, H.C. Ji, R. Venkataramanan, M. Mondelli, Mathematical Statistics and Learning 8 (2025) 193–304.","apa":"Zhang, Y., Ji, H. C., Venkataramanan, R., &#38; Mondelli, M. (2025). Spectral estimators for structured generalized linear models via approximate message passing. <i>Mathematical Statistics and Learning</i>. EMS Press. <a href=\"https://doi.org/10.4171/MSL/52\">https://doi.org/10.4171/MSL/52</a>","ista":"Zhang Y, Ji HC, Venkataramanan R, Mondelli M. 2025. Spectral estimators for structured generalized linear models via approximate message passing. Mathematical Statistics and Learning. 8(3–4), 193–304.","ama":"Zhang Y, Ji HC, Venkataramanan R, Mondelli M. Spectral estimators for structured generalized linear models via approximate message passing. <i>Mathematical Statistics and Learning</i>. 2025;8(3-4):193-304. doi:<a href=\"https://doi.org/10.4171/MSL/52\">10.4171/MSL/52</a>","mla":"Zhang, Yihan, et al. “Spectral Estimators for Structured Generalized Linear Models via Approximate Message Passing.” <i>Mathematical Statistics and Learning</i>, vol. 8, no. 3–4, EMS Press, 2025, pp. 193–304, doi:<a href=\"https://doi.org/10.4171/MSL/52\">10.4171/MSL/52</a>.","ieee":"Y. Zhang, H. C. Ji, R. Venkataramanan, and M. Mondelli, “Spectral estimators for structured generalized linear models via approximate message passing,” <i>Mathematical Statistics and Learning</i>, vol. 8, no. 3–4. EMS Press, pp. 193–304, 2025."},"publication_identifier":{"issn":["2520-2316"],"eissn":["2520-2324"]},"doi":"10.4171/MSL/52","_id":"20734","page":"193-304","status":"public","date_updated":"2025-12-09T13:53:31Z","article_processing_charge":"No","department":[{"_id":"MaMo"}],"intvolume":"         8","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":8,"year":"2025","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"abstract":[{"text":"We consider the problem of parameter estimation in a high-dimensional generalized linear model. Spectral methods obtained via the principal eigenvector of a suitable data-dependent matrix provide a simple yet surprisingly effective solution. However, despite their wide use, a rigorous performance characterization, as well as a principled way to preprocess the data, are available only for unstructured (i.i.d. Gaussian and Haar orthogonal) designs. In contrast, real-world data matrices are highly structured and exhibit non-trivial correlations. To address the problem, we consider correlated Gaussian designs capturing the anisotropic nature of the features via a covariance matrix Σ. Our main result is a precise asymptotic characterization of the performance of spectral estimators. This allows us to identify the optimal preprocessing that minimizes the number of samples needed for parameter estimation. Surprisingly, such preprocessing is universal across a broad set of designs, which partly addresses a conjecture on optimal spectral estimators for rotationally invariant models. Our principled approach vastly improves upon previous heuristic methods, including for designs common in computational imaging and genetics. The proposed methodology, based on approximate message passing, is broadly applicable and opens the way to the precise characterization of spiked matrices and of the corresponding spectral methods in a variety of settings.","lang":"eng"}],"corr_author":"1","file":[{"checksum":"55a1bd9c1b6b0198c42504fb94f4ad4c","content_type":"application/pdf","file_id":"20752","relation":"main_file","access_level":"open_access","date_updated":"2025-12-09T13:50:03Z","date_created":"2025-12-09T13:50:03Z","creator":"dernst","file_name":"2025_MathStatLearning_Zhang.pdf","file_size":1379626,"success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was done when Y. Z. and H. C. J. were at the Institute of Science and Technology Austria. Y. Z. thanks Hugo Latourelle-Vigeant for bringing [53] to the authors’ attention.\r\nY. Z. and M. M. are partially supported by the 2019 Lopez-Loreta Prize and by the Interdisciplinary Projects Committee (IPC) at ISTA. H. C. J. is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.","oa":1,"ddc":["000"],"has_accepted_license":"1","publisher":"EMS Press"},{"publication_identifier":{"isbn":["978-3-99078-072-5"],"issn":["2663-337X"]},"citation":{"chicago":"Casado Polanco, Raquel. “Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20737\">https://doi.org/10.15479/AT-ISTA-20737</a>.","short":"R. Casado Polanco, Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression, Institute of Science and Technology Austria, 2025.","mla":"Casado Polanco, Raquel. <i>Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20737\">10.15479/AT-ISTA-20737</a>.","ista":"Casado Polanco R. 2025. Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria.","ama":"Casado Polanco R. Role of NOTCH signaling in radial glial progenitor lineage progression. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20737\">10.15479/AT-ISTA-20737</a>","apa":"Casado Polanco, R. (2025). <i>Role of NOTCH signaling in radial glial progenitor lineage progression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20737\">https://doi.org/10.15479/AT-ISTA-20737</a>","ieee":"R. Casado Polanco, “Role of NOTCH signaling in radial glial progenitor lineage progression,” Institute of Science and Technology Austria, 2025."},"doi":"10.15479/AT-ISTA-20737","title":"Role of NOTCH signaling in radial glial progenitor lineage progression","day":"09","fulldoi":"https://doi.org/10.15479/AT-ISTA-20737","file_date_updated":"2025-12-11T11:18:37Z","publication_status":"published","date_published":"2025-12-09T00:00:00Z","OA_place":"publisher","type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"author":[{"id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","last_name":"Casado Polanco","orcid":"0000-0001-8293-4568","first_name":"Raquel","full_name":"Casado Polanco, Raquel"}],"month":"12","date_created":"2025-12-09T09:04:18Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"acknowledgement":"I also want to thank ISTA and the Austrian Science Fund FWF SFB F78 (F7805) for financially\r\nsupporting my research.","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"file":[{"checksum":"71e0fdf4619b0d70d03657ad7348137d","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20793","relation":"source_file","access_level":"closed","date_created":"2025-12-11T09:28:09Z","date_updated":"2025-12-11T11:18:37Z","creator":"rcasadop","file_name":"2025_CasadoPolanco_Raquel_Thesis.docx","file_size":78207207},{"date_updated":"2025-12-11T09:28:04Z","date_created":"2025-12-11T09:28:04Z","embargo_to":"open_access","creator":"rcasadop","embargo":"2026-12-01","file_size":6261874,"file_name":"2025_CasadoPolanco_Raquel_Thesis.pdf","checksum":"58cf2f25c33567723bc754a019c3e396","content_type":"application/pdf","file_id":"20794","relation":"main_file","access_level":"closed"}],"corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2025","keyword":["NOTCH","radial glial progenitor","lineage progression","cortical development"],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"page":"133","_id":"20737","article_processing_charge":"No","date_updated":"2026-04-14T08:16:58Z","status":"public"},{"month":"11","_id":"20749","contributor":[{"first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","last_name":"Hübl"},{"last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X","first_name":"Galien M"}],"author":[{"last_name":"Shi","id":"5c5b9247-15b2-11ec-abd3-fd958715639c","first_name":"Sue","full_name":"Shi, Sue"}],"date_updated":"2026-05-20T08:41:14Z","date_created":"2025-12-09T13:36:16Z","related_material":{"record":[{"relation":"used_in_publication","id":"20727","status":"public"}]},"status":"public","article_processing_charge":"No","department":[{"_id":"ScWa"},{"_id":"CaGo"}],"type":"research_data_reference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa_version":"Published Version","OA_place":"repository","year":"2025","fulldoi":"https://doi.org/10.5281/ZENODO.15752991","day":"10","OA_type":"green","corr_author":"1","abstract":[{"lang":"eng","text":"Datasets and code for publication \"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter\""}],"date_published":"2025-11-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["530"],"publisher":"Zenodo","title":"Datasets and code for manuscript \"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter\"","has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.15752991","open_access":"1"}],"citation":{"short":"S. Shi, (2025).","chicago":"Shi, Sue. “Datasets and Code for Manuscript ‘Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.’” Zenodo, 2025. <a href=\"https://doi.org/10.5281/ZENODO.15752991\">https://doi.org/10.5281/ZENODO.15752991</a>.","ieee":"S. Shi, “Datasets and code for manuscript ‘Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.’” Zenodo, 2025.","ama":"Shi S. Datasets and code for manuscript “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.” 