[{"status":"public","corr_author":"1","ec_funded":1,"arxiv":1,"citation":{"ista":"Henzinger M, Safavi Hemami R, Vadhan S. 2026. Concurrent composition for differentially private continual mechanisms. Proceedings of the ACM on Management of Data. 4(2), 1–26.","mla":"Henzinger, Monika, et al. “Concurrent Composition for Differentially Private Continual Mechanisms.” <i>Proceedings of the ACM on Management of Data</i>, vol. 4, no. 2, Association for Computing Machinery, 2026, pp. 1–26, doi:<a href=\"https://doi.org/10.1145/3801895\">10.1145/3801895</a>.","chicago":"Henzinger, Monika, Roodabeh Safavi Hemami, and Salil Vadhan. “Concurrent Composition for Differentially Private Continual Mechanisms.” <i>Proceedings of the ACM on Management of Data</i>. Association for Computing Machinery, 2026. <a href=\"https://doi.org/10.1145/3801895\">https://doi.org/10.1145/3801895</a>.","short":"M. Henzinger, R. Safavi Hemami, S. Vadhan, Proceedings of the ACM on Management of Data 4 (2026) 1–26.","ama":"Henzinger M, Safavi Hemami R, Vadhan S. Concurrent composition for differentially private continual mechanisms. <i>Proceedings of the ACM on Management of Data</i>. 2026;4(2):1-26. doi:<a href=\"https://doi.org/10.1145/3801895\">10.1145/3801895</a>","apa":"Henzinger, M., Safavi Hemami, R., &#38; Vadhan, S. (2026). Concurrent composition for differentially private continual mechanisms. <i>Proceedings of the ACM on Management of Data</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3801895\">https://doi.org/10.1145/3801895</a>","ieee":"M. Henzinger, R. Safavi Hemami, and S. Vadhan, “Concurrent composition for differentially private continual mechanisms,” <i>Proceedings of the ACM on Management of Data</i>, vol. 4, no. 2. Association for Computing Machinery, pp. 1–26, 2026."},"date_published":"2026-06-01T00:00:00Z","intvolume":"         4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","file_date_updated":"2026-07-16T09:09:53Z","department":[{"_id":"MoHe"}],"doi":"10.1145/3801895","month":"06","_id":"22318","oa_version":"Published Version","quality_controlled":"1","date_updated":"2026-07-16T09:14:49Z","date_created":"2026-07-13T14:59:14Z","volume":4,"scopus_import":"1","project":[{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms"}],"keyword":["differential privacy","concurrent composition","continual release","continual observation","data streaming","continual mechanisms","concurrent parallel composition","concurrent filter composition"],"supplementarymaterial":"no","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","type":"journal_article","year":"2026","article_type":"original","researchdata_availability":"no","external_id":{"arxiv":["2411.03299"]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2836-6573"]},"das_tickbox":"0","file":[{"content_type":"application/pdf","access_level":"open_access","date_created":"2026-07-16T09:09:53Z","date_updated":"2026-07-16T09:09:53Z","file_size":655405,"success":1,"creator":"dernst","checksum":"c6c5e256d02b90682c0690c3bee94040","file_id":"22345","relation":"main_file","file_name":"2026_ACMMgmtData_Henzinger.pdf"}],"publication":"Proceedings of the ACM on Management of Data","publication_status":"published","page":"1-26","acknowledgement":"1Salil Vadhan was supported by NSF grant BCS-2218803, a grant from the Sloan Foundation, and\r\na Simons Investigator Award. Work began while a Visiting Researcher at the Bocconi University\r\nDepartment of Computing Sciences, supported by Luca Trevisan’s ERC Project GA-834861.\r\n2Monika Henzinger and Roodabeh Safavi were supported by the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (Grant agreement\r\nNo. 101019564), and the Austrian Science Fund (FWF) under grants DOI 10.55776/Z422, DOI\r\n10.55776/I5982, and DOI 10.55776/P33775. For open access purposes, the author has applied a CC BY\r\npublic copyright license to any author-accepted manuscript version arising from this submission.\r\nViews and opinions expressed are however those of the author(s)\r\nonly and do not necessarily reflect those of the European Union\r\nor the European Research Council Executive Agency. Neither the\r\nEuropean Union nor the granting authority can be held responsible for them.","abstract":[{"lang":"eng","text":"Many intended uses of differential privacy involve a continual mechanism that is set up to run continuously\r\nover a long period of time, making more statistical releases as either queries come in or the dataset is updated.