[{"file_date_updated":"2025-12-01T08:19:46Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"publication":"Physical Review Letters","date_updated":"2025-12-01T08:22:37Z","status":"public","PlanS_conform":"1","scopus_import":"1","issue":"21","ec_funded":1,"quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2507.17591"]},"language":[{"iso":"eng"}],"_id":"20705","abstract":[{"lang":"eng","text":"Optical tweezers are widely used as a highly sensitive tool to measure forces on micron-scale particles. One such application is the measurement of the electric charge of a particle, which can be done with high precision in liquids, air, or vacuum. We experimentally investigate how the trapping laser itself can electrically charge such a particle, in our case a ∼1  μ⁢m SiO2 sphere in air. We model the charging mechanism as a two-photon process which reproduces the experimental data with high fidelity."}],"day":"21","citation":{"chicago":"Stöllner, Andrea, Isaac C Lenton, Artem Volosniev, James Millen, Renjiro Shibuya, Hisao Ishii, Dmytro Rak, et al. “Using Optical Tweezers to Simultaneously Trap, Charge, and Measure the Charge of a Microparticle in Air.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/5xd9-4tjj.","ista":"Stöllner A, Lenton IC, Volosniev A, Millen J, Shibuya R, Ishii H, Rak D, Alpichshev Z, David G, Signorell R, Muller CJ, Waitukaitis SR. 2025. Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. 135(21), 218202.","ama":"Stöllner A, Lenton IC, Volosniev A, et al. Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. 2025;135(21). doi:10.1103/5xd9-4tjj","apa":"Stöllner, A., Lenton, I. C., Volosniev, A., Millen, J., Shibuya, R., Ishii, H., … Waitukaitis, S. R. (2025). Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. American Physical Society. https://doi.org/10.1103/5xd9-4tjj","ieee":"A. Stöllner et al., “Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air,” Physical Review Letters, vol. 135, no. 21. American Physical Society, 2025.","short":"A. Stöllner, I.C. Lenton, A. Volosniev, J. Millen, R. Shibuya, H. Ishii, D. Rak, Z. Alpichshev, G. David, R. Signorell, C.J. Muller, S.R. Waitukaitis, Physical Review Letters 135 (2025).","mla":"Stöllner, Andrea, et al. “Using Optical Tweezers to Simultaneously Trap, Charge, and Measure the Charge of a Microparticle in Air.” Physical Review Letters, vol. 135, no. 21, 218202, American Physical Society, 2025, doi:10.1103/5xd9-4tjj."},"has_accepted_license":"1","ddc":["530","550"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","article_number":"218202","intvolume":" 135","OA_place":"publisher","date_published":"2025-11-21T00:00:00Z","oa":1,"doi":"10.1103/5xd9-4tjj","acknowledgement":"We thank Todor Asenov and Abdulhamid Baghdadi for their outstanding technical support and Dr. Michael Gleichweit and Mercede Azizbaig Mohajer for the helpful discussions. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 949120 and No. 805041) and the Swiss National Science Foundation (SNSF, Project No. 200021-236446). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop and the Scientific Computing service unit.","month":"11","department":[{"_id":"ZhAl"},{"_id":"CaMu"},{"_id":"ScWa"}],"article_type":"original","project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"},{"grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"volume":135,"author":[{"id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed","first_name":"Andrea","orcid":"0000-0002-0464-8440","full_name":"Stöllner, Andrea","last_name":"Stöllner"},{"full_name":"Lenton, Isaac C","last_name":"Lenton","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525"},{"first_name":"James","full_name":"Millen, James","last_name":"Millen"},{"last_name":"Shibuya","full_name":"Shibuya, Renjiro","first_name":"Renjiro"},{"first_name":"Hisao","full_name":"Ishii, Hisao","last_name":"Ishii"},{"id":"70313b46-47c2-11ec-9e88-cd79101918fe","first_name":"Dmytro","full_name":"Rak, Dmytro","last_name":"Rak"},{"last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"},{"first_name":"Grégory","last_name":"David","full_name":"David, Grégory"},{"last_name":"Signorell","full_name":"Signorell, Ruth","first_name":"Ruth"},{"full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"publisher":"American Physical Society","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publication_status":"published","file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","file_size":1761373,"date_created":"2025-12-01T08:19:46Z","checksum":"a5f76b1230cc7b039ecd0dbd6f99e775","file_name":"2025_PhysReviewLetters_Stoellner.pdf","relation":"main_file","creator":"dernst","date_updated":"2025-12-01T08:19:46Z","file_id":"20717"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"arxiv":1,"OA_type":"hybrid","oa_version":"Published Version","title":"Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air","date_created":"2025-11-30T23:02:07Z"},{"date_created":"2025-11-30T23:02:07Z","title":"Entropic costs of extracting classical ticks from a quantum clock","oa_version":"Published Version","OA_type":"hybrid","arxiv":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_size":444198,"date_created":"2025-12-01T08:28:00Z","checksum":"e5c89b95d0f52a38f2d2ada3483f3576","file_name":"2025_PhysReviewLetters_Wadhia.pdf","creator":"dernst","file_id":"20718","date_updated":"2025-12-01T08:28:00Z","relation":"main_file"}],"publication_status":"published","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","publisher":"American Physical Society","volume":135,"author":[{"first_name":"Vivek","full_name":"Wadhia, Vivek","last_name":"Wadhia"},{"full_name":"Meier, Florian","last_name":"Meier","first_name":"Florian"},{"first_name":"Federico","last_name":"Fedele","full_name":"Fedele, Federico"},{"full_name":"Silva, Ralph","last_name":"Silva","first_name":"Ralph"},{"first_name":"Nuriya","full_name":"Nurgalieva, Nuriya","last_name":"Nurgalieva"},{"first_name":"David L.","full_name":"Craig, David L.","last_name":"Craig"},{"last_name":"Jirovec","full_name":"Jirovec, Daniel","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"first_name":"Marcus","last_name":"Huber","full_name":"Huber, Marcus"},{"last_name":"Mitchison","full_name":"Mitchison, Mark T.","first_name":"Mark T."},{"first_name":"Paul","full_name":"Erker, Paul","last_name":"Erker"},{"first_name":"Natalia","full_name":"Ares, Natalia","last_name":"Ares"}],"article_type":"original","department":[{"_id":"GeKa"}],"month":"11","acknowledgement":"The authors thank Georgios Katsaros for providing the device for this experiment, and Tony Apollaro, Ilia Khomchenko, and Gerard Milburn for discussions. V. W. acknowledges funding from UK Research and Innovation Grant No. EP/T517811/1. F. M., M. H., and P. E. acknowledge funding from the European Research Council (Consolidator Grant “Cocoquest” No. 101043705). M. H. and P. E. acknowledge funding from the Austrian Federal Ministry of Education, Science, and Research via the Austrian Research Promotion Agency (FFG) through Quantum Austria. R. S. acknowledges funding from the Swiss National Science Foundation via an Ambizione Grant No. PZ00P2_185986. M. T. M. is supported by a Royal Society University Research Fellowship. N. A. acknowledges support from the European Research Council (Grant Agreement No, 948932) and the Royal Society (No. URF-R1-191150). This project is cofunded by the European Union (Quantum Flagship project ASPECTS, Grant Agreement No. 101080167) and UK Research and Innovation (UKRI). Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union, Research Executive Agency, or UKRI. Neither the European Union nor UKRI can be held responsible for them.","oa":1,"doi":"10.1103/5rtj-djfk","date_published":"2025-11-14T00:00:00Z","OA_place":"publisher","intvolume":" 135","article_number":"200407","year":"2025","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"apa":"Wadhia, V., Meier, F., Fedele, F., Silva, R., Nurgalieva, N., Craig, D. L., … Ares, N. (2025). Entropic costs of extracting classical ticks from a quantum clock. Physical Review Letters. American Physical Society. https://doi.org/10.1103/5rtj-djfk","short":"V. Wadhia, F. Meier, F. Fedele, R. Silva, N. Nurgalieva, D.L. Craig, D. Jirovec, J. Saez Mollejo, A. Ballabio, D. Chrastina, G. Isella, M. Huber, M.T. Mitchison, P. Erker, N. Ares, Physical Review Letters 135 (2025).","ieee":"V. Wadhia et al., “Entropic costs of extracting classical ticks from a quantum clock,” Physical Review Letters, vol. 135, no. 20. American Physical Society, 2025.","mla":"Wadhia, Vivek, et al. “Entropic Costs of Extracting Classical Ticks from a Quantum Clock.” Physical Review Letters, vol. 135, no. 20, 200407, American Physical Society, 2025, doi:10.1103/5rtj-djfk.","chicago":"Wadhia, Vivek, Florian Meier, Federico Fedele, Ralph Silva, Nuriya Nurgalieva, David L. Craig, Daniel Jirovec, et al. “Entropic Costs of Extracting Classical Ticks from a Quantum Clock.