2025. doi:<a href=\"https://doi.org/10.5281/ZENODO.15752991\">10.5281/ZENODO.15752991</a>","ista":"Shi S. 2025. Datasets and code for manuscript ‘Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.15752991\">10.5281/ZENODO.15752991</a>.","apa":"Shi, S. (2025). Datasets and code for manuscript “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.15752991\">https://doi.org/10.5281/ZENODO.15752991</a>","mla":"Shi, Sue. <i>Datasets and Code for Manuscript “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.”</i> Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/ZENODO.15752991\">10.5281/ZENODO.15752991</a>."},"doi":"10.5281/ZENODO.15752991"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["530"],"has_accepted_license":"1","publisher":"Zenodo","title":"All rf-based tuning algorithm for quantum devices using machine learning","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.17352653","open_access":"1"}],"citation":{"ieee":"B. Van Straaten <i>et al.</i>, “All rf-based tuning algorithm for quantum devices using machine learning.” Zenodo, 2025.","mla":"Van Straaten, Barnaby, et al. <i>All Rf-Based Tuning Algorithm for Quantum Devices Using Machine Learning</i>. Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/ZENODO.17352653\">10.5281/ZENODO.17352653</a>.","ista":"Van Straaten B, Fedele F, Vigneau F, Hickie J, Jirovec D, Chrastina D, Isella G, Ares N. 2025. All rf-based tuning algorithm for quantum devices using machine learning, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.17352653\">10.5281/ZENODO.17352653</a>.","apa":"Van Straaten, B., Fedele, F., Vigneau, F., Hickie, J., Jirovec, D., Chrastina, D., … Ares, N. (2025). All rf-based tuning algorithm for quantum devices using machine learning. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.17352653\">https://doi.org/10.5281/ZENODO.17352653</a>","ama":"Van Straaten B, Fedele F, Vigneau F, et al. All rf-based tuning algorithm for quantum devices using machine learning. 2025. doi:<a href=\"https://doi.org/10.5281/ZENODO.17352653\">10.5281/ZENODO.17352653</a>","short":"B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, D. Chrastina, G. Isella, N. Ares, (2025).","chicago":"Van Straaten, Barnaby, Federico Fedele, Florian Vigneau, Joseph Hickie, Daniel Jirovec, Daniel Chrastina, Giovanni Isella, and Natalia Ares. “All Rf-Based Tuning Algorithm for Quantum Devices Using Machine Learning.” Zenodo, 2025. <a href=\"https://doi.org/10.5281/ZENODO.17352653\">https://doi.org/10.5281/ZENODO.17352653</a>."},"doi":"10.5281/ZENODO.17352653","_id":"20750","month":"10","author":[{"full_name":"Van Straaten, Barnaby","last_name":"Van Straaten","first_name":"Barnaby"},{"first_name":"Federico","last_name":"Fedele","full_name":"Fedele, Federico"},{"full_name":"Vigneau, Florian","last_name":"Vigneau","first_name":"Florian"},{"first_name":"Joseph","last_name":"Hickie","full_name":"Hickie, Joseph"},{"last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"full_name":"Ares, Natalia","first_name":"Natalia","last_name":"Ares"}],"date_created":"2025-12-09T13:36:29Z","related_material":{"record":[{"relation":"used_in_publication","id":"20730","status":"public"}]},"status":"public","date_updated":"2025-12-09T14:49:36Z","article_processing_charge":"No","department":[{"_id":"GeKa"}],"type":"research_data_reference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa_version":"Published Version","OA_place":"repository","year":"2025","fulldoi":"https://doi.org/10.5281/ZENODO.17352653","OA_type":"green","day":"14","date_published":"2025-10-14T00:00:00Z"},{"keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"year":"2025","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"corr_author":"1","file_date_updated":"2025-12-11T11:00:53Z","file":[{"checksum":"251e7aab01917c2ad2fbccf465492ea1","content_type":"application/zip","file_id":"20799","relation":"main_file","access_level":"open_access","date_created":"2025-12-11T10:47:15Z","date_updated":"2025-12-11T10:47:15Z","creator":"llayanaf","file_size":4575,"file_name":"Perl_scripts.zip","success":1},{"success":1,"file_name":"Supplementary_Datasets.zip","file_size":19052849,"date_updated":"2025-12-11T10:52:17Z","date_created":"2025-12-11T10:52:17Z","creator":"llayanaf","relation":"main_file","access_level":"open_access","checksum":"daf1c03149dd170b14e5c8e109ee3c77","file_id":"20800","content_type":"application/zip"},{"relation":"main_file","access_level":"open_access","checksum":"658d6e95a361b0a3db058b7b4e1733d4","file_id":"20801","content_type":"application/zip","success":1,"file_name":"Supplementary_Tables.zip","file_size":566476,"date_created":"2025-12-11T10:52:11Z","date_updated":"2025-12-11T10:52:11Z","creator":"llayanaf"},{"file_id":"20802","content_type":"text/plain","checksum":"2a2b92eb9fade0015719190596a8c5b7","access_level":"open_access","relation":"main_file","creator":"llayanaf","date_updated":"2025-12-11T11:00:53Z","date_created":"2025-12-11T11:00:53Z","success":1,"file_size":1204,"file_name":"README.txt"}],"date_published":"2025-12-01T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20780","status":"public","date_created":"2025-12-10T23:40:14Z","date_updated":"2026-06-10T08:27:48Z","article_processing_charge":"No","month":"12","_id":"20780","author":[{"orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra"},{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeVi"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"research_data","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","title":"Causes and consequences of sex-chromosome turnovers in Diptera","doi":"10.15479/AT-ISTA-20780","citation":{"short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025).","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>.","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria, 2025.","mla":"Layana Franco, Lorena Alexandra, et al. <i>Causes and Consequences of Sex-Chromosome Turnovers in Diptera</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>","ista":"Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>"},"oa":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d"},{"_id":"20795","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/hidden-in-plain-sight/","description":"News on ISTA website"}]},"date_updated":"2026-05-20T08:11:56Z","status":"public","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"CaMu"}],"intvolume":"       122","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["41284872"]},"volume":122,"year":"2025","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041"}],"abstract":[{"text":"The tropical climate variability is characterized by various oscillations across a range of timescales. Oscillations that imprint the tropical mean state are generally attributed to slow processes, such as the seasonal cycle or interannual variability. Here, we identify a pronounced tropics-wide intraseasonal oscillation (TWISO) in satellite observations and reanalyses. This oscillation, with a period of 30 to 60 d, is evident across multiple variables and involves interactions between convection, radiation, surface fluxes, and large-scale circulation. It is primarily manifested as convective perturbations in the tropical Indo-Pacific warm pool accompanied by oscillations in the large-scale tropical overturning circulation. Here, we examine the relationship between TWISO, the Madden–Julian Oscillation (MJO), and the instability of radiative-convective equilibrium. Certain phases of TWISO coincide with specific phases of the MJO, suggesting a potential connection between the two. However, although the MJO can amplify the oscillation amplitude of TWISO, it is not essential for TWISO to occur. Finally, due to its broad manifestation across the tropics, TWISO potentially exerts widespread influence on tropical weather and climate at regional scales.","lang":"eng"}],"corr_author":"1","file":[{"content_type":"application/pdf","file_id":"20822","checksum":"093a8685170e4a1de9176f68ee449493","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-12-15T09:17:33Z","date_updated":"2025-12-15T09:17:33Z","success":1,"file_name":"2025_PNAS_Bao.pdf","file_size":30890293}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement No. 101034413). S.