\r\nIn this paper, we give the first general treatment of privacy against adaptive adversaries for mechanisms that\r\nsupport dataset updates and a variety of queries, all arbitrarily interleaved. It also models a very general notion\r\nof neighboring, that includes both event-level and user-level privacy. We prove several concurrent composition\r\ntheorems for continual mechanisms, which ensure privacy even when an adversary can interleave its queries\r\nand dataset updates to the different composed mechanisms. Previous concurrent composition theorems for\r\ndifferential privacy were only for the case when the dataset is static, with no adaptive updates. We also give\r\nthe first interactive and continual generalizations of the “parallel composition theorem” for noninteractive\r\ndifferential privacy. Specifically, we show that the analogue of the noninteractive parallel composition theorem\r\nholds if either there are no adaptive dataset updates or each of the composed mechanisms satisfies pure\r\ndifferential privacy, but it fails to hold for composing approximately differentially private mechanisms with\r\ndataset updates. Thus, we prove a tight new composition theorem for this case. In addition, we prove concurrent\r\nfilter compositions theorems for the scenarios in which the privacy parameters are adaptively chosen. We\r\nextend these results to other measures of differential privacy, including Rényi DP and 𝑓 -DP.\r\nWe then formalize a set of general conditions on a continual mechanism M that runs multiple continual submechanisms such that the privacy guarantees of M follow directly using the above concurrent composition\r\ntheorems on the sub-mechanisms, without further privacy loss. This enables us to give a simpler and modular\r\nprivacy analysis of a recent continual histogram mechanism of Henzinger, Sricharan, and Steiner. In the\r\ncase of approximate DP, ours is the first proof that shows that its privacy holds against adaptive adversaries.\r\nWe also provide a framework that simplifies the analysis of local differential privacy when the protocol\r\nincludes multi-round server-user interactions. Using this result, we simplify the privacy analysis of the core\r\ndecomposition protocol of Dhulipala, Henzinger, Li, Liu, Sricharan, and Zhu [5]."}],"title":"Concurrent composition for differentially private continual mechanisms","issue":"2","author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Safavi Hemami","id":"72ed2640-8972-11ed-ae7b-f9c81ec75154","first_name":"Roodabeh","full_name":"Safavi Hemami, Roodabeh"},{"last_name":"Vadhan","full_name":"Vadhan, Salil","first_name":"Salil"}],"day":"01","ddc":["000"],"OA_place":"publisher","oa":1,"OA_type":"gold","article_processing_charge":"Yes"},{"publication":"Proceedings of the 18th International Conference on Agents and Artificial Intelligence","das_tickbox":"1","publication_identifier":{"eissn":["2184-433X"],"isbn":["9789897587962"]},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2410.22374"]},"year":"2026","oa":1,"OA_place":"repository","article_processing_charge":"No","OA_type":"green","day":"30","author":[{"full_name":"Hatua, Amartya","first_name":"Amartya","last_name":"Hatua"},{"first_name":"Trung","full_name":"Nguyen, Trung","last_name":"Nguyen"},{"first_name":"Filip","full_name":"Cano Cordoba, Filip","last_name":"Cano Cordoba","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","orcid":"0000-0002-0783-904X"},{"last_name":"Sung","first_name":"Andrew","full_name":"Sung, Andrew"}],"abstract":[{"text":"Modern computer systems store vast amounts of personal data, enabling advances in AI and ML but risking user privacy and trust. For privacy reasons, it is sometimes desired for an ML model to forget part of the data it was trained on. In this paper, we introduce a novel unlearning approach based on Forgetting Neural Networks (FNNs), a neuroscience-inspired architecture that explicitly encodes forgetting through multiplicative decay factors. While FNNs had previously been studied as a theoretical construct, we provide the first concrete implementation and demonstrate their effectiveness for targeted unlearning. We propose several variants with per-neuron forgetting factors, including rank-based assignments guided by activation levels, and evaluate them on MNIST and Fashion-MNIST benchmarks. Our method systematically removes information associated with forget sets while preserving performance on retained data. Membership inference attacks confirm the effectiveness of FNN-based unlearning in erasing information about the training data from the neural network. These results establish FNNs as a promising foundation for efficient and interpretable unlearning. ","lang":"eng"}],"title":"Machine unlearning using forgetting neural networks","page":"1536-1546","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"SciTePress","date_published":"2026-06-30T00:00:00Z","citation":{"ieee":"A. Hatua, T. Nguyen, F. Cano Cordoba, and A. Sung, “Machine unlearning using forgetting neural networks,” in <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, Marbella, Spain, 2026, vol. 2, pp. 1536–1546.","apa":"Hatua, A., Nguyen, T., Cano Cordoba, F., &#38; Sung, A. (2026). Machine unlearning using forgetting neural networks. In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i> (Vol. 2, pp. 1536–1546). Marbella, Spain: SciTePress. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>","ama":"Hatua A, Nguyen T, Cano Cordoba F, Sung A. Machine unlearning using forgetting neural networks. In: <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>. Vol 2. SciTePress; 2026:1536-1546. doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>","short":"A. Hatua, T. Nguyen, F. Cano Cordoba, A. Sung, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, SciTePress, 2026, pp. 1536–1546.","chicago":"Hatua, Amartya, Trung Nguyen, Filip Cano Cordoba, and Andrew Sung. “Machine Unlearning Using Forgetting Neural Networks.” In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, 2:1536–46. SciTePress, 2026. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>.","mla":"Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, vol. 2, SciTePress, 2026, pp. 1536–46, doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>.","ista":"Hatua A, Nguyen T, Cano Cordoba F, Sung A. 2026. Machine unlearning using forgetting neural networks. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 2, 1536–1546."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         2","status":"public","arxiv":1,"conference":{"name":"ICAART: International Conference on Agents and Artificial Intelligence","location":"Marbella, Spain","end_date":"2026-03-08","start_date":"2026-03-05"},"type":"conference","keyword":["Machine Unlearning","Neuroscience-Inspired Machine Learning","Membership Inference Attacks"],"volume":2,"quality_controlled":"1","date_created":"2026-07-13T09:46:46Z","date_updated":"2026-07-16T09:02:53Z","_id":"22294","oa_version":"Preprint","month":"06","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2410.22374"}],"doi":"10.5220/0014326500004052"},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["2512.15981"]},"researchdata_availability":"no","article_type":"original","year":"2026","publication":"Proceedings of the ACM on Management of Data","file":[{"checksum":"21a48a620e415a31a3874077c55bc6c3","relation":"main_file","file_id":"22349","file_name":"2026_ACMMgmtData_Aryanfard.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-07-16T09:29:08Z","date_created":"2026-07-16T09:29:08Z","file_size":934963,"success":1,"creator":"dernst"}],"das_tickbox":"0","publication_identifier":{"issn":["2836-6573"]},"title":"Improved lower bounds for privacy under continual release","abstract":[{"lang":"eng","text":"We study the problem of continually releasing statistics of an evolving dataset under differential privacy. In the event-level setting, we show the first polynomial lower bounds on the additive error for insertions-only graph problems such as maximum matching, degree histogram and k-core number computation. These results represent an exponential improvement on the polylogarithmic lower bounds of Fichtenberger, Henzinger and Ost [ESA 2021] for the former two problems, and are the first lower bounds in the continual release setting for the latter problem. Our results run counter to the intuition that the difference between insertions-only vs fully dynamic updates causes the gap between polylogarithmic and polynomial additive error. Indeed, we show that for estimating the size of the maximum matching or k-core number of a vertex, allowing small multiplicative approximations is what brings the additive error down to polylogarithmic. We complement these results with improved upper bounds on the additive error when no multiplicative approximation is allowed.\r\nBeyond graphs, our techniques also show that polynomial additive error is unavoidable for the Simultaneous Norm Estimation problem in the insertions-only setting. When multiplicative approximations are allowed, we circumvent this lower bound by giving the first continual mechanism with polylogarithmic additive error under (1 + ζ) multiplicative approximations, for any ζ > 0, for estimating all monotone symmetric norms simultaneously.\r\nIn the item-level setting, we show polynomial lower bounds on the product of the multiplicative and the additive error of continual mechanisms for a large range of graph problems. To the best of our knowledge, these are the first lower bounds shown for any differentially private mechanism under continual release with multiplicative error. To obtain these results, we prove a new lower bound on the product of multiplicative and additive error for the 1-Way-Marginals problem, and give reductions from 1-Way-Marginals to our desired graph problems. This generalizes the prior results of Hardt and Talwar [STOC 2010] and Bun, Ullman and Vadhan [STOC 2014, SIAM J. Comput. 2018], who gave lower bounds on the additive error for the special case of mechanisms with no multiplicative error."}],"acknowledgement":"Bardiya Aryanfard and Monika Henzinger were supported by the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (Grant agreement\r\nNo. 101019564). For open access purposes, the author has applied a CC BY public copyright\r\nlicense to any author-accepted manuscript version arising from this submission. Funded by the\r\nEuropean union. Views and opinions expressed are however those of the author(s) only and do\r\nnot necessarily reflect those of the European Union or the European Research Council Executive\r\nAgency. Neither the European Union nor the granting authority can be held responsible for them","page":"1-27","publication_status":"published","article_processing_charge":"Yes","OA_type":"gold","OA_place":"publisher","oa":1,"day":"01","ddc":["000"],"author":[{"last_name":"Aryanfard","id":"1e8f4084-31df-11ee-b195-f706b4b77091","full_name":"Aryanfard, Bardiya","first_name":"Bardiya"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","first_name":"David","full_name":"Saulpic, David"},{"last_name":"Sricharan","full_name":"Sricharan, A. R.","first_name":"A. R."