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/5rtj-djfk.","ista":"Wadhia V, Meier F, Fedele F, Silva R, Nurgalieva N, Craig DL, Jirovec D, Saez Mollejo J, Ballabio A, Chrastina D, Isella G, Huber M, Mitchison MT, Erker P, Ares N. 2025. Entropic costs of extracting classical ticks from a quantum clock. Physical Review Letters. 135(20), 200407.","ama":"Wadhia V, Meier F, Fedele F, et al. Entropic costs of extracting classical ticks from a quantum clock. Physical Review Letters. 2025;135(20). doi:10.1103/5rtj-djfk"},"day":"14","_id":"20706","language":[{"iso":"eng"}],"abstract":[{"text":"We experimentally realize a quantum clock by using a charge sensor to count charges tunneling through a double quantum dot (DQD). Individual tunneling events are used as the clock’s ticks. We quantify the clock’s precision while measuring the power dissipated by the DQD and, separately, the charge sensor in both direct-current and radio-frequency readout modes. This allows us to probe the thermodynamic cost of creating ticks microscopically and recording them macroscopically. Our experiment is the first to explore the interplay between the entropy produced by a microscopic clockwork and its macroscopic measurement apparatus. We show that the latter contribution not only dwarfs the former but also unlocks greatly increased precision, because the measurement record can be exploited to optimally estimate time even when the DQD is at equilibrium. Our results suggest that the entropy produced by the amplification and measurement of a clock’s ticks, which has often been ignored in the literature, is the most important and fundamental thermodynamic cost of timekeeping at the quantum scale.","lang":"eng"}],"external_id":{"isi":["001619305100001"],"arxiv":["2502.00096"]},"type":"journal_article","quality_controlled":"1","issue":"20","scopus_import":"1","PlanS_conform":"1","status":"public","publication":"Physical Review Letters","date_updated":"2025-12-01T15:39:14Z","isi":1,"file_date_updated":"2025-12-01T08:28:00Z"},{"publisher":"American Physical Society","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","article_processing_charge":"Yes","acknowledgement":"The authors thank Andela Saric, Christoph Zechner, and Paul Robin for helpful discussions. J. P. acknowledges support by ERC grant (VULCAN, 101086998) and U.S. ARO under Award No. W911NF2310008. Y. I. L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","doi":"10.1103/rjk2-q2wh","oa":1,"article_type":"original","project":[{"grant_number":"101086998","_id":"bdac72da-d553-11ed-ba76-eae56e802b74","name":"VULCAN: matter, powered from within"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"month":"10","department":[{"_id":"EdHa"},{"_id":"JePa"}],"volume":15,"author":[{"first_name":"Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","orcid":"0000-0002-2916-6632","last_name":"Martinet","full_name":"Martinet, Quentin"},{"first_name":"Yuting I","id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb","full_name":"Li, Yuting I","last_name":"Li"},{"first_name":"A.","last_name":"Aubret","full_name":"Aubret, A."},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"publication_identifier":{"eissn":["2160-3308"]},"arxiv":1,"oa_version":"Published Version","OA_type":"gold","title":"Emergent dynamics of active elastic microbeams","date_created":"2025-11-30T23:02:08Z","publication_status":"published","file":[{"file_size":5902259,"date_created":"2025-12-01T07:30:00Z","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"20714","date_updated":"2025-12-01T07:30:00Z","file_name":"2025_PhysicalReviewX_Martinet.pdf","checksum":"bb64ea9f2c400205fd89e9bdd15cc850"}],"status":"public","PlanS_conform":"1","scopus_import":"1","DOAJ_listed":"1","ec_funded":1,"issue":"4","file_date_updated":"2025-12-01T07:30:00Z","date_updated":"2025-12-01T07:44:06Z","publication":"Physical Review X","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"intvolume":" 15","article_number":"041017","date_published":"2025-10-31T00:00:00Z","OA_place":"publisher","type":"journal_article","quality_controlled":"1","_id":"20708","abstract":[{"lang":"eng","text":"In equilibrium, the physical properties of matter are set by the interactions between the constituents. In contrast, the energy input of the individual components controls the behavior of synthetic or living active matter. Great progress has been made in understanding the emergent phenomena in active fluids, though their inability to resist shear forces hinders their practical use. This motivates the exploration of active solids as shape-shifting materials, yet, we lack controlled synthetic systems to devise active solids with unconventional properties. Here we build active elastic beams from dozens of active colloids and unveil complex emergent behaviors such as self-oscillations or persistent rotations. Developing tensile tests at the microscale, we show that the active beams are ultrasoft materials, with large (nonequilibrium) fluctuations. Combining experiments, theory, and stochastic inference, we show that the dynamics of the active beams can be mapped on different phase transitions which are tuned by boundary conditions. More quantitatively, we assess all relevant parameters by independent measurements or first-principles calculations, and find that our theoretical description agrees with the experimental observations. Our results demonstrate that the simple addition of activity to an elastic beam unveils novel physics and can inspire design strategies for active solids and functional microscopic machines."}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2508.20642"]},"has_accepted_license":"1","citation":{"ama":"Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. Emergent dynamics of active elastic microbeams. Physical Review X. 2025;15(4). doi:10.1103/rjk2-q2wh","ista":"Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. 2025. Emergent dynamics of active elastic microbeams. Physical Review X. 15(4), 041017.","chicago":"Martinet, Quentin, Yuting I Li, A. Aubret, Edouard B Hannezo, and Jérémie A Palacci. “Emergent Dynamics of Active Elastic Microbeams.” Physical Review X. American Physical Society, 2025. https://doi.org/10.1103/rjk2-q2wh.","mla":"Martinet, Quentin, et al. “Emergent Dynamics of Active Elastic Microbeams.” Physical Review X, vol. 15, no. 4, 041017, American Physical Society, 2025, doi:10.1103/rjk2-q2wh.","short":"Q. Martinet, Y.I. Li, A. Aubret, E.B. Hannezo, J.A. Palacci, Physical Review X 15 (2025).","ieee":"Q. Martinet, Y. I. Li, A. Aubret, E. B. Hannezo, and J. A. Palacci, “Emergent dynamics of active elastic microbeams,” Physical Review X, vol. 15, no. 4. American Physical Society, 2025.","apa":"Martinet, Q., Li, Y. I., Aubret, A., Hannezo, E. B., & Palacci, J. A. (2025). Emergent dynamics of active elastic microbeams. Physical Review X. American Physical Society. https://doi.org/10.1103/rjk2-q2wh"},"day":"31"},{"arxiv":1,"publication_identifier":{"eissn":["2643-1564"]},"title":"Finite steady-state current defies non-Hermitian many-body localization","date_created":"2025-11-30T23:02:08Z","OA_type":"gold","oa_version":"Published Version","publication_status":"published","file":[{"file_name":"2025_PhysReviewResearch_Brighi.pdf","checksum":"c4e582ab64ab9f8fface70bf2fd31882","relation":"main_file","date_updated":"2025-12-01T08:00:19Z","file_id":"20715","creator":"dernst","access_level":"open_access","file_size":483879,"date_created":"2025-12-01T08:00:19Z","content_type":"application/pdf","success":1}],"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"American Physical Society","oa":1,"doi":"10.1103/crwj-x7j8","acknowledgement":"F.B. thanks Giuseppe de Tomasi and Oskar A. Prośniak for discussion. P.B. acknowledges support by the Austrian Science Fund (FWF) (Grant Agreement No. 10.55776/ESP9057324). This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/COE1]. The numerical simulations were performed using the ITensor library [73] on the Vienna Scientific Cluster (VSC) and on the MPIPKS