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project Mesoscale organization of tropical convection, grant agreement No 101098063). D.T. acknowledges funding from the Japan Society for the Promotion of Science (JSPS) (Project JSPS Grants-in-Aid for Scientific Research, grant No. JP24K22893). C.M. gratefully acknowledges funding from the ERC under the European Union’s Horizon 2020 research and innovation program (Project organisation of CLoUdS, and implications for Tropical cyclones and for the Energetics of the tropics, in current and in a waRming climate, grant agreement No. 805041). We thank Martin Singh, Steven Sherwood, Bjorn Stevens, and Lokahith Agasthya for helpful discussions. JSPS Core-to-Core Program, “International Core-to-Core Project on Global Storm Resolving Analysis” (Grant Number: JPJSCCA20220001)","ddc":["550"],"oa":1,"has_accepted_license":"1","publisher":"National Academy of Sciences","article_number":"e2511549122","month":"12","author":[{"first_name":"Jiawei","last_name":"Bao","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei"},{"first_name":"Sandrine","last_name":"Bony","full_name":"Bony, Sandrine"},{"full_name":"Takasuka, Daisuke","last_name":"Takasuka","first_name":"Daisuke"},{"full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350"}],"date_created":"2025-12-11T10:41:13Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"ec_funded":1,"OA_place":"publisher","PlanS_conform":"1","fulldoi":"https://doi.org/10.1073/pnas.2511549122","day":"02","OA_type":"hybrid","scopus_import":"1","article_type":"original","date_published":"2025-12-02T00:00:00Z","publication_status":"published","file_date_updated":"2025-12-15T09:17:33Z","issue":"48","quality_controlled":"1","pmid":1,"title":"Tropics-wide intraseasonal oscillations","APC_amount":"5651,35 EUR","publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"citation":{"chicago":"Bao, Jiawei, Sandrine Bony, Daisuke Takasuka, and Caroline J Muller. “Tropics-Wide Intraseasonal Oscillations.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2511549122\">https://doi.org/10.1073/pnas.2511549122</a>.","short":"J. Bao, S. Bony, D. Takasuka, C.J. Muller, Proceedings of the National Academy of Sciences 122 (2025).","mla":"Bao, Jiawei, et al. “Tropics-Wide Intraseasonal Oscillations.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48, e2511549122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2511549122\">10.1073/pnas.2511549122</a>.","ama":"Bao J, Bony S, Takasuka D, Muller CJ. Tropics-wide intraseasonal oscillations. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(48). doi:<a href=\"https://doi.org/10.1073/pnas.2511549122\">10.1073/pnas.2511549122</a>","ista":"Bao J, Bony S, Takasuka D, Muller CJ. 2025. Tropics-wide intraseasonal oscillations. Proceedings of the National Academy of Sciences. 122(48), e2511549122.","apa":"Bao, J., Bony, S., Takasuka, D., &#38; Muller, C. J. (2025). Tropics-wide intraseasonal oscillations. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2511549122\">https://doi.org/10.1073/pnas.2511549122</a>","ieee":"J. Bao, S. Bony, D. Takasuka, and C. J. Muller, “Tropics-wide intraseasonal oscillations,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48. National Academy of Sciences, 2025."},"doi":"10.1073/pnas.2511549122"},{"publication_identifier":{"eissn":["2041-1723"]},"citation":{"chicago":"Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi, Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>.","short":"D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications 16 (2025).","mla":"Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>, vol. 16, 10446, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>.","ama":"Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>","apa":"Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>","ista":"Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 16, 10446.","ieee":"D. Paouneskou <i>et al.</i>, “BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"doi":"10.1038/s41467-025-65420-9","title":"BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity","publication":"Nature Communications","DOAJ_listed":"1","pmid":1,"quality_controlled":"1","day":"25","OA_type":"gold","fulldoi":"https://doi.org/10.1038/s41467-025-65420-9","file_date_updated":"2025-12-15T09:25:51Z","article_type":"original","publication_status":"published","date_published":"2025-11-25T00:00:00Z","scopus_import":"1","PlanS_conform":"1","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","author":[{"full_name":"Paouneskou, Dimitra","last_name":"Paouneskou","first_name":"Dimitra"},{"first_name":"Antoine","last_name":"Baudrimont","full_name":"Baudrimont, Antoine"},{"orcid":"0000-0002-8489-9281","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","full_name":"Kelemen, Réka K"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"first_name":"Angela","last_name":"Graf","full_name":"Graf, Angela"},{"first_name":"Shehab","last_name":"Moukbel Ali Aldawla","full_name":"Moukbel Ali Aldawla, Shehab"},{"last_name":"Kölbl","first_name":"Claudia","full_name":"Kölbl, Claudia"},{"first_name":"Irene","last_name":"Tiemann-Boege","full_name":"Tiemann-Boege, Irene"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"last_name":"Jantsch","first_name":"Verena","full_name":"Jantsch, Verena"}],"article_number":"10446","month":"11","date_created":"2025-12-11T10:45:06Z","publisher":"Springer Nature","has_accepted_license":"1","acknowledgement":"We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and Nick Wedige) for training and support in image acquisition. We also thank the members of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B (ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory for helpful discussions. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa":1,"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"file":[{"access_level":"open_access","relation":"main_file","file_id":"20823","content_type":"application/pdf","checksum":"a952f7ea050242b79008540de49a0e61","file_size":8096309,"success":1,"file_name":"2025_NatureComm_Paouneskou.pdf","creator":"dernst","date_updated":"2025-12-15T09:25:51Z","date_created":"2025-12-15T09:25:51Z"}],"abstract":[{"text":"Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","volume":16,"year":"2025","external_id":{"pmid":["41290579"]},"department":[{"_id":"BeVi"}],"intvolume":"        16","_id":"20796","article_processing_charge":"Yes","date_updated":"2025-12-15T09:28:37Z","status":"public"},{"department":[{"_id":"MaRo"}],"intvolume":"        26","_id":"20816","article_processing_charge":"Yes","date_updated":"2025-12-15T13:19:41Z","status":"public","file":[{"relation":"main_file","access_level":"open_access","checksum":"7c92919af1b5820d01e91e08906a411f","file_id":"20825","content_type":"application/pdf","file_name":"2025_GenomeBiology_Robertson.pdf","file_size":2206991,"success":1,"date_created":"2025-12-15T13:18:07Z","date_updated":"2025-12-15T13:18:07Z","creator":"dernst"}],"abstract":[{"text":"Background: DNA methylation (DNAm) can regulate gene expression, and its genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for complex traits. The relative stability of methylation profiles may enable better assessment of chronic exposures compared to single time-point protein measures. We present the first large-scale epigenetic study of the highly-abundant serum proteome measured via ultra-high throughput mass spectrometry in 14,671 samples from the Generation Scotland cohort. We further demonstrate the first large-scale comparison of protein EpiScores and their respective proteins as predictors of incident cardiovascular disease.\r\n\r\nResults: Marginal epigenome-wide association models, adjusting for age, sex, measurement batch, estimated white cell proportions, BMI, smoking and methylation principal components, reveal 15,855 significant CpG – protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10. Bayesian epigenome-wide association studies of the same 133 proteins reveal 697 CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein EpiScores correlate significantly with their respective protein in a holdout test-set. Of these, sixteen associate significantly with incident all-cause cardiovascular disease (Nevents=191) compared to one measured protein.\r\n\r\nConclusions: We highlight a complex interplay between the blood-based methylome and proteome. Importantly, we show that protein EpiScores correlate with measured proteins and demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically relevant biomarkers. The protein EpiScores demonstrate more significant associations with cardiovascular disease than directly measured proteins, suggesting their potential as clinical biomarkers for monitoring or predicting disease risk. We suggest that biomarker development could be enhanced by the consideration of protein EpiScores alongside measured proteins.