}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         4","date_published":"2026-06-01T00:00:00Z","citation":{"ista":"Aryanfard B, Henzinger M, Saulpic D, Sricharan AR. 2026. Improved lower bounds for privacy under continual release. Proceedings of the ACM on Management of Data. 4(2), 1–27.","short":"B. Aryanfard, M. Henzinger, D. Saulpic, A.R. Sricharan, Proceedings of the ACM on Management of Data 4 (2026) 1–27.","chicago":"Aryanfard, Bardiya, Monika Henzinger, David Saulpic, and A. R. Sricharan. “Improved Lower Bounds for Privacy under Continual Release.” <i>Proceedings of the ACM on Management of Data</i>. Association for Computing Machinery, 2026. <a href=\"https://doi.org/10.1145/3801903\">https://doi.org/10.1145/3801903</a>.","mla":"Aryanfard, Bardiya, et al. “Improved Lower Bounds for Privacy under Continual Release.” <i>Proceedings of the ACM on Management of Data</i>, vol. 4, no. 2, Association for Computing Machinery, 2026, pp. 1–27, doi:<a href=\"https://doi.org/10.1145/3801903\">10.1145/3801903</a>.","ama":"Aryanfard B, Henzinger M, Saulpic D, Sricharan AR. Improved lower bounds for privacy under continual release. <i>Proceedings of the ACM on Management of Data</i>. 2026;4(2):1-27. doi:<a href=\"https://doi.org/10.1145/3801903\">10.1145/3801903</a>","ieee":"B. Aryanfard, M. Henzinger, D. Saulpic, and A. R. Sricharan, “Improved lower bounds for privacy under continual release,” <i>Proceedings of the ACM on Management of Data</i>, vol. 4, no. 2. Association for Computing Machinery, pp. 1–27, 2026.","apa":"Aryanfard, B., Henzinger, M., Saulpic, D., &#38; Sricharan, A. R. (2026). Improved lower bounds for privacy under continual release. <i>Proceedings of the ACM on Management of Data</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3801903\">https://doi.org/10.1145/3801903</a>"},"arxiv":1,"ec_funded":1,"corr_author":"1","status":"public","department":[{"_id":"MoHe"},{"_id":"GradSch"}],"file_date_updated":"2026-07-16T09:29:08Z","publisher":"Association for Computing Machinery","project":[{"call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures"}],"scopus_import":"1","quality_controlled":"1","date_updated":"2026-07-16T09:30:31Z","date_created":"2026-07-14T05:33:58Z","volume":4,"_id":"22322","oa_version":"Published Version","month":"06","doi":"10.1145/3801903","type":"journal_article","PlanS_conform":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","supplementarymaterial":"no"},{"ddc":["530"],"day":"15","author":[{"first_name":"Chen Y","full_name":"Zhang, Chen Y","id":"81b43fb8-c9d5-11ef-bf68-ade532a1f204","last_name":"Zhang"},{"full_name":"Mateu Hoyos, Pablo","first_name":"Pablo","last_name":"Mateu Hoyos","id":"50b236c7-50c1-11ef-bb9a-a2375694f8b5"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","oa":1,"OA_place":"publisher","acknowledgement":"This work was supported in part\r\nby European Research Council No. ERC-2023-SyG\r\n“DynaTrans” Grant No. 101118866 (G. T.). We thank\r\nPieter Rein ten Wolde and Vahe Galstyan for stimulating\r\ndiscussions.","publication_status":"published","title":"Nonlocal decoding of positional and correlational information during development","abstract":[{"text":"In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be improved by nonlocal information, e.g., via cell-cell communication? Using a Bayes-optimal framework, we show that positional inference depends crucially on morphogen spatial correlations and on the \"structural prior\" that encodes the geometry of the cellular lattice performing the readout, thereby determining what a cell can reliably assume about the position of its neighbors when interpreting nonlocal morphogen signals. We derive upper bounds on positional information gain due to nonlocal readout and identify signal processing algorithms that approximate optimal positional inference, as well as simple chemical reaction schemes which implement such algorithms. Our theory suggests that correlational information can be exploited to significantly enhance developmental precision.","lang":"eng"}],"file":[{"checksum":"28861d31d0f6cf541aaca04faaed1767","file_name":"2026_PhysicalReviewLetters_Zhang.pdf","relation":"main_file","file_id":"22352","access_level":"open_access","content_type":"application/pdf","success":1,"creator":"dernst","date_updated":"2026-07-16T09:54:55Z","date_created":"2026-07-16T09:54:55Z","file_size":2550345}],"das_tickbox":"1","publication_identifier":{"issn":["0031-9007"],"eissn":[" 1079-7114"]},"publication":"Physical Review Letters","article_type":"original","year":"2026","language":[{"iso":"eng"}],"dataavailabilitystatement":"Code to evaluate PI, to run algorithmic implementations of ALP and RLP decoding, and to\r\nperform simulations is publicly available at https://github.com/alex-chenyi-zhang/nonlocdec_pici.","researchdata_availability":"no","supplementarymaterial":"no","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","has_accepted_license":"1","doi":"10.1103/mbjk-v4ym","project":[{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"}],"scopus_import":"1","quality_controlled":"1","date_updated":"2026-07-16T09:58:04Z","date_created":"2026-07-14T05:38:28Z","volume":137,"_id":"22326","month":"07","oa_version":"Published Version","publisher":"American Physical Society","department":[{"_id":"GaTk"},{"_id":"EdHa"},{"_id":"GradSch"}],"file_date_updated":"2026-07-16T09:54:55Z","article_number":"038401","status":"public","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       137","date_published":"2026-07-15T00:00:00Z","citation":{"chicago":"Zhang, Chen Y, Pablo Mateu Hoyos, David Brückner, and Gašper Tkačik. “Nonlocal Decoding of Positional and Correlational Information during Development.