HPC cluster. M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. F.R. acknowledges support by the European Union-Next Generation EU with the project “Quantum Optics in Many-Body photonic Environments” (QOMBE) code SOE2024_0000084-CUP B77G24000480006. Open\r\naccess publication funded by Max Planck Society.","volume":7,"author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729"},{"orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","full_name":"Ljubotina, Marko","last_name":"Ljubotina"},{"first_name":"Federico","full_name":"Roccati, Federico","last_name":"Roccati"},{"first_name":"Federico","full_name":"Balducci, Federico","last_name":"Balducci"}],"department":[{"_id":"MaSe"}],"month":"10","article_type":"original","article_number":"L042014","intvolume":" 7","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","OA_place":"publisher","date_published":"2025-10-01T00:00:00Z","external_id":{"arxiv":["2504.02460"]},"_id":"20709","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Non-Hermitian many-body localization (NH MBL) has emerged as a possible scenario for stable localization in open systems, as suggested by spectral indicators identifying a putative transition for finite system sizes. In this work, we shift the focus to dynamical probes, specifically the steady-state spin current, to investigate transport properties in a disordered, non-Hermitian XXZ spin chain. Through exact diagonalization for small systems and tensor-network methods for larger chains, we demonstrate that the steady-state current remains finite and decays exponentially with disorder strength, showing no evidence of a transition up to disorder values far beyond the previously claimed critical point. Our results reveal a stark discrepancy between spectral indicators, which suggest localization, and transport behavior, which indicates delocalization. This highlights the importance of dynamical observables in characterizing NH MBL and suggests that traditional spectral measures may not fully capture the physics of non-Hermitian systems. Additionally, we observe a noncommutativity of limits in system size and time, further complicating the interpretation of finite-size studies. These findings challenge the existence of NH MBL in the studied model and underscore the need for alternative approaches to understanding localization in non-Hermitian settings."}],"quality_controlled":"1","type":"journal_article","citation":{"chicago":"Brighi, Pietro, Marko Ljubotina, Federico Roccati, and Federico Balducci. “Finite Steady-State Current Defies Non-Hermitian Many-Body Localization.” Physical Review Research. American Physical Society, 2025. https://doi.org/10.1103/crwj-x7j8.","ama":"Brighi P, Ljubotina M, Roccati F, Balducci F. Finite steady-state current defies non-Hermitian many-body localization. Physical Review Research. 2025;7(4). doi:10.1103/crwj-x7j8","ista":"Brighi P, Ljubotina M, Roccati F, Balducci F. 2025. Finite steady-state current defies non-Hermitian many-body localization. Physical Review Research. 7(4), L042014.","apa":"Brighi, P., Ljubotina, M., Roccati, F., & Balducci, F. (2025). Finite steady-state current defies non-Hermitian many-body localization. Physical Review Research. American Physical Society. https://doi.org/10.1103/crwj-x7j8","mla":"Brighi, Pietro, et al. “Finite Steady-State Current Defies Non-Hermitian Many-Body Localization.” Physical Review Research, vol. 7, no. 4, L042014, American Physical Society, 2025, doi:10.1103/crwj-x7j8.","ieee":"P. Brighi, M. Ljubotina, F. Roccati, and F. Balducci, “Finite steady-state current defies non-Hermitian many-body localization,” Physical Review Research, vol. 7, no. 4. American Physical Society, 2025.","short":"P. Brighi, M. Ljubotina, F. Roccati, F. Balducci, Physical Review Research 7 (2025)."},"day":"01","has_accepted_license":"1","PlanS_conform":"1","status":"public","DOAJ_listed":"1","issue":"4","scopus_import":"1","file_date_updated":"2025-12-01T08:00:19Z","date_updated":"2025-12-01T08:02:13Z","publication":"Physical Review Research"},{"external_id":{"arxiv":["2406.14374"]},"_id":"20723","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Information-flow interfaces is a formalism recently proposed for specifying, composing, and refining system-wide security requirements. In this work, we show how the widely used concept of security lattices provides a natural semantic interpretation for information-flow interfaces."}],"quality_controlled":"1","type":"book_chapter","day":"02","citation":{"chicago":"Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da Costa. “Information-Flow Interfaces and Security Lattices.” In Engineering Safe and Trustworthy Cyber Physical Systems, 15471:251–63. Cham: Springer Nature, 2025. https://doi.org/10.1007/978-3-031-97537-0_15.","ista":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2025.Information-Flow Interfaces and Security Lattices. In: Engineering Safe and Trustworthy Cyber Physical Systems. LNCS, vol. 15471, 251–263.","ama":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Information-Flow Interfaces and Security Lattices. In: Engineering Safe and Trustworthy Cyber Physical Systems. Vol 15471. Cham: Springer Nature; 2025:251-263. doi:10.1007/978-3-031-97537-0_15","apa":"Bartocci, E., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A. (2025). Information-Flow Interfaces and Security Lattices. In Engineering Safe and Trustworthy Cyber Physical Systems (Vol. 15471, pp. 251–263). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-97537-0_15","short":"E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, Engineering Safe and Trustworthy Cyber Physical Systems, Springer Nature, Cham, 2025, pp. 251–263.","ieee":"E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Information-Flow Interfaces and Security Lattices,” in Engineering Safe and Trustworthy Cyber Physical Systems, vol. 15471, Cham: Springer Nature, 2025, pp. 251–263.","mla":"Bartocci, Ezio, et al. “Information-Flow Interfaces and Security Lattices.” Engineering Safe and Trustworthy Cyber Physical Systems, vol. 15471, Springer Nature, 2025, pp. 251–63, doi:10.1007/978-3-031-97537-0_15."},"intvolume":" 15471","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","OA_place":"repository","date_published":"2025-10-02T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.14374","open_access":"1"}],"date_updated":"2025-12-09T07:57:55Z","publication":"Engineering Safe and Trustworthy Cyber Physical Systems","status":"public","page":"251-263","ec_funded":1,"scopus_import":"1","publication_status":"published","place":"Cham","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783031975370"],"isbn":["9783031975363"]},"arxiv":1,"title":"Information-Flow Interfaces and Security Lattices","alternative_title":["LNCS"],"date_created":"2025-12-01T15:44:58Z","OA_type":"green","oa_version":"Preprint","oa":1,"doi":"10.1007/978-3-031-97537-0_15","acknowledgement":"This project was funded in part by the Austrian Science Fund (FWF) SFB project SpyCoDe F8502 and by the ERC-2020-AdG 101020093.","author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Oliveira da Costa, Ana","last_name":"Oliveira da Costa","first_name":"Ana","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4","orcid":"0000-0002-8741-5799"}],"volume":15471,"department":[{"_id":"ToHe"}],"month":"10","project":[{"name":"Interface Theory for Security and Privacy","_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","grant_number":"F8502"},{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"article_processing_charge":"No","corr_author":"1","publisher":"Springer Nature"},{"oa":1,"doi":"10.1016/j.tplants.2025.10.018","acknowledgement":"I apologize to colleagues whose relevant work I was unable to cite due to space limitations. This work was funded by the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; 37051-B). I thank Drs Huihuang Chen, Yuanrong Pei, Jason Reed, Linlin Qi, and Dolf Weijers for inspiration and critical input.","author":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"department":[{"_id":"JiFr"}],"month":"11","project":[{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"article_type":"review","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Elsevier","pmid":1,"publication_status":"epub_ahead","publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]},"date_created":"2025-12-02T16:29:22Z","title":"Role of cAMP in TIR1/AFB auxin signaling: Open issues","OA_type":"hybrid","oa_version":"Published Version","publication":"Trends in Plant Science","date_updated":"2025-12-09T08:04:58Z","PlanS_conform":"1","status":"public","page":"S1360-1385(25)00300-0","scopus_import":"1","external_id":{"pmid":["41249070"]},"language":[{"iso":"eng"}],"_id":"20725","abstract":[{"text":"The canonical mechanism by which the phytohormone auxin regulates transcription has been one of the cornerstones of plant signaling. The recent unexpected discovery of cyclic AMP (cAMP) as a second messenger in this pathway has revised its foundations while leaving many open questions and gaps in our understanding; these will be discussed in this forum article.","lang":"eng"}],"type":"journal_article","citation":{"chicago":"Friml, Jiří. “Role of CAMP in TIR1/AFB Auxin Signaling: Open Issues.” Trends in Plant Science. Elsevier, 2025. https://doi.org/10.1016/j.tplants.2025.10.018.","ista":"Friml J. 2025. Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science., S1360-1385(25)00300–0.","ama":"Friml J. Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science. 2025:S1360-1385(25)00300-0. doi:10.1016/j.tplants.2025.10.018","apa":"Friml, J. (2025). Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2025.10.018","ieee":"J. Friml, “Role of cAMP in TIR1/AFB auxin signaling: Open issues,” Trends in Plant Science. Elsevier, pp. S1360-1385(25)00300–0, 2025.","short":"J. Friml, Trends in Plant Science (2025) S1360-1385(25)00300–0.","mla":"Friml, Jiří. “Role of CAMP in TIR1/AFB Auxin Signaling: Open Issues.” Trends in Plant Science, Elsevier, 2025, pp. S1360-1385(25)00300-0, doi:10.1016/j.tplants.2025.10.018."},"day":"16","has_accepted_license":"1","ddc":["580"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","OA_place":"publisher","date_published":"2025-11-16T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1016/j.tplants.2025.10.018","open_access":"1"}]},{"date_updated":"2026-02-16T12:33:43Z","publication":"Proceedings of the National Academy of Sciences","acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2025-12-09T12:45:53Z","issue":"50","scopus_import":"1","page":"e2516865122","status":"public","day":"16","citation":{"mla":"Shi, Sue, et al. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.” Proceedings of the National Academy of Sciences, vol. 122, no. 50, National Academy of Sciences, 2025, p. e2516865122, doi:10.1073/pnas.2516865122.","short":"S. Shi, M. Hübl, G.M. Grosjean, C.P. Goodrich, S.R. Waitukaitis, Proceedings of the National Academy of Sciences 122 (2025) e2516865122.","ieee":"S. Shi, M. Hübl, G. M. Grosjean, C. P. Goodrich, and S. R. Waitukaitis, “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter,” Proceedings of the National Academy of Sciences, vol. 122, no. 50. National Academy of Sciences, p. e2516865122, 2025.","apa":"Shi, S., Hübl, M., Grosjean, G. M., Goodrich, C. P., & Waitukaitis, S. R. (2025). Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2516865122","ama":"Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings of the National Academy of Sciences. 2025;122(50):e2516865122. doi:10.1073/pnas.2516865122","ista":"Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. 2025. Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings of the National Academy of Sciences. 122(50), e2516865122.","chicago":"Shi, Sue, Maximilian Hübl, Galien M Grosjean, Carl Peter Goodrich, and Scott R Waitukaitis. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2516865122."},"has_accepted_license":"1","external_id":{"arxiv":["2507.01739"]},"abstract":[{"lang":"eng","text":"Acoustic levitation provides a unique method for manipulating small particles as it completely evades effects from gravity, container walls, or physical handling. These advantages make it a tantalizing platform for studying complex phenomena in many-particle systems. In most standing-wave traps, however, particles interact via acoustic scattering forces that cause them to merge into a single dense object. Here, we introduce a complementary approach that combines acoustic levitation with electrostatic charging to assemble, adapt, and activate complex, separated many-particle systems. The key idea is to superimpose electrostatic repulsion on the intrinsic acoustic attraction, rendering a so-called “mermaid” potential where interactions are attractive at short range and repulsive at long range. By controlling the attraction–repulsion balance, we can levitate expanded structures where all particles are separated, collapsed structures where they are in contact, and hybrid ones consisting of both expanded and collapsed components. We find that collapsed and expanded structures are inherently stable, whereas hybrid ones exhibit transient stability governed by acoustically unstable dimers. Furthermore, we show how electrostatics allow us to adapt between configurations on the fly, either by quasistatic discharge or discrete up/down charge steps. Finally, we demonstrate how large structures experience selective energy pumping from the acoustic field—thrusting some particles into motion while others remain stationary—leading to complex dynamics including coupled rotations and oscillations. Our approach establishes a design space beyond acoustic collapse, offering possibilities to study many-particle systems with complex interactions, while suggesting pathways toward scalable integration into materials processing and other applications."}],"_id":"20727","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","OA_place":"publisher","date_published":"2025-12-16T00:00:00Z","intvolume":" 122","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"year":"2025","volume":122,"author":[{"full_name":"Shi, Sue","last_name":"Shi","first_name":"Sue","id":"5c5b9247-15b2-11ec-abd3-fd958715639c"},{"first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","last_name":"Hübl","full_name":"Hübl, Maximilian"},{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M","orcid":"0000-0001-5154-417X","last_name":"Grosjean","full_name":"Grosjean, Galien M"},{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"month":"12","department":[{"_id":"ScWa"},{"_id":"CaGo"}],"project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","grant_number":"FTI23-G-011"}],"article_type":"original","oa":1,"doi":"10.1073/pnas.2516865122","acknowledgement":"We thank Dustin Kleckner, Jack-William Barotta, and Daniel M. Harris for insightful discussions. We acknowledge the Miba machine shop at the Institute of Science and Technology Austria for instrumentation support. M.C.H. and C.P.G. acknowledge funding by the Gesellschaft für Forschungsförderung Niederösterreich under project FTI23-G-011.","related_material":{"record":[{"relation":"research_data","status":"public","id":"20749"}]},"article_processing_charge":"Yes (in subscription journal)","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"corr_author":"1","publisher":"National Academy of Sciences","file":[{"file_id":"20744","relation":"main_file","date_updated":"2025-12-09T12:45:53Z","creator":"dernst","file_name":"2025_PNAS_Shi.pdf","checksum":"c40dc4c909724b9d1146636612e8821a","file_size":10621381,"date_created":"2025-12-09T12:45:53Z","content_type":"application/pdf","success":1,"access_level":"open_access"}],"publication_status":"published","title":"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter","date_created":"2025-12-07T23:02:00Z","OA_type":"hybrid","oa_version":"Published Version","arxiv":1,"publication_identifier":{"eissn":["1091-6490"]}},{"title":"All-rf-based coarse-tuning algorithm for quantum devices using machine learning","date_created":"2025-12-07T23:02:01Z","OA_type":"hybrid","oa_version":"Published Version","publication_identifier":{"eissn":["2331-7019"]},"file":[{"file_size":5754118,"date_created":"2025-12-09T13:34:38Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","date_updated":"2025-12-09T13:34:38Z","file_id":"20748","file_name":"2025_PhysReviewApplied_vanStraaten.pdf","checksum":"9906b32c7e3c79ed13d05ef88ff15586"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"20750","relation":"research_data"}]},"article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"American Physical Society","volume":24,"author":[{"first_name":"Barnaby","full_name":"Van Straaten, Barnaby","last_name":"Van Straaten"},{"first_name":"Federico","full_name":"Fedele, Federico","last_name":"Fedele"},{"first_name":"Florian","full_name":"Vigneau, Florian","last_name":"Vigneau"},{"first_name":"Joseph","last_name":"Hickie","full_name":"Hickie, Joseph"},{"full_name":"Jirovec, Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"},{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"}],"department":[{"_id":"GeKa"}],"month":"11","article_type":"original","project":[{"call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"},{"name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"}],"oa":1,"doi":"10.1103/v11m-dbhm","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.","OA_place":"publisher","date_published":"2025-11-01T00:00:00Z","intvolume":" 24","article_number":"054030","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"year":"2025","citation":{"ama":"Van Straaten B, Fedele F, Vigneau F, et al. All-rf-based coarse-tuning algorithm for quantum devices using machine learning. Physical Review Applied. 