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2025","volume":26,"external_id":{"pmid":["41361833"]},"acknowledgement":"Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006] and is currently supported by the Wellcome Trust [216767/Z/19/Z]. Genotyping of the Generation Scotland samples was carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, University of Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) Reference 104036/Z/14/Z). The DNA methylation profiling and analysis was supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI: Prof AM McIntosh) and through funding from NARSAD (Ref: 27404; awardee: Dr DM Howard) and the Royal College of Physicians of Edinburgh (Sim Fellowship; Awardee: Prof HC Whalley).\r\nJAR is a University of Edinburgh Clinical Academic Track PhD student, supported by the Wellcome Trust (319878/Z/24/Z). ADC was supported by a Medical Research Council PhD Studentship in Precision Medicine with funding from the Medical Research Council Doctoral Training Program and the University of Edinburgh College of Medicine and Veterinary Medicine. HMS is a student on the University of Edinburgh Translational Neuroscience PhD programme funded by the Wellcome Trust (218493/Z/19/Z). CH was funded by MRC Human Genetics Unit program (QTL in Health and Disease) (grant U.MC_UU_00007/10). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (221890/Z/20/Z). JM and REM were supported by Alzheimer’s Society project grant AS-PG-19b-010.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["570"],"has_accepted_license":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","author":[{"first_name":"Josephine A.","last_name":"Robertson","full_name":"Robertson, Josephine A."},{"full_name":"Bajzik, Jakub","id":"b995e25b-8c4b-11ed-a6d8-f71b7bcd6122","last_name":"Bajzik","first_name":"Jakub"},{"full_name":"Vernardis, Spyros","last_name":"Vernardis","first_name":"Spyros"},{"full_name":"Chybowska, Aleksandra D.","first_name":"Aleksandra D.","last_name":"Chybowska"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Grauslys, Arturas","last_name":"Grauslys","first_name":"Arturas"},{"full_name":"Mur, Jure","first_name":"Jure","last_name":"Mur"},{"full_name":"Smith, Hannah M.","last_name":"Smith","first_name":"Hannah M."},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Drake","first_name":"Camilla","full_name":"Drake, Camilla"},{"first_name":"Hannah","last_name":"Grant","full_name":"Grant, Hannah"},{"last_name":"Pearce","first_name":"Jamie","full_name":"Pearce, Jamie"},{"full_name":"Russ, Tom C.","first_name":"Tom C.","last_name":"Russ"},{"first_name":"Poppy","last_name":"Adkin","full_name":"Adkin, Poppy"},{"full_name":"White, Matthew","first_name":"Matthew","last_name":"White"},{"full_name":"Brigden, Charles","first_name":"Charles","last_name":"Brigden"},{"full_name":"Messner, Christoph B.","first_name":"Christoph B.","last_name":"Messner"},{"first_name":"David J.","last_name":"Porteous","full_name":"Porteous, David J."},{"full_name":"Hayward, Caroline","last_name":"Hayward","first_name":"Caroline"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"full_name":"Zelezniak, Aleksej","first_name":"Aleksej","last_name":"Zelezniak"},{"first_name":"Markus","last_name":"Ralser","full_name":"Ralser, Markus"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard"},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."}],"month":"12","article_number":"417","date_created":"2025-12-14T23:02:04Z","day":"08","OA_type":"gold","fulldoi":"https://doi.org/10.1186/s13059-025-03892-0","publication_status":"published","date_published":"2025-12-08T00:00:00Z","article_type":"original","file_date_updated":"2025-12-15T13:18:07Z","scopus_import":"1","OA_place":"publisher","pmid":1,"quality_controlled":"1","publication_identifier":{"eissn":["1474-760X"],"issn":["1474-7596"]},"citation":{"ista":"Robertson JA, Bajzik J, Vernardis S, Chybowska AD, Mccartney DL, Grauslys A, Mur J, Smith HM, Campbell A, Drake C, Grant H, Pearce J, Russ TC, Adkin P, White M, Brigden C, Messner CB, Porteous DJ, Hayward C, Cox SR, Zelezniak A, Ralser M, Robinson MR, Marioni RE. 2025. Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. Genome Biology. 26, 417.","apa":"Robertson, J. A., Bajzik, J., Vernardis, S., Chybowska, A. D., Mccartney, D. L., Grauslys, A., … Marioni, R. E. (2025). Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-025-03892-0\">https://doi.org/10.1186/s13059-025-03892-0</a>","ama":"Robertson JA, Bajzik J, Vernardis S, et al. Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. <i>Genome Biology</i>. 2025;26. doi:<a href=\"https://doi.org/10.1186/s13059-025-03892-0\">10.1186/s13059-025-03892-0</a>","mla":"Robertson, Josephine A., et al. “Methylome-Wide Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins in 14,671 Generation Scotland Participants.” <i>Genome Biology</i>, vol. 26, 417, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s13059-025-03892-0\">10.1186/s13059-025-03892-0</a>.","ieee":"J. A. Robertson <i>et al.</i>, “Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants,” <i>Genome Biology</i>, vol. 26. Springer Nature, 2025.","chicago":"Robertson, Josephine A., Jakub Bajzik, Spyros Vernardis, Aleksandra D. Chybowska, Daniel L. Mccartney, Arturas Grauslys, Jure Mur, et al. “Methylome-Wide Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins in 14,671 Generation Scotland Participants.” <i>Genome Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s13059-025-03892-0\">https://doi.org/10.1186/s13059-025-03892-0</a>.","short":"J.A. Robertson, J. Bajzik, S. Vernardis, A.D. Chybowska, D.L. Mccartney, A. Grauslys, J. Mur, H.M. Smith, A. Campbell, C. Drake, H. Grant, J. Pearce, T.C. Russ, P. Adkin, M. White, C. Brigden, C.B. Messner, D.J. Porteous, C. Hayward, S.R. Cox, A. Zelezniak, M. Ralser, M.R. Robinson, R.E. Marioni, Genome Biology 26 (2025)."},"doi":"10.1186/s13059-025-03892-0","title":"Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants","publication":"Genome Biology","DOAJ_listed":"1"},{"quality_controlled":"1","citation":{"short":"W.F. Podlaski, E.J. Agnes, T.P. Vogels, Physical Review X 15 (2025).","chicago":"Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>Physical Review X</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">https://doi.org/10.1103/PhysRevX.15.011057</a>.","ieee":"W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” <i>Physical Review X</i>, vol. 15. American Physical Society, 2025.","ama":"Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>Physical Review X</i>. 2025;15. doi:<a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">10.1103/PhysRevX.15.011057</a>","apa":"Podlaski, W. F., Agnes, E. J., &#38; Vogels, T. P. (2025). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">https://doi.org/10.1103/PhysRevX.15.011057</a>","ista":"Podlaski WF, Agnes EJ, Vogels TP. 2025. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. Physical Review X. 15, 011057.","mla":"Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>Physical Review X</i>, vol. 15, 011057, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">10.1103/PhysRevX.15.011057</a>."},"publication_identifier":{"eissn":["2160-3308"]},"doi":"10.1103/PhysRevX.15.011057","title":"High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating","APC_amount":"4910,08 EUR","publication":"Physical Review X","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","article_number":"011057","month":"03","author":[{"orcid":"0000-0001-6619-7502","first_name":"William F.","last_name":"Podlaski","full_name":"Podlaski, William F."},{"full_name":"Agnes, Everton J.","last_name":"Agnes","first_name":"Everton J.","orcid":"0000-0001-7184-7311"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels"}],"date_created":"2020-07-16T12:24:28Z","fulldoi":"https://doi.org/10.1103/PhysRevX.15.011057","OA_type":"gold","day":"13","scopus_import":"1","article_type":"original","date_published":"2025-03-13T00:00:00Z","file_date_updated":"2025-03-20T12:47:17Z","publication_status":"published","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Helen Barron, Vezha Boboeva, Adam Packer, João Sacramento, Andrew Saxe, Misha Tsodyks, and Friedemann Zenke for helpful comments at various stages of this work, and Rubem Erichsen, Jr. for carefully reading the manuscript and valuable comments. This work was\r\nsupported by a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society [No. WT100000 (W. F. P., E. J. A., and T. P. V.)], a Wellcome Trust Senior Research Fellowship [No. 214316/Z/18/Z (E. J. A. and T. P. V.)], and a Research Project Grant by the Leverhulme Trust\r\n[No. RPG-2016-446 (E. J. A.)]