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/mbjk-v4ym\">https://doi.org/10.1103/mbjk-v4ym</a>.","short":"C.Y. Zhang, P. Mateu Hoyos, D. Brückner, G. Tkačik, Physical Review Letters 137 (2026).","mla":"Zhang, Chen Y., et al. “Nonlocal Decoding of Positional and Correlational Information during Development.” <i>Physical Review Letters</i>, vol. 137, 038401, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/mbjk-v4ym\">10.1103/mbjk-v4ym</a>.","ista":"Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. 2026. Nonlocal decoding of positional and correlational information during development. Physical Review Letters. 137, 038401.","ieee":"C. Y. Zhang, P. Mateu Hoyos, D. Brückner, and G. Tkačik, “Nonlocal decoding of positional and correlational information during development,” <i>Physical Review Letters</i>, vol. 137. American Physical Society, 2026.","apa":"Zhang, C. Y., Mateu Hoyos, P., Brückner, D., &#38; Tkačik, G. (2026). Nonlocal decoding of positional and correlational information during development. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/mbjk-v4ym\">https://doi.org/10.1103/mbjk-v4ym</a>","ama":"Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. Nonlocal decoding of positional and correlational information during development. <i>Physical Review Letters</i>. 2026;137. doi:<a href=\"https://doi.org/10.1103/mbjk-v4ym\">10.1103/mbjk-v4ym</a>"}},{"doi":"10.1038/s41467-026-75416-8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-026-75416-8"}],"biorxivid":1,"scopus_import":"1","_id":"22333","oa_version":"Published Version","month":"07","date_created":"2026-07-14T07:27:59Z","date_updated":"2026-07-16T11:29:31Z","quality_controlled":"1","supplementarymaterial":"yes","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","has_accepted_license":"1","status":"public","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","date_published":"2026-07-13T00:00:00Z","citation":{"short":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky, Nature Communications (2026).","chicago":"Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka, Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-75416-8\">https://doi.org/10.1038/s41467-026-75416-8</a>.","mla":"Hlavata, Annamaria, et al. “Structure of Cytoplasmic RNA Polymerase II.” <i>Nature Communications</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-75416-8\">10.1038/s41467-026-75416-8</a>.","ista":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. 2026. Structure of cytoplasmic RNA polymerase II. Nature Communications.","ieee":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C. Bernecky, “Structure of cytoplasmic RNA polymerase II,” <i>Nature Communications</i>. Springer Nature, 2026.","apa":"Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &#38; Bernecky, C. (2026). Structure of cytoplasmic RNA polymerase II. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-75416-8\">https://doi.org/10.1038/s41467-026-75416-8</a>","ama":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. <i>Nature Communications</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41467-026-75416-8\">10.1038/s41467-026-75416-8</a>"},"publisher":"Springer Nature","department":[{"_id":"CaBe"}],"acknowledgement":"We thank A. Salmazo for assistance with Pol II purification. We thank staff at the Vienna BioCenter Core Facilities (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 ISTA through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF). F.H. was funded by the Endowed Professorship of the Lower Austria Research Funding Agency (GFF NÖ) and by the Austrian Research Promotion Agency (FFG) through the COIN Establishment Grant n.o. 45624401.","publication_status":"epub_ahead","title":"Structure of cytoplasmic RNA polymerase II","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 assembly 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 contains Gdown1 and three biogenesis factors – RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex reveals how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis reveals how RPAP2 tethers 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 molecular switch regulating biogenesis factor association, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes."}],"author":[{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Neuditschko","first_name":"Benjamin","full_name":"Neuditschko, Benjamin"},{"first_name":"Ulla","full_name":"Schellhaas, Ulla","last_name":"Schellhaas"},{"full_name":"Plaschka, Clemens","first_name":"Clemens","last_name":"Plaschka"},{"last_name":"Herzog","full_name":"Herzog, Franz","first_name":"Franz"},{"full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036"}],"day":"13","ddc":["570"],"OA_type":"gold","article_processing_charge":"Yes","OA_place":"publisher","oa":1,"year":"2026","article_type":"original","dataavailabilitystatement":"The\r\nc ryo EM maps generated in this study were deposited to the EM Data Bank under the\r\naccession codes: EMD 55583 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55583\r\n(Pol II Gdown1 RPAP2 composite map), EMD 55578\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55578 Pol II Gdown1 RPAP2 Pol II core\r\nmap EMD 55579 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55579 Pol II\r\nGdown1 RPAP2 Pol II stalk map EMD 55580\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55580 Pol II Gdown1 RPAP2 RPAP2\r\nmap EMD 55581 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55 581 Pol II\r\nGdown1 RPAP2 Gdown1 N terminus map EMD 55582\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD 55582 Pol II Gdown1 RPAP2 Gdown1\r\nC terminus map and EMD 55585 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD\r\n55585 RPAP2 GPN1 GPN3 map Model coordi nates were deposited to the PDBe under\r\nthe accession codes: 9T5H [http://doi.org/10.2210/pdb 9T5H / (Pol II Gdown1\r\nRPAP2 complex structure) and 9T5J [http://doi.org/10.2210/pdb 9T5H / (GPN1\r\nGPN3 RPAP2 structure). Immunoprecipitation mass spectrometry and crosslinking mass\r\nspectrometry proteomics data have been deposited to the ProteomeXchange Consortium\r\nvia the PRIDE partner repository with the dataset identifiers PXD071638\r\n[http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD 071638 and\r\nP XD070852\r\n[http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD 070852\r\nAlphaFold3 structure predictions have been deposited to the Zenodo repository\r\nhttps://doi.org/10.5281/zenodo.20687910 P reviously published model coordinates\r\nwere utilized and are available at the PDB under the accession codes 8QEP\r\n[http://doi.org/10.2210/pdb 8QEP / 9BZ 0 [http://doi.org/10.2210/pdb 9BZ 0 /\r\nand 7B7U [http://doi.org/10.2210/pdb 7B7U / Source Data are provided with this\r\npaper.","external_id":{"biorxivid":["10.64898/2025.12.10.692585"]},"language":[{"iso":"eng"}],"researchdata_availability":"yes","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"publication_identifier":{"eissn":["2041-1723"]},"das_tickbox":"1","publication":"Nature Communications"},{"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"date_updated":"2026-07-17T07:09:42Z","date_created":"2026-06-18T08:00:03Z","_id":"22017","month":"06","oa_version":"Published Version","doi":"10.15479/AT-ISTA-22017","type":"dissertation","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"15182"},{"relation":"part_of_dissertation","id":"20326","status":"public"},{"relation":"part_of_dissertation","id":"12237","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Kleinhanns T. Unraveling the origin and evolution of defects to enable advanced thermoelectric performance. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22017\">10.15479/AT-ISTA-22017</a>","apa":"Kleinhanns, T. (2026). <i>Unraveling the origin and evolution of defects to enable advanced thermoelectric performance</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22017\">https://doi.org/10.15479/AT-ISTA-22017</a>","ieee":"T. Kleinhanns, “Unraveling the origin and evolution of defects to enable advanced thermoelectric performance,” Institute of Science and Technology Austria, 2026.","ista":"Kleinhanns T. 2026. Unraveling the origin and evolution of defects to enable advanced thermoelectric performance. Institute of Science and Technology Austria.","mla":"Kleinhanns, Tobias. <i>Unraveling the Origin and Evolution of Defects to Enable Advanced Thermoelectric Performance</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22017\">10.15479/AT-ISTA-22017</a>.","chicago":"Kleinhanns, Tobias. “Unraveling the Origin and Evolution of Defects to Enable Advanced Thermoelectric Performance.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22017\">https://doi.org/10.15479/AT-ISTA-22017</a>.","short":"T. Kleinhanns, Unraveling the Origin and Evolution of Defects to Enable Advanced Thermoelectric Performance, Institute of Science and Technology Austria, 2026."},"doi_confirm":"1","date_published":"2026-06-18T00:00:00Z","alternative_title":["ISTA Thesis"],"status":"public","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"file_date_updated":"2026-07-01T07:35:17Z","publisher":"Institute of Science and Technology Austria","title":"Unraveling the origin and evolution of defects to enable advanced thermoelectric