2025;24(5). doi:10.1103/v11m-dbhm","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.","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.” Physical Review Applied. American Physical Society, 2025. https://doi.org/10.1103/v11m-dbhm.","mla":"Van Straaten, Barnaby, et al. “All-Rf-Based Coarse-Tuning Algorithm for Quantum Devices Using Machine Learning.” Physical Review Applied, vol. 24, no. 5, 054030, American Physical Society, 2025, doi:10.1103/v11m-dbhm.","ieee":"B. Van Straaten et al., “All-rf-based coarse-tuning algorithm for quantum devices using machine learning,” Physical Review Applied, vol. 24, no. 5. American Physical Society, 2025.","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).","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. Physical Review Applied. American Physical Society. https://doi.org/10.1103/v11m-dbhm"},"day":"01","has_accepted_license":"1","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"}],"_id":"20730","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","issue":"5","scopus_import":"1","PlanS_conform":"1","status":"public","date_updated":"2025-12-09T14:49:35Z","publication":"Physical Review Applied","acknowledged_ssus":[{"_id":"NanoFab"}],"file_date_updated":"2025-12-09T13:34:38Z"},{"oa":1,"doi":"10.1146/annurev-genet-111523-102424","acknowledgement":"Funding provided by the European Union (grant 101057429) to G.N.","author":[{"full_name":"Marano, Domenico","last_name":"Marano","first_name":"Domenico","id":"3b004c42-803f-11ed-ab7e-ecee8f08bd58"},{"last_name":"Mariano","full_name":"Mariano, Vittoria","first_name":"Vittoria","id":"ee829c33-edb3-11ed-b4fb-c020aaca4b01"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"volume":59,"department":[{"_id":"GaNo"}],"month":"11","article_type":"review","project":[{"name":"Reducing the impact of major environmental challenges on mental health","grant_number":"101057429","_id":"349d1832-11ca-11ed-8bc3-d79b574010e0"}],"article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Annual Reviews","pmid":1,"publication_status":"published","file":[{"checksum":"1000228dc9aca3d48e92605607a99c41","file_name":"2025_AnnualRevGenetics_Marano.pdf","creator":"dernst","date_updated":"2025-12-09T12:53:09Z","relation":"main_file","file_id":"20745","access_level":"open_access","success":1,"content_type":"application/pdf","date_created":"2025-12-09T12:53:09Z","file_size":3629986}],"publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"title":"Fueling the mind: Brain metabolism in health and neurodevelopmental disorders","date_created":"2025-12-07T23:02:01Z","OA_type":"hybrid","oa_version":"Published Version","file_date_updated":"2025-12-09T12:53:09Z","publication":"Annual Review of Genetics","date_updated":"2025-12-09T12:55:11Z","PlanS_conform":"1","page":"415-434","status":"public","scopus_import":"1","external_id":{"pmid":["40902207"]},"language":[{"iso":"eng"}],"_id":"20731","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."}],"quality_controlled":"1","type":"journal_article","day":"03","citation":{"chicago":"Marano, Domenico, Vittoria Mariano, and Gaia Novarino. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review of Genetics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-genet-111523-102424.","ama":"Marano D, Mariano V, Novarino G. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 2025;59:415-434. doi:10.1146/annurev-genet-111523-102424","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., & Novarino, G. (2025). Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-111523-102424","mla":"Marano, Domenico, et al. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review of Genetics, vol. 59, Annual Reviews, 2025, pp. 415–34, doi:10.1146/annurev-genet-111523-102424.","short":"D. Marano, V. Mariano, G. Novarino, Annual Review of Genetics 59 (2025) 415–434.","ieee":"D. Marano, V. Mariano, and G. Novarino, “Fueling the mind: Brain metabolism in health and neurodevelopmental disorders,” Annual Review of Genetics, vol. 59. Annual Reviews, pp. 415–434, 2025."},"has_accepted_license":"1","intvolume":" 59","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"year":"2025","OA_place":"publisher","date_published":"2025-11-03T00:00:00Z"},{"quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2412.06916"]},"_id":"20733","language":[{"iso":"eng"}],"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."}],"citation":{"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. Physical Review Research. American Physical Society. https://doi.org/10.1103/q3dx-kyqj","mla":"Aggarwal, Kushagra, et al. “Rapid Optimal Work Extraction from a Quantum-Dot Information Engine.” Physical Review Research, vol. 7, no. 3, L032017, American Physical Society, 2025, doi:10.1103/q3dx-kyqj.","ieee":"K. Aggarwal et al., “Rapid optimal work extraction from a quantum-dot information engine,” Physical Review Research, vol. 7, no. 3. American Physical Society, 2025.","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.” Physical Review Research. American Physical Society, 2025. https://doi.org/10.1103/q3dx-kyqj.","ama":"Aggarwal K, Rolandi A, Yang Y, et al. Rapid optimal work extraction from a quantum-dot information engine. Physical Review Research. 2025;7(3). doi:10.1103/q3dx-kyqj","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."},"day":"01","has_accepted_license":"1","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","article_number":"L032017","intvolume":" 7","OA_place":"publisher","date_published":"2025-07-01T00:00:00Z","file_date_updated":"2025-12-09T14:05:56Z","date_updated":"2025-12-09T14:07:49Z","publication":"Physical Review Research","status":"public","PlanS_conform":"1","scopus_import":"1","issue":"3","publication_status":"published","file":[{"access_level":"open_access","file_size":536624,"date_created":"2025-12-09T14:05:56Z","content_type":"application/pdf","success":1,"file_name":"2025_PhysReviewResearch_Aggarwal.pdf","checksum":"66f2b572a36a7b5fe611a7639a8b6f12","file_id":"20753","relation":"main_file","creator":"dernst","date_updated":"2025-12-09T14:05:56Z"}],"publication_identifier":{"eissn":["2643-1564"]},"arxiv":1,"OA_type":"gold","oa_version":"Published Version","date_created":"2025-12-07T23:02:02Z","title":"Rapid optimal work extraction from a quantum-dot information engine","oa":1,"doi":"10.1103/q3dx-kyqj","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.","month":"07","department":[{"_id":"GeKa"}],"article_type":"letter_note","volume":7,"author":[{"first_name":"Kushagra","full_name":"Aggarwal, Kushagra","last_name":"Aggarwal"},{"first_name":"Alberto","full_name":"Rolandi, Alberto","last_name":"Rolandi"},{"first_name":"Yikai","full_name":"Yang, Yikai","last_name":"Yang"},{"full_name":"Hickie, Joseph","last_name":"Hickie","first_name":"Joseph"},{"full_name":"Jirovec, Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"last_name":"Ballabio","full_name":"Ballabio, Andrea","first_name":"Andrea"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"first_name":"Mark T.","full_name":"Mitchison, Mark T.","last_name":"Mitchison"},{"last_name":"Perarnau-Llobet","full_name":"Perarnau-Llobet, Martí","first_name":"Martí"},{"first_name":"Natalia","full_name":"Ares, Natalia","last_name":"Ares"}],"publisher":"American Physical Society","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.14516009"}]}},{"oa":1,"doi":"10.5281/ZENODO.17352653","date_updated":"2025-12-09T14:49:36Z","author":[{"last_name":"Van Straaten","full_name":"Van Straaten, Barnaby","first_name":"Barnaby"},{"first_name":"Federico","full_name":"Fedele, Federico","last_name":"Fedele"},{"first_name":"Florian","full_name":"Vigneau, Florian","last_name":"Vigneau"},{"first_name":"Joseph","last_name":"Hickie","full_name":"Hickie, Joseph"},{"full_name":"Jirovec, Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"first_name":"Natalia","full_name":"Ares, Natalia","last_name":"Ares"}],"month":"10","department":[{"_id":"GeKa"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"Zenodo","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20730"}]},"_id":"20750","type":"research_data_reference","has_accepted_license":"1","day":"14","citation":{"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. https://doi.org/10.5281/ZENODO.17352653.","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, 10.5281/ZENODO.17352653.","ama":"Van Straaten B, Fedele F, Vigneau F, et al. All rf-based tuning algorithm for quantum devices using machine learning. 