. ","ddc":["530"],"oa":1,"publisher":"American Physical Society","has_accepted_license":"1","department":[{"_id":"TiVo"}],"intvolume":"        15","_id":"8125","status":"public","related_material":{"link":[{"relation":"software","url":"https://github.com/wpodlaski/contextual-memory-nets"}]},"date_updated":"2026-05-06T12:44:27Z","article_processing_charge":"Yes","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"isi":1,"abstract":[{"text":"Biological memory is known to be flexible—memory formation and recall depend on factors such as the behavioral context of the organism. However, this property is often ignored in associative memory models, leaving it unclear how memories can be organized and recalled when subject to contextual control. Because of the lack of a rigorous analytical framework, it is also unknown how contextual control affects memory stability, storage capacity, and information content. Here, we bring the dynamic nature of memory to the fore by introducing a novel model of associative memory, which we refer to as the context-modular memory network. In our model, stored memory patterns are associated to one of several background network states, or contexts. Memories are accessible when their corresponding context is active, and are otherwise inaccessible. Context modulates the effective network connectivity by imposing a specific\r\nconfiguration of neuronal and synaptic gating—gated neurons (synapses) have their activity (weights) momentarily silenced, thereby reducing interference from memories belonging to other contexts. Memory patterns are randomly and independently chosen, while neuronal and synaptic gates may be selected randomly or optimized through a process of contextual synaptic refinement. Through analytic and numerical results, we show that context-modular memory networks can exhibit both improved memory capacity and differential control of memory stability with random gating (especially for neuronal gating). For contextual synaptic refinement, we devise a method in which synapses are gated off for a given context if they destabilize the memory patterns in that context, drastically improving memory capacity and enabling even more precise control over memory stability. Notably, synaptic refinement allows for patterns to be\r\naccessible in multiple contexts, stabilizing memory patterns even for weight matrices that alone do not contain any information about the memory patterns, such as Gaussian random matrices. Overall, our model integrates recent ideas about context-dependent memory organization with classic associative memory models and proposes a rigorous theory which can act as a framework for future work. Furthermore, our work carries important implications for the understanding of biological memory storage and recall in the brain, such as highlighting an intriguing trade-off between memory capacity and accessibility.","lang":"eng"}],"corr_author":"1","file":[{"file_name":"2025_PhysReviewX_Podlaski.pdf","file_size":1373704,"success":1,"date_created":"2025-03-20T12:47:17Z","date_updated":"2025-03-20T12:47:17Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"1f27ee469ab51a3e1ce1e2df0022e81d","content_type":"application/pdf","file_id":"19432"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"locked":"1","external_id":{"isi":["001451378900002"]},"year":"2025","volume":15},{"volume":16,"year":"2025","external_id":{"isi":["001523450500035"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","file":[{"file_id":"19971","content_type":"application/pdf","checksum":"f59748cb67232cfb210035d9aef60836","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-07-07T09:52:46Z","date_updated":"2025-07-07T09:52:46Z","file_name":"2025_NatureComm_Gao.pdf","file_size":17018106,"success":1}],"abstract":[{"text":"The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we report that a substantial proportion of blood vessels in the adult mouse brain sporadically occlude and regress. Their regression proceeds through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels are found to be widespread in mouse, monkey and human brains. We further reveal that blood vessel regression cause a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"isi":1,"article_processing_charge":"Yes","status":"public","date_updated":"2025-09-04T07:08:37Z","_id":"8616","intvolume":"        16","department":[{"_id":"SiHi"}],"publisher":"Springer Nature","has_accepted_license":"1","ddc":["570"],"oa":1,"acknowledgement":"The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies.  Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","date_published":"2025-07-01T00:00:00Z","article_type":"original","publication_status":"published","file_date_updated":"2025-07-07T09:52:46Z","scopus_import":"1","OA_type":"gold","day":"01","fulldoi":"https://doi.org/10.1038/s41467-025-60308-0","date_created":"2020-10-06T08:58:59Z","author":[{"last_name":"Gao","first_name":"Xiaofei","full_name":"Gao, Xiaofei"},{"full_name":"Li, Jun-Liszt","last_name":"Li","first_name":"Jun-Liszt"},{"last_name":"Chen","first_name":"Xingjun","full_name":"Chen, Xingjun"},{"first_name":"Bo","last_name":"Ci","full_name":"Ci, Bo"},{"first_name":"Fei","last_name":"Chen","full_name":"Chen, Fei"},{"last_name":"Lu","first_name":"Nannan","full_name":"Lu, Nannan"},{"full_name":"Shen, Bo","first_name":"Bo","last_name":"Shen"},{"full_name":"Zheng, Lijun","first_name":"Lijun","last_name":"Zheng"},{"last_name":"Jia","first_name":"Jie-Min","full_name":"Jia, Jie-Min"},{"full_name":"Yi, Yating","last_name":"Yi","first_name":"Yating"},{"full_name":"Zhang, Shiwen","last_name":"Zhang","first_name":"Shiwen"},{"full_name":"Shi, Ying-Chao","first_name":"Ying-Chao","last_name":"Shi"},{"full_name":"Shi, Kaibin","last_name":"Shi","first_name":"Kaibin"},{"first_name":"Nicholas E","last_name":"Propson","full_name":"Propson, Nicholas E"},{"full_name":"Huang, Yubin","last_name":"Huang","first_name":"Yubin"},{"first_name":"Katherine","last_name":"Poinsatte","full_name":"Poinsatte, Katherine"},{"first_name":"Zhaohuan","last_name":"Zhang","full_name":"Zhang, Zhaohuan"},{"first_name":"Yuanlei","last_name":"Yue","full_name":"Yue, Yuanlei"},{"full_name":"Bosco, Dale B","first_name":"Dale B","last_name":"Bosco"},{"full_name":"Lu, Ying-mei","first_name":"Ying-mei","last_name":"Lu"},{"last_name":"Yang","first_name":"Shi-bing","full_name":"Yang, Shi-bing"},{"full_name":"Adams, Ralf H.","last_name":"Adams","first_name":"Ralf H."},{"full_name":"Lindner, Volkhard","last_name":"Lindner","first_name":"Volkhard"},{"full_name":"Huang, Fen","last_name":"Huang","first_name":"Fen"},{"last_name":"Wu","first_name":"Long-Jun","full_name":"Wu, Long-Jun"},{"full_name":"Zheng, Hui","first_name":"Hui","last_name":"Zheng"},{"first_name":"Feng","last_name":"Han","full_name":"Han, Feng"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Stowe, Ann M.","last_name":"Stowe","first_name":"Ann M."},{"full_name":"Peng, Bo","first_name":"Bo","last_name":"Peng"},{"full_name":"Margeta, Marta","last_name":"Margeta","first_name":"Marta"},{"full_name":"Wang, Xiaoqun","last_name":"Wang","first_name":"Xiaoqun"},{"last_name":"Liu","first_name":"Qiang","full_name":"Liu, Qiang"},{"first_name":"Jakob","last_name":"Körbelin","full_name":"Körbelin, Jakob"},{"last_name":"Trepel","first_name":"Martin","full_name":"Trepel, Martin"},{"full_name":"Lu, Hui","first_name":"Hui","last_name":"Lu"},{"full_name":"Zhou, Bo O.","last_name":"Zhou","first_name":"Bo O."},{"full_name":"Zhao, Hu","first_name":"Hu","last_name":"Zhao"},{"full_name":"Su, Wenzhi","first_name":"Wenzhi","last_name":"Su"},{"full_name":"Bachoo, Robert M.","last_name":"Bachoo","first_name":"Robert M."},{"full_name":"Ge, Woo-ping","first_name":"Woo-ping","last_name":"Ge"}],"month":"07","article_number":"5840","ec_funded":1,"type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"Nature Communications","DOAJ_listed":"1","title":"Reduction of neuronal activity mediated by blood-vessel regression in the brain","doi":"10.1038/s41467-025-60308-0","publication_identifier":{"eissn":["2041-1723"]},"citation":{"chicago":"Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-60308-0\">https://doi.org/10.1038/s41467-025-60308-0</a>.","short":"X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, Nature Communications 16 (2025).","mla":"Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>Nature Communications</i>, vol. 16, 5840, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-60308-0\">10.1038/s41467-025-60308-0</a>.","ama":"Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-60308-0\">10.1038/s41467-025-60308-0</a>","ista":"Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. 