2025. doi:10.5281/ZENODO.17352653","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. https://doi.org/10.5281/ZENODO.17352653","short":"B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, D. Chrastina, G. Isella, N. Ares, (2025).","ieee":"B. Van Straaten et al., “All rf-based tuning algorithm for quantum devices using machine learning.” Zenodo, 2025.","mla":"Van Straaten, Barnaby, et al. All Rf-Based Tuning Algorithm for Quantum Devices Using Machine Learning. Zenodo, 2025, doi:10.5281/ZENODO.17352653."},"year":"2025","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-10-14T00:00:00Z","date_created":"2025-12-09T13:36:29Z","title":"All rf-based tuning algorithm for quantum devices using machine learning","OA_place":"repository","oa_version":"Published Version","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.17352653"}]},{"type":"research_data","_id":"20780","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."}],"file":[{"checksum":"251e7aab01917c2ad2fbccf465492ea1","file_name":"Perl_scripts.zip","file_id":"20799","creator":"llayanaf","date_updated":"2025-12-11T10:47:15Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"file_size":4575,"date_created":"2025-12-11T10:47:15Z"},{"file_id":"20800","date_updated":"2025-12-11T10:52:17Z","relation":"main_file","creator":"llayanaf","file_name":"Supplementary_Datasets.zip","checksum":"daf1c03149dd170b14e5c8e109ee3c77","date_created":"2025-12-11T10:52:17Z","file_size":19052849,"success":1,"content_type":"application/zip","access_level":"open_access"},{"file_name":"Supplementary_Tables.zip","checksum":"658d6e95a361b0a3db058b7b4e1733d4","relation":"main_file","file_id":"20801","date_updated":"2025-12-11T10:52:11Z","creator":"llayanaf","access_level":"open_access","date_created":"2025-12-11T10:52:11Z","file_size":566476,"content_type":"application/zip","success":1},{"checksum":"2a2b92eb9fade0015719190596a8c5b7","file_name":"README.txt","file_id":"20802","creator":"llayanaf","date_updated":"2025-12-11T11:00:53Z","relation":"main_file","access_level":"open_access","success":1,"content_type":"text/plain","date_created":"2025-12-11T11:00:53Z","file_size":1204}],"citation":{"apa":"Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20780","mla":"Layana Franco, Lorena Alexandra, et al. Causes and Consequences of Sex-Chromosome Turnovers in Diptera. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20780.","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.","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. https://doi.org/10.15479/AT-ISTA-20780.","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:10.15479/AT-ISTA-20780","ista":"Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20780."},"has_accepted_license":"1","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","year":"2025","oa_version":"None","title":"Causes and consequences of sex-chromosome turnovers in Diptera","date_created":"2025-12-10T23:40:14Z","date_published":"2025-12-01T00:00:00Z","file_date_updated":"2025-12-11T11:00:53Z","oa":1,"doi":"10.15479/AT-ISTA-20780","department":[{"_id":"BeVi"}],"month":"12","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","full_name":"Toups, Melissa A"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-12-15T11:13:32Z","status":"public","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"publication_identifier":{"eissn":["2041-1723"]},"date_created":"2025-12-11T10:45:06Z","title":"BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity","OA_type":"gold","oa_version":"Published Version","publication_status":"published","file":[{"creator":"dernst","file_id":"20823","relation":"main_file","date_updated":"2025-12-15T09:25:51Z","checksum":"a952f7ea050242b79008540de49a0e61","file_name":"2025_NatureComm_Paouneskou.pdf","success":1,"content_type":"application/pdf","file_size":8096309,"date_created":"2025-12-15T09:25:51Z","access_level":"open_access"}],"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Springer Nature","pmid":1,"doi":"10.1038/s41467-025-65420-9","oa":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).","author":[{"last_name":"Paouneskou","full_name":"Paouneskou, Dimitra","first_name":"Dimitra"},{"first_name":"Antoine","full_name":"Baudrimont, Antoine","last_name":"Baudrimont"},{"orcid":"0000-0002-8489-9281","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","full_name":"Kelemen, Réka K"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"last_name":"Graf","full_name":"Graf, Angela","first_name":"Angela"},{"first_name":"Shehab","last_name":"Moukbel Ali Aldawla","full_name":"Moukbel Ali Aldawla, Shehab"},{"last_name":"Kölbl","full_name":"Kölbl, Claudia","first_name":"Claudia"},{"first_name":"Irene","full_name":"Tiemann-Boege, Irene","last_name":"Tiemann-Boege"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"last_name":"Jantsch","full_name":"Jantsch, Verena","first_name":"Verena"}],"volume":16,"department":[{"_id":"BeVi"}],"month":"11","article_type":"original","project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"intvolume":" 16","article_number":"10446","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"year":"2025","OA_place":"publisher","date_published":"2025-11-25T00:00:00Z","external_id":{"pmid":["41290579"]},"_id":"20796","language":[{"iso":"eng"}],"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"}],"quality_controlled":"1","type":"journal_article","day":"25","citation":{"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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65420-9","mla":"Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications, vol. 16, 10446, Springer Nature, 2025, doi:10.1038/s41467-025-65420-9.","ieee":"D. Paouneskou et al., “BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity,” Nature Communications, vol. 16. Springer Nature, 2025.","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).","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.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65420-9.","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. Nature Communications. 2025;16. doi:10.1038/s41467-025-65420-9","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."},"has_accepted_license":"1","PlanS_conform":"1","status":"public","DOAJ_listed":"1","scopus_import":"1","file_date_updated":"2025-12-15T09:25:51Z","date_updated":"2025-12-15T09:28:37Z","publication":"Nature Communications"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","title":"Structure of cytoplasmic RNA polymerase II","date_created":"2025-12-11T13:33:27Z","date_published":"2025-12-10T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.64898/2025.12.10.692585","open_access":"1"}],"oa_version":"None","_id":"20804","abstract":[{"lang":"eng","text":"RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contained Gdown1 and three biogenesis factors – RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex revealed how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis revealed how RPAP2 recruits GPN1–GPN3 to the complex, and how the assembly of the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a GTP-controlled switch during the final stages of Pol II biogenesis, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes."}],"language":[{"iso":"eng"}],"publication_status":"published","type":"preprint","day":"10","citation":{"apa":"Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., & Bernecky, C. (2025). Structure of cytoplasmic RNA polymerase II. bioRxiv. https://doi.org/10.64898/2025.12.10.692585","ieee":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C. Bernecky, “Structure of cytoplasmic RNA polymerase II.” bioRxiv, 2025.","short":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky, (2025).","mla":"Hlavata, Annamaria, et al. Structure of Cytoplasmic RNA Polymerase II. bioRxiv, 2025, doi:10.64898/2025.12.10.692585.","chicago":"Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka, Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.” bioRxiv, 2025. https://doi.org/10.64898/2025.12.10.692585.","ista":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. 2025. Structure of cytoplasmic RNA polymerase II. 10.64898/2025.12.10.692585.","ama":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. 2025. doi:10.64898/2025.12.10.692585"},"article_processing_charge":"No","corr_author":"1","status":"public","publisher":"bioRxiv","oa":1,"doi":"10.64898/2025.12.10.692585","acknowledgement":"We thank A. Salmazo for assistance with Pol II purification. We thank staff at the VBCF Proteomics facility for immunoprecipitation-mass spectrometry analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research was further supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","author":[{"last_name":"Hlavata","full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria"},{"first_name":"Benjamin","full_name":"Neuditschko, Benjamin","last_name":"Neuditschko"},{"full_name":"Schellhaas, Ulla","last_name":"Schellhaas","first_name":"Ulla"},{"first_name":"Clemens","last_name":"Plaschka","full_name":"Plaschka, Clemens"},{"last_name":"Herzog","full_name":"Herzog, Franz","first_name":"Franz"},{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky"}],"date_updated":"2025-12-15T09:48:22Z","month":"12","department":[{"_id":"CaBe"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}]},{"article_processing_charge":"No","publisher":"Wiley","pmid":1,"doi":"10.1111/pce.70295","acknowledgement":"The authors sincerely thank Dr. Shutang Tan for experimental support and Dr. Barbara Kloeckener Gruissem for critical reading and constructive advice on the manuscript. This study was supported by the European Research Council Advanced Grant (ETAP-742985 to H.T. and J.F.), by the Ministry of Science and Technology (grant 112-2636-B-005-001- to K.-J.L.), and by the Ministry of Education (grant MOE-109-YSFAG-0006-001-P1 to K.-J.L.).","author":[{"last_name":"Tang","full_name":"Tang, Han","orcid":"0000-0001-6152-6637","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","first_name":"Han"},{"first_name":"Adrijana","id":"cced8a85-223e-11ed-af04-b0596c55053b","full_name":"Smoljan, Adrijana","last_name":"Smoljan"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","last_name":"Zou","full_name":"Zou, Minxia"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","full_name":"Zhang, Yuzhou"},{"last_name":"Lu","full_name":"Lu, Kuan Ju","first_name":"Kuan Ju"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"}],"month":"12","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"article_type":"comment","publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"title":"The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha","date_created":"2025-12-14T23:02:05Z","OA_type":"closed access","oa_version":"None","publication_status":"epub_ahead","status":"public","ec_funded":1,"scopus_import":"1","publication":"Plant Cell and Environment","date_updated":"2025-12-15T13:56:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","date_published":"2025-12-03T00:00:00Z","external_id":{"pmid":["41340422"]},"_id":"20818","abstract":[{"text":"This study demonstrates that Marchantia non-canonical PINs are predominantly localized to the plasma membrane, with MpPINX and MpPINW exhibiting asymmetric distribution.\r\nA newly identified miniW domain within the MpPINW hydrophilic loop governs subcellular trafficking and asymmetric PM localization of non-canonical PINs in Marchantia.","lang":"eng"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"ista":"Tang H, Smoljan A, Zou M, Zhang Y, Lu KJ, Friml J. 2025. The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha. Plant Cell and Environment.","ama":"Tang H, Smoljan A, Zou M, Zhang Y, Lu KJ, Friml J. The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha. Plant Cell and Environment. 2025. doi:10.1111/pce.70295","chicago":"Tang, Han, Adrijana Smoljan, Minxia Zou, Yuzhou Zhang, Kuan Ju Lu, and Jiří Friml. “The MiniW Domain Directs Polarized Membrane Localization of Non-Canonical PINs in Marchantia Polymorpha.” Plant Cell and Environment. Wiley, 2025. https://doi.org/10.1111/pce.70295.","short":"H. Tang, A. Smoljan, M. Zou, Y. Zhang, K.J. Lu, J. Friml, Plant Cell and Environment (2025).","ieee":"H. Tang, A. Smoljan, M. Zou, Y. Zhang, K. J. Lu, and J. Friml, “The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha,” Plant Cell and Environment. Wiley, 2025.","mla":"Tang, Han, et al. “The MiniW Domain Directs Polarized Membrane Localization of Non-Canonical PINs in Marchantia Polymorpha.” Plant Cell and Environment, Wiley, 2025, doi:10.1111/pce.70295.","apa":"Tang, H., Smoljan, A., Zou, M., Zhang, Y., Lu, K. J., & Friml, J. (2025). The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.70295"},"day":"03"},{"publication_status":"published","place":"New York, NY","publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781071643099"],"eisbn":["9781071643105"]},"alternative_title":["Methods in Molecular Biology"],"date_created":"2025-01-07T08:36:47Z","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","oa_version":"None","OA_type":"closed access","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","doi":"10.1007/978-1-0716-4310-5_7","author":[{"last_name":"Cheung","full_name":"Cheung, Giselle T","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"volume":2886,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"department":[{"_id":"SiHi"}],"month":"01","corr_author":"1","article_processing_charge":"No","publisher":"Springer Nature","series_title":"MIMB","pmid":1,"abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution."}],"_id":"18765","language":[{"iso":"eng"}],"external_id":{"pmid":["39745639"]},"type":"book_chapter","quality_controlled":"1","day":"03","citation":{"chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. Lineage Tracing. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7","apa":"Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in Lineage Tracing, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7."},"intvolume":" 2886","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-01-03T00:00:00Z","publication":"Lineage Tracing","date_updated":"2025-04-14T07:43:46Z","acknowledged_ssus":[{"_id":"Bio"}],"status":"public","page":"139-151","ec_funded":1,"scopus_import":"1","editor":[{"last_name":"Garcia-Marques","full_name":"Garcia-Marques, Jorge","first_name":"Jorge"},{"first_name":"Tzumin","last_name":"Lee","full_name":"Lee, Tzumin"}]},{"acknowledgement":"We thank the members of the Bernecky laboratory for helpful discussions and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade (Max Perutz Laboratories and Medical University of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This research was further supported by the Scientific Service Units of ISTA through resources provided by the Laboratory Support Facility, Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.","oa":1,"doi":"10.1038/s41594-024-01448-7","article_type":"original","project":[{"grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","name":"Regulation of mammalian transcription by noncoding RNA"}],"month":"04","department":[{"_id":"CaBe"}],"volume":32,"author":[{"last_name":"Tluckova","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"full_name":"Bernecky, Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036"}],"publisher":"Springer Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","article_processing_charge":"Yes (in subscription journal)","pmid":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"14644"}]},"publication_status":"published","file":[{"access_level":"open_access","date_created":"2025-04-16T08:17:27Z","file_size":9306639,"success":1,"content_type":"application/pdf","file_name":"2025_NatureStrucMolBiol_Tluckova.pdf","checksum":"2919b30b271f395888e880076a680d73","date_updated":"2025-04-16T08:17:27Z","creator":"dernst","file_id":"19573","relation":"main_file"}],"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"oa_version":"Published Version","OA_type":"hybrid","date_created":"2025-01-08T11:20:20Z","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","file_date_updated":"2025-04-16T08:17:27Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"isi":1,"publication":"Nature Structural & Molecular Biology","date_updated":"2025-11-20T10:28:36Z","status":"public","page":"607-612","scopus_import":"1","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"18778","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.","lang":"eng"}],"external_id":{"pmid":["39762629"],"isi":["001390268000001"]},"has_accepted_license":"1","day":"01","citation":{"apa":"Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7","short":"K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural & Molecular Biology 32 (2025) 607–612.","ieee":"K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” Nature Structural & Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025.","mla":"Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32, Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7.","chicago":"Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7.","ista":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. 