2025. Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. 16, 5840.","apa":"Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (2025). Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-60308-0\">https://doi.org/10.1038/s41467-025-60308-0</a>","ieee":"X. Gao <i>et al.</i>, “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"quality_controlled":"1"},{"arxiv":1,"publication_identifier":{"issn":["0021-8693"],"eissn":["1090-266X"]},"citation":{"chicago":"Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for GLn.” <i>Journal of Algebra</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">https://doi.org/10.1016/j.jalgebra.2024.08.033</a>.","short":"J. Löwit, Journal of Algebra 663 (2025) 81–118.","mla":"Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for GLn.” <i>Journal of Algebra</i>, vol. 663, no. 2, Elsevier, 2025, pp. 81–118, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">10.1016/j.jalgebra.2024.08.033</a>.","ama":"Löwit J. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. <i>Journal of Algebra</i>. 2025;663(2):81-118. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">10.1016/j.jalgebra.2024.08.033</a>","ista":"Löwit J. 2025. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. Journal of Algebra. 663(2), 81–118.","apa":"Löwit, J. (2025). On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">https://doi.org/10.1016/j.jalgebra.2024.08.033</a>","ieee":"J. Löwit, “On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn,” <i>Journal of Algebra</i>, vol. 663, no. 2. Elsevier, pp. 81–118, 2025."},"doi":"10.1016/j.jalgebra.2024.08.033","title":"On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn","publication":"Journal of Algebra","issue":"2","quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.jalgebra.2024.08.033","OA_type":"hybrid","day":"01","scopus_import":"1","article_type":"original","file_date_updated":"2025-01-13T08:57:57Z","publication_status":"published","date_published":"2025-02-01T00:00:00Z","OA_place":"publisher","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"month":"02","author":[{"full_name":"Löwit, Jakub","first_name":"Jakub","id":"e3b80ae2-eb8e-11eb-b029-9aef4a9108a0","last_name":"Löwit"}],"date_created":"2024-09-29T22:01:37Z","has_accepted_license":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"oa":1,"isi":1,"abstract":[{"text":"In 1976, Deligne and Lusztig realized the representation theory of finite groups of Lie type inside étale cohomology of certain algebraic varieties. Recently, a p-adic version of this theory started to emerge: there are p-adic Deligne–Lusztig spaces, whose cohomology encodes representation theoretic information for p-adic groups – for instance, it partially realizes the local Langlands correspondence with characteristic zero coefficients. However, the parallel case of coefficients of positive characteristic  ℓ≠p has not been inspected so far. The purpose of this article is to initiate such an inspection. In particular, we relate cohomology of certain p-adic Deligne–Lusztig spaces to Vignéras's modular local Langlands correspondence for GLn.","lang":"eng"}],"corr_author":"1","file":[{"checksum":"eb240e93c178e48429ad918c9058f1fe","file_id":"18830","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-01-13T08:57:57Z","date_created":"2025-01-13T08:57:57Z","creator":"dernst","success":1,"file_size":731175,"file_name":"2024_JourAlgebra_Loewit.pdf"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"arxiv":["2404.11176"],"isi":["001325207800001"]},"volume":663,"year":"2025","department":[{"_id":"TaHa"}],"intvolume":"       663","_id":"18154","page":"81-118","date_updated":"2025-02-27T12:32:40Z","status":"public","article_processing_charge":"Yes (via OA deal)"},{"date_created":"2024-10-06T22:01:10Z","month":"02","article_number":"103212","author":[{"first_name":"Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"orcid":"0000-0003-1548-0177","first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","full_name":"Mühlböck, Fabian"},{"full_name":"Muroya Lei, Stefanie","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","last_name":"Muroya Lei"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","OA_place":"publisher","scopus_import":"1","file_date_updated":"2025-01-13T09:02:47Z","date_published":"2025-02-01T00:00:00Z","publication_status":"published","article_type":"original","fulldoi":"https://doi.org/10.1016/j.scico.2024.103212","day":"01","OA_type":"hybrid","quality_controlled":"1","issue":"2","publication":"Science of Computer Programming","title":"VAMOS: Middleware for best-effort third-party monitoring","doi":"10.1016/j.scico.2024.103212","citation":{"mla":"Chalupa, Marek, et al. “VAMOS: Middleware for Best-Effort Third-Party Monitoring.” <i>Science of Computer Programming</i>, vol. 240, no. 2, 103212, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.scico.2024.103212\">10.1016/j.scico.2024.103212</a>.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2025. VAMOS: Middleware for best-effort third-party monitoring. Science of Computer Programming. 240(2), 103212.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for best-effort third-party monitoring. <i>Science of Computer Programming</i>. 2025;240(2). doi:<a href=\"https://doi.org/10.1016/j.scico.2024.103212\">10.1016/j.scico.2024.103212</a>","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2025). VAMOS: Middleware for best-effort third-party monitoring. <i>Science of Computer Programming</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scico.2024.103212\">https://doi.org/10.1016/j.scico.2024.103212</a>","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “VAMOS: Middleware for best-effort third-party monitoring,” <i>Science of Computer Programming</i>, vol. 240, no. 2. Elsevier, 2025.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “VAMOS: Middleware for Best-Effort Third-Party Monitoring.” <i>Science of Computer Programming</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.scico.2024.103212\">https://doi.org/10.1016/j.scico.2024.103212</a>.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, Science of Computer Programming 240 (2025)."},"publication_identifier":{"issn":["0167-6423"]},"date_updated":"2025-09-09T12:25:29Z","status":"public","related_material":{"record":[{"status":"public","id":"12856","relation":"earlier_version"}]},"article_processing_charge":"Yes (via OA deal)","_id":"18169","intvolume":"       240","department":[{"_id":"ToHe"}],"external_id":{"isi":["001327852600001"]},"volume":240,"year":"2025","oa_version":"Published Version","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of runtime monitoring. Third-party and best-effort monitoring are especially valuable, yet under-explored areas of runtime monitoring. In this context, third-party monitoring means monitoring with a limited knowledge of the monitored software (as it has been developed by a third party). Best-effort monitoring keeps pace with the monitored software at the cost of possibly imprecise verdicts when keeping up with the monitored software would not be feasible. Most existing monitoring frameworks do not support the combination of third-party and best-effort monitoring because they either require the full access to the monitored code or the ability to process all observable events, or both.\r\nWe present a middleware framework, Vamos, for the runtime monitoring of software. Vamos is explicitly designed to support third-party and best-effort scenarios. The design goals of Vamos are (i) efficiency (tracing events with low overhead), (ii) flexibility (the ability to monitor a variety of different event channels, and to connect to a wide range of monitors), and (iii) ease-of-use. To achieve its goals, Vamos combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for Vamos and conducted a set of experiments demonstrating the usability of the scheme. The results indicate that Vamos enables writing useful yet efficient monitors, and simplifies key aspects of setting up a monitoring system from scratch."