32, 607–612.","ama":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7"},"year":"2025","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","date_published":"2025-04-01T00:00:00Z","APC_amount":"12348 EUR","OA_place":"publisher"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","article_number":"013303","intvolume":" 111","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2408.10052","open_access":"1"}],"OA_place":"repository","date_published":"2025-01-03T00:00:00Z","quality_controlled":"1","type":"journal_article","external_id":{"isi":["001398791400004"],"arxiv":["2408.10052"]},"_id":"18821","language":[{"iso":"eng"}],"abstract":[{"text":"Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.","lang":"eng"}],"day":"03","citation":{"chicago":"Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” Physical Review A. American Physical Society, 2025. https://doi.org/10.1103/PhysRevA.111.013303.","ista":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 111(1), 013303.","ama":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 2025;111(1). doi:10.1103/PhysRevA.111.013303","apa":"Brauneis, F., Hammer, H. W., Reimann, S. M., & Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.111.013303","ieee":"F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of renormalized interactions using one-dimensional few-body systems as a testbed,” Physical Review A, vol. 111, no. 1. American Physical Society, 2025.","short":"F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025).","mla":"Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” Physical Review A, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:10.1103/PhysRevA.111.013303."},"status":"public","scopus_import":"1","issue":"1","isi":1,"publication":"Physical Review A","date_updated":"2025-02-27T12:41:58Z","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"arxiv":1,"OA_type":"green","oa_version":"Preprint","title":"Comparison of renormalized interactions using one-dimensional few-body systems as a testbed","date_created":"2025-01-12T23:04:00Z","publication_status":"published","publisher":"American Physical Society","article_processing_charge":"No","oa":1,"doi":"10.1103/PhysRevA.111.013303","acknowledgement":"We thank J. Cremon and J. Bjerlin for earlier contributions to the configuration-interaction calculations used in this work (see Refs. [49,50]). F.B. and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter, and Lila Chergui. We further want to thank Lila Chergui for helpful comments on the paper. This research was financially supported by the Knut and Alice Wallenberg Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No. 2022-03654 VR).","department":[{"_id":"MiLe"}],"month":"01","article_type":"original","volume":111,"author":[{"first_name":"Fabian","last_name":"Brauneis","full_name":"Brauneis, Fabian"},{"first_name":"Hans Werner","full_name":"Hammer, Hans Werner","last_name":"Hammer"},{"first_name":"Stephanie M.","last_name":"Reimann","full_name":"Reimann, Stephanie M."},{"last_name":"Volosniev","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}]},{"related_material":{"record":[{"relation":"used_in_publication","id":"19003","status":"public"}]},"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"corr_author":"1","status":"public","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"}],"date_updated":"2025-10-08T08:43:55Z","department":[{"_id":"JoDa"}],"month":"04","oa":1,"doi":"10.15479/AT:ISTA:18837","file_date_updated":"2025-03-07T11:09:13Z","date_created":"2025-01-13T09:51:29Z","title":"Research Data for the publication \"Super-resolution expansion microscopy in plant roots\"","date_published":"2025-04-01T00:00:00Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","citation":{"ista":"Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution expansion microscopy in plant roots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18837.","ama":"Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution expansion microscopy in plant roots.” 2025. doi:10.15479/AT:ISTA:18837","chicago":"Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication ‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18837.","short":"J.G. Danzl, C. Kreuzinger, (2025).","ieee":"J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution expansion microscopy in plant roots.’” Institute of Science and Technology Austria, 2025.","mla":"Danzl, Johann G., and Caroline Kreuzinger. Research Data for the Publication “Super-Resolution Expansion Microscopy in Plant Roots.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:18837.","apa":"Danzl, J. G., & Kreuzinger, C. (2025). 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Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens.","lang":"eng"}],"type":"research_data"},{"acknowledgement":"We thank Nicholas H. Barton for his comments on the manuscript, Benjamin Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many persistently inspiring conversations. This work was supported in part by the Human Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730, and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).","oa":1,"doi":"10.1073/pnas.2402925121","volume":122,"author":[{"full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"article_type":"original","project":[{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"month":"01","department":[{"_id":"GaTk"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"corr_author":"1","article_processing_charge":"Yes (in subscription journal)","publisher":"National Academy of Sciences","pmid":1,"publication_status":"published","file":[{"checksum":"8dbfc7d495413340225ebfae69b0cf9a","file_name":"2025_PNAS_Sokolowski.pdf","date_updated":"2025-01-20T10:10:04Z","creator":"dernst","relation":"main_file","file_id":"18862","access_level":"open_access","content_type":"application/pdf","success":1,"file_size":19073585,"date_created":"2025-01-20T10:10:04Z"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_created":"2025-01-19T23:01:50Z","title":"Deriving a genetic regulatory network from an optimization principle","oa_version":"Published Version","OA_type":"hybrid","file_date_updated":"2025-01-20T10:10:04Z","date_updated":"2026-02-16T12:26:51Z","publication":"Proceedings of the National Academy of Sciences","isi":1,"status":"public","issue":"1","scopus_import":"1","language":[{"iso":"eng"}],"_id":"18849","abstract":[{"text":"Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks.","lang":"eng"}],"external_id":{"isi":["001392772400001"],"pmid":["39752518"]},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","day":"07","citation":{"mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings of the National Academy of Sciences, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:10.1073/pnas.2402925121.","ieee":"T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” Proceedings of the National Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.","short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","apa":"Sokolowski, T. R., Gregor, T., Bialek, W., & Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2402925121","ama":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2402925121","ista":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 122(1), e2402925121.","chicago":"Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2402925121."},"intvolume":" 122","article_number":"e2402925121","year":"2025","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-01-07T00:00:00Z","OA_place":"publisher"}]