}],"corr_author":"1","file":[{"creator":"dernst","date_created":"2025-01-13T09:02:47Z","date_updated":"2025-01-13T09:02:47Z","file_size":1173677,"success":1,"file_name":"2024_ScienceCompProg_Chalupa.pdf","content_type":"application/pdf","file_id":"18831","checksum":"cd93c0c356e479ffccfbe8499b6ba8e2","access_level":"open_access","relation":"main_file"}],"isi":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"ddc":["000"],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the STTT reviewers for their valuable feedback and suggestions.","publisher":"Elsevier","has_accepted_license":"1"},{"volume":267,"year":"2025","external_id":{"pmid":["39341071"],"isi":["001328413700001"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","file":[{"access_level":"open_access","relation":"main_file","file_id":"18843","content_type":"application/pdf","checksum":"208ac27dab27af792d198fcb74af8756","file_size":4135372,"success":1,"file_name":"2025_BiosensorsBioelectronics_Herdina.pdf","creator":"dernst","date_created":"2025-01-13T11:14:32Z","date_updated":"2025-01-13T11:14:32Z"}],"abstract":[{"lang":"eng","text":"This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making."}],"isi":1,"article_processing_charge":"Yes (in subscription journal)","status":"public","date_updated":"2025-02-27T12:34:07Z","_id":"18170","intvolume":"       267","department":[{"_id":"LeSa"}],"publisher":"Elsevier","has_accepted_license":"1","oa":1,"ddc":["570"],"acknowledgement":"This research was funded in whole by the Austrian Science Fund (FWF) [P 35103-B, Grant-DOI: 10.55776/P35103]. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. We would like to thank Olfert Landt for advice on ssDNA probe design; Rui Qiang Chen, Jennifer Stock, and Christine Wukotitsch for their excellent support with ONT sequencing; Christoph Köppl and Andreas Fischer for excellent support in recombinant N protein expression and purification; and the whole team at the division of clinical virology for their support with standard diagnostics.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","article_type":"original","publication_status":"published","file_date_updated":"2025-01-13T11:14:32Z","date_published":"2025-01-01T00:00:00Z","scopus_import":"1","day":"01","OA_type":"hybrid","fulldoi":"https://doi.org/10.1016/j.bios.2024.116807","date_created":"2024-10-06T22:01:11Z","author":[{"last_name":"Herdina","first_name":"Anna Nele","full_name":"Herdina, Anna Nele"},{"last_name":"Bozdogan","first_name":"Anil","full_name":"Bozdogan, Anil"},{"full_name":"Aspermair, Patrik","first_name":"Patrik","last_name":"Aspermair"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"last_name":"Klausberger","first_name":"Miriam","full_name":"Klausberger, Miriam"},{"first_name":"Nico","last_name":"Lingg","full_name":"Lingg, Nico"},{"first_name":"Monika","last_name":"Cserjan-Puschmann","full_name":"Cserjan-Puschmann, Monika"},{"first_name":"Patricia Pereira","last_name":"Aguilar","full_name":"Aguilar, Patricia Pereira"},{"full_name":"Auer, Simone","first_name":"Simone","last_name":"Auer"},{"full_name":"Demirtas, Halil","first_name":"Halil","last_name":"Demirtas"},{"id":"3a5f4167-9bd9-11ed-bd12-a1446d38776f","last_name":"Andersson","first_name":"Jakob","full_name":"Andersson, Jakob"},{"full_name":"Lötsch, Felix","first_name":"Felix","last_name":"Lötsch"},{"first_name":"Barbara","last_name":"Holzer","full_name":"Holzer, Barbara"},{"last_name":"Steinrigl","first_name":"Adi","full_name":"Steinrigl, Adi"},{"first_name":"Florian","last_name":"Thalhammer","full_name":"Thalhammer, Florian"},{"first_name":"Julia","last_name":"Schellnegger","full_name":"Schellnegger, Julia"},{"full_name":"Breuer, Monika","last_name":"Breuer","first_name":"Monika"},{"full_name":"Knoll, Wolfgang","first_name":"Wolfgang","last_name":"Knoll"},{"last_name":"Strassl","first_name":"Robert","full_name":"Strassl, Robert"}],"article_number":"116807","month":"01","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication":"Biosensors and Bioelectronics","title":"Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements","doi":"10.1016/j.bios.2024.116807","citation":{"mla":"Herdina, Anna Nele, et al. “Bridging Basic Science and Applied Diagnostics: Comprehensive Viral Diagnostics Enabled by Graphene-Based Electronic Biosensor Technology Advancements.” <i>Biosensors and Bioelectronics</i>, vol. 267, 116807, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bios.2024.116807\">10.1016/j.bios.2024.116807</a>.","apa":"Herdina, A. N., Bozdogan, A., Aspermair, P., Dostalek, J., Klausberger, M., Lingg, N., … Strassl, R. (2025). Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. <i>Biosensors and Bioelectronics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bios.2024.116807\">https://doi.org/10.1016/j.bios.2024.116807</a>","ista":"Herdina AN, Bozdogan A, Aspermair P, Dostalek J, Klausberger M, Lingg N, Cserjan-Puschmann M, Aguilar PP, Auer S, Demirtas H, Andersson J, Lötsch F, Holzer B, Steinrigl A, Thalhammer F, Schellnegger J, Breuer M, Knoll W, Strassl R. 2025. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. Biosensors and Bioelectronics. 267, 116807.","ama":"Herdina AN, Bozdogan A, Aspermair P, et al. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. <i>Biosensors and Bioelectronics</i>. 2025;267. doi:<a href=\"https://doi.org/10.1016/j.bios.2024.116807\">10.1016/j.bios.2024.116807</a>","ieee":"A. N. Herdina <i>et al.</i>, “Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements,” <i>Biosensors and Bioelectronics</i>, vol. 267. Elsevier, 2025.","chicago":"Herdina, Anna Nele, Anil Bozdogan, Patrik Aspermair, Jakub Dostalek, Miriam Klausberger, Nico Lingg, Monika Cserjan-Puschmann, et al. “Bridging Basic Science and Applied Diagnostics: Comprehensive Viral Diagnostics Enabled by Graphene-Based Electronic Biosensor Technology Advancements.” <i>Biosensors and Bioelectronics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bios.2024.116807\">https://doi.org/10.1016/j.bios.2024.116807</a>.","short":"A.N. Herdina, A. Bozdogan, P. Aspermair, J. Dostalek, M. Klausberger, N. Lingg, M. Cserjan-Puschmann, P.P. Aguilar, S. Auer, H. Demirtas, J. Andersson, F. Lötsch, B. Holzer, A. Steinrigl, F. Thalhammer, J. Schellnegger, M. Breuer, W. Knoll, R. Strassl, Biosensors and Bioelectronics 267 (2025)."},"publication_identifier":{"eissn":["1873-4235"],"issn":["0956-5663"]},"pmid":1,"quality_controlled":"1"},{"oa_version":"Published Version","language":[{"iso":"eng"}],"conference":{"location":"Vienna, Austria & Virtual","name":"EGU General Assembly","end_date":"2025-05-02","start_date":"2025-04-27"},"year":"2025","_id":"22120","date_updated":"2026-07-02T06:41:43Z","status":"public","article_processing_charge":"No","department":[{"_id":"FrPe"},{"_id":"GradSch"}],"publisher":"European Geosciences Union","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["550"],"OA_place":"publisher","fulldoi":"https://doi.org/10.5194/egusphere-egu25-17446","OA_type":"gold","day":"14","date_published":"2025-05-14T00:00:00Z","publication_status":"published","article_number":"EGU25-17446","month":"05","author":[{"last_name":"Muñoz Hermosilla","id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","first_name":"José M","orcid":"0000-0002-1990-8508","full_name":"Muñoz Hermosilla, José M"},{"full_name":"Miles, Evan","first_name":"Evan","last_name":"Miles"},{"first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"full_name":"Hardmeier, Florian","first_name":"Florian","last_name":"Hardmeier"},{"full_name":"Melo Velasco, Juan Vicente","first_name":"Juan Vicente","last_name":"Melo Velasco","id":"2611dec0-b9c6-11ed-9bea-a81c2b17a549"},{"first_name":"Guillaume","last_name":"Jouvet","full_name":"Jouvet, Guillaume"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087","first_name":"Francesca"}],"date_created":"2026-06-22T12:17:47Z","type":"conference_abstract","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"main_file_link":[{"url":"https://doi.org/10.5194/egusphere-egu25-17446","open_access":"1"}],"title":"Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier","publication":"EGU General Assembly 2025","citation":{"ieee":"J. M. Muñoz Hermosilla <i>et al.</i>, “Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier,” in <i>EGU General Assembly 2025</i>, Vienna, Austria &#38; Virtual, 2025.","mla":"Muñoz Hermosilla, José M., et al. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” <i>EGU General Assembly 2025</i>, EGU25-17446, European Geosciences Union, 2025, doi:<a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">10.5194/egusphere-egu25-17446</a>.","ama":"Muñoz Hermosilla JM, Miles E, McCarthy M, et al. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In: <i>EGU General Assembly 2025</i>. European Geosciences Union; 2025. doi:<a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">10.5194/egusphere-egu25-17446</a>","apa":"Muñoz Hermosilla, J. M., Miles, E., McCarthy, M., Hardmeier, F., Melo Velasco, J. V., Jouvet, G., &#38; Pellicciotti, F. (2025). Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In <i>EGU General Assembly 2025</i>. Vienna, Austria &#38; Virtual: European Geosciences Union. <a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">https://doi.org/10.5194/egusphere-egu25-17446</a>","ista":"Muñoz Hermosilla JM, Miles E, McCarthy M, Hardmeier F, Melo Velasco JV, Jouvet G, Pellicciotti F. 2025. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. EGU General Assembly 2025. EGU General Assembly, EGU25-17446.","short":"J.M. Muñoz Hermosilla, E. Miles, M. McCarthy, F. Hardmeier, J.V. Melo Velasco, G. Jouvet, F. Pellicciotti, in:, EGU General Assembly 2025, European Geosciences Union, 2025.","chicago":"Muñoz Hermosilla, José M, Evan Miles, Michael McCarthy, Florian Hardmeier, Juan Vicente Melo Velasco, Guillaume Jouvet, and Francesca Pellicciotti. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” In <i>EGU General Assembly 2025</i>. European Geosciences Union, 2025. <a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">https://doi.org/10.5194/egusphere-egu25-17446</a>."},"doi":"10.5194/egusphere-egu25-17446"},{"quality_controlled":"1","doi":"10.4171/jems/1692","arxiv":1,"citation":{"ieee":"M. Glasgow, M. A. Kwan, A. Sah, and M. Sawhney, “The exact rank of sparse random graphs,” <i>Journal of the European Mathematical Society</i>. EMS Press, 2025.","mla":"Glasgow, Margalit, et al. “The Exact Rank of Sparse Random Graphs.” <i>Journal of the European Mathematical Society</i>, EMS Press, 2025, doi:<a href=\"https://doi.org/10.4171/jems/1692\">10.4171/jems/1692</a>.","ista":"Glasgow M, Kwan MA, Sah A, Sawhney M. 2025. The exact rank of sparse random graphs. Journal of the European Mathematical Society.","apa":"Glasgow, M., Kwan, M. A., Sah, A., &#38; Sawhney, M. (2025). The exact rank of sparse random graphs. <i>Journal of the European Mathematical Society</i>. EMS Press. <a href=\"https://doi.org/10.4171/jems/1692\">https://doi.org/10.4171/jems/1692</a>","ama":"Glasgow M, Kwan MA, Sah A, Sawhney M. The exact rank of sparse random graphs. <i>Journal of the European Mathematical Society</i>. 2025. doi:<a href=\"https://doi.org/10.4171/jems/1692\">10.4171/jems/1692</a>","short":"M. Glasgow, M.A. Kwan, A. Sah, M. Sawhney, Journal of the European Mathematical Society (2025).","chicago":"Glasgow, Margalit, Matthew Alan Kwan, Ashwin Sah, and Mehtaab Sawhney. “The Exact Rank of Sparse Random Graphs.” <i>Journal of the European Mathematical Society</i>. EMS Press, 2025. <a href=\"https://doi.org/10.4171/jems/1692\">https://doi.org/10.4171/jems/1692</a>."},"publication_identifier":{"eissn":["1435-9863"],"issn":["1435-9855"]},"DOAJ_listed":"1","publication":"Journal of the European Mathematical Society","title":"The exact rank of sparse random graphs","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4171/JEMS/1692"}],"type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_created":"2026-02-17T07:41:59Z","month":"09","author":[{"full_name":"Glasgow, Margalit","first_name":"Margalit","last_name":"Glasgow"},{"full_name":"Kwan, Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"first_name":"Ashwin","last_name":"Sah","full_name":"Sah, Ashwin"},{"full_name":"Sawhney, Mehtaab","first_name":"Mehtaab","last_name":"Sawhney"}],"date_published":"2025-09-02T00:00:00Z","publication_status":"epub_ahead","article_type":"original","fulldoi":"https://doi.org/10.4171/jems/1692","OA_type":"diamond","day":"02","OA_place":"publisher","PlanS_conform":"1","das_tickbox":"1","oa":1,"ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank Noga Alon for suggesting that our main result gives\r\na linear-time algorithm for computing the rank. We also thank the referees for a number of thoughtful comments and suggestions. Glasgow was supported by NSF graduate research fellowship program award DGE1656518. Kwan was supported by ERC Starting Grant “RANDSTRUCT” No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302.\r\n","has_accepted_license":"1","publisher":"EMS Press","department":[{"_id":"MaKw"}],"date_updated":"2026-07-06T11:51:31Z","status":"public","article_processing_charge":"No","_id":"21263","abstract":[{"text":"Two landmark results in combinatorial random matrix theory, due to Komlós and Costello–Tao–Vu, show that discrete random matrices and symmetric discrete random matrices are typically nonsingular. In particular, in the language of graph theory, when p is a fixed constant, the biadjacency matrix of a random Erdős–Rényi bipartite graph G(n,n,p) and the adjacency matrix of an Erdős–Rényi random graph G(n,p) are both nonsingular with high probability. However, very sparse random graphs (i.e., where p is allowed to decay rapidly with n) are typically singular, due to the presence of “local” dependencies such as isolated vertices and pairs of degree-1 vertices with the same neighbour. In this paper, we give a combinatorial description of the rank of a sparse random graph G(n,n,c/n) or G(n,c/n) in terms of such local dependencies, for all constants c=e (and we present some evidence that the situation is very different for c=e). This gives an essentially complete answer to a question raised by Vu (2014). As applications of our main theorem and its proof, we also determine the asymptotic singularity probability of the 2-core of a sparse random graph, we show that the rank of a sparse random graph is extremely well approximated by its matching number, and we deduce a central limit theorem for the rank of G(n,c/n).","lang":"eng"}],"corr_author":"1","project":[{"grant_number":"101076777","name":"Randomness and structure in combinatorics","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"external_id":{"arxiv":["2303.05435"]},"year":"2025","oa_version":"Published Version","language":[{"iso":"eng"}]},{"OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT-ISTA-20441","day":"12","date_published":"2025-10-12T00:00:00Z","file_date_updated":"2025-10-28T13:10:26Z","publication_status":"published","month":"10","author":[{"first_name":"Suyash","orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","last_name":"Naik","full_name":"Naik, Suyash"}],"date_created":"2025-10-10T14:58:30Z","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"dissertation","title":"Keratins act as global coordinators of tissue spreading through mechanosensitive feedback","license":"https://creativecommons.org/licenses/by-sa/4.0/","publication_identifier":{"isbn":["978-3-99078-069-5"],"issn":["2663-337X"]},"citation":{"short":"S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025.","chicago":"Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>.","ieee":"S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025.","ista":"Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria.","apa":"Naik, S. (2025). <i>Keratins act as global coordinators of tissue spreading through mechanosensitive feedback</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>","ama":"Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>","mla":"Naik, Suyash. <i>Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>."},"doi":"10.15479/AT-ISTA-20441","oa_version":"Published Version","language":[{"iso":"eng"}],"year":"2025","project":[{"_id":"8f060199-16d5-11f0-9cad-f3253b266c46","grant_number":"PAT 5044023","name":"Keratins in epithelial tissue spreading"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W 1250-B20","_id":"25AA5F24-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"abstract":[{"text":"Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium.","lang":"eng"}],"corr_author":"1","file":[{"access_level":"open_access","relation":"main_file","file_id":"20567","content_type":"application/pdf","checksum":"2892f04d4a5c18677871c3e06ac1244a","file_name":"Thesis_PDFA_.pdf","file_size":6846189,"success":1,"creator":"snaik","date_updated":"2025-10-28T13:10:08Z","date_created":"2025-10-28T13:10:08Z"},{"access_level":"open_access","relation":"source_file","content_type":"application/zip","file_id":"20568","checksum":"15934d4465cd0e9b7c32678da9a33a2f","file_size":8839300,"file_name":"Thesis.zip","creator":"snaik","date_created":"2025-10-28T13:10:26Z","date_updated":"2025-10-28T13:10:26Z"}],"_id":"20441","page":"105","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20465"}]},"date_updated":"2026-07-06T12:51:41Z","status":"public","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences.","ddc":["596","597","532"],"oa":1}]