performance","page":"59","publication_status":"published","article_processing_charge":"No","OA_place":"publisher","degree_awarded":"PhD","ddc":["546","530"],"day":"18","author":[{"full_name":"Kleinhanns, Tobias","first_name":"Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","orcid":"0000-0003-1537-7436"}],"supervisor":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria"}],"language":[{"iso":"eng"}],"year":"2026","file":[{"file_name":"2026_Kleinhanns_Tobias_Thesis_Source_File.docx","relation":"source_file","file_id":"22226","checksum":"3df7e865a7d1da8972ccd8acb8b4c16c","creator":"tkleinha","date_created":"2026-06-30T09:17:15Z","file_size":15658266,"date_updated":"2026-06-30T09:17:15Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","file_id":"22232","file_name":"2026_Kleinhanns_Tobias_Thesis_Main_File_A4.pdf","embargo_to":"open_access","embargo":"2026-12-18","checksum":"40ec279272a963636ff29c964032dcba","date_created":"2026-07-01T07:35:17Z","file_size":9909375,"date_updated":"2026-07-01T07:35:17Z","creator":"tkleinha","access_level":"closed","content_type":"application/pdf"}],"das_tickbox":"1","publication_identifier":{"isbn":["978-3-99078-081-7"],"issn":["2663-337X"]}},{"abstract":[{"text":"Characterizing protein dynamics at the atomic level is essential for our understanding of biological mechanisms. Whether it is to facilitate metabolite transport, catalyze reactions, transmit signals, or regulate metabolism – proteins are constantly in motion and sample multiple conformational states to fulfill their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly well suited to elucidate the dynamics of biomolecules on their complex free-energy landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the study of large molecular assemblies, protein crystals, or insoluble proteins at atomic resolution without an inherent molecular size limitation. MAS NMR experiments to probe protein dynamics are extremely versatile and sensitive to motional timescales from picoseconds to seconds. Over the past decades, technological advances, developments in experimental design, and new isotope-labeling approaches have further expanded the possibilities of this technique and significantly improved the accuracy of the determined motional parameters.\r\nFunctionally important sites of proteins often contain aromatic residues. Their side-chain motions have therefore long served as valuable indicators of mechanistically relevant dynamics in NMR studies. In this thesis, site-specifically labeled aromatic residues act as sensitive reporters for MAS NMR studies of protein dynamics. The first part addresses how different environments impact side-chain motion by probing ring flips of phenylalanines and tyrosines in crystalline proteins and amyloid fibrils. It provides important insights for the analysis of dynamics obtained in non-native protein environments and emphasizes the complex factors that determine the timescale of internal dynamics. In the second part, the focus shifts towards methodological questions regarding the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits promising characteristics for NMR studies but also presents significant challenges, which is why the full methodological potential of 19F MAS NMR has not been fully realized yet. This work demonstrates that paramagnetic doping can considerably reduce the measurement time and improve the sensitivity of fluorinated samples. Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics on the example of tryptophans. The results illustrate the challenges in analyzing such experiments and lay the foundation for further development of 19F MAS NMR relaxation studies.\r\nTaken together, this thesis highlights the potential of combining specific isotope labeling, MAS NMR, and complementary methods such as crystallography and computational simulations to elucidate internal protein dynamics. The further development of such integrative approaches will be crucial to improving our understanding of complex mechanisms and protein function.\r\n","lang":"eng"}],"title":"Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR","publication_status":"published","page":"205","acknowledgement":"During the work on this thesis, I was the recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01).","degree_awarded":"PhD","oa":1,"OA_place":"publisher","article_processing_charge":"No","supervisor":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul"}],"author":[{"first_name":"Lea Marie","full_name":"Becker, Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"}],"day":"13","ddc":["572"],"language":[{"iso":"eng"}],"year":"2026","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-084-8"]},"das_tickbox":"1","file":[{"access_level":"closed","content_type":"application/zip","creator":"lbecker","file_size":99472908,"date_created":"2026-07-16T09:17:08Z","date_updated":"2026-07-16T09:17:08Z","checksum":"8b85114eff543916c0e1445cd2189555","file_name":"2026_Becker_Lea_source_files.zip","relation":"source_file","file_id":"22346"},{"date_created":"2026-07-16T09:17:05Z","file_size":74647289,"date_updated":"2026-07-16T09:17:05Z","success":1,"creator":"lbecker","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"22347","file_name":"2026_Becker_Lea_Thesis.pdf","checksum":"6c526862bc6dbd1e4c80ecb34580bc58"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"NMR"}],"month":"07","_id":"22334","oa_version":"Published Version","date_updated":"2026-07-20T09:49:13Z","date_created":"2026-07-14T08:08:51Z","project":[{"grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"doi":"10.15479/AT-ISTA-22334","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"22105"},{"status":"public","relation":"part_of_dissertation","id":"12675"},{"relation":"part_of_dissertation","id":"21777","status":"public"},{"id":"12114","relation":"part_of_dissertation","status":"public"}]},"date_published":"2026-07-13T00:00:00Z","doi_confirm":"1","citation":{"ieee":"L. M. Becker, “Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026.","apa":"Becker, L. M. (2026). <i>Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22334\">https://doi.org/10.15479/AT-ISTA-22334</a>","ama":"Becker LM. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22334\">10.15479/AT-ISTA-22334</a>","chicago":"Becker, Lea Marie. “Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22334\">https://doi.org/10.15479/AT-ISTA-22334</a>.","short":"L.M. Becker, Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR, Institute of Science and Technology Austria, 2026.","mla":"Becker, Lea Marie. <i>Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22334\">10.15479/AT-ISTA-22334</a>.","ista":"Becker LM. 2026. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","corr_author":"1","status":"public","alternative_title":["ISTA Thesis"],"file_date_updated":"2026-07-16T09:17:08Z","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"publisher":"Institute of Science and Technology Austria"},{"researchdata_availability":"yes","language":[{"iso":"eng"}],"pmid":1,"dataavailabilitystatement":"The cryo and room-temperature crystal structures of GB1QDD are deposited at the PDB under the access codes 9I2I and 9T8Z, respectively. The solid-state NMR backbone assignment of GB1QDD is deposited at the BMRB under the access code 53330. NMR spectra, analysis scripts and raw data are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-20641)120. Files to reproduce the enhanced-sampling MD simulations are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-21145)121.","external_id":{"pmid":["42271006"]},"article_type":"original","year":"2026","publication":"Nature Chemistry","publication_identifier":{"eissn":["17554349"],"issn":["17554330"]},"das_tickbox":"1","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"abstract":[{"text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein–protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labelling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a crystal structure of a GB1 variant reported in this work, reproduce these elevated barriers and reveal how the crystal restrains motions.","lang":"eng"}],"title":"Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes","publication_status":"epub_ahead","acknowledgement":"We thank N. R. Skrynnikov and O. O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to T. Schubeis (Lyon) for advice on GB1 crystallization and R. Schmid for initial crystallization trials. We thank C. Mueller-Dieckmann for assistance with room-temperature X-ray crystallography data collection on beamline ID30B at the ESRF, which is acknowledged for providing beamtime through its In-House Research programme. We thank S. Falkner for assistance with constructing the structural model of the IgG:GB1 complex. We thank J. Lewandowski for providing feedback on the paper and granting access to backbone relaxation data of IgG:GB1T2Q and GB1T2Q microcrystals. This research was supported by the Scientific Service Units (SSU) of the Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank P. Rovó and M. V. Falcón for excellent support of the NMR facility. L.M.B. is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant number PR10660EAW01). C.C. acknowledges the European Research Council (grant project 101097272 ‘MilliInMicro’) and the Métropole du Grand Nancy (grant project ‘ARC’). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.Open access funding provided by Institute of Science and Technology (IST Austria).","OA_place":"publisher","oa":1,"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","ddc":["540"],"day":"10","author":[{"full_name":"Becker, Lea Marie","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","orcid":"0000-0002-6401-5151"},{"full_name":"Fu, Haohao","first_name":"Haohao","last_name":"Fu"},{"id":"71cda2f3-e604-11ee-a1df-da10587eda3f","last_name":"Tatman","first_name":"Benjamin","full_name":"Tatman, Benjamin"},{"full_name":"Dreydoppel, Matthias","first_name":"Matthias","last_name":"Dreydoppel"},{"id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova","full_name":"Kapitonova, Anna","first_name":"Anna"},{"first_name":"Daniel","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Weininger","full_name":"Weininger, Ulrich","first_name":"Ulrich"},{"last_name":"Engilberge","full_name":"Engilberge, Sylvain","first_name":"Sylvain"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"citation":{"apa":"Becker, L. M., Fu, H., Tatman, B., Dreydoppel, M., Kapitonova, A., Balazs, D., … Schanda, P. (2026). Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-026-02155-0\">https://doi.org/10.1038/s41557-026-02155-0</a>","ieee":"L. M. Becker <i>et al.</i>, “Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes,” <i>Nature Chemistry</i>. Springer Nature, 2026.","ama":"Becker LM, Fu H, Tatman B, et al. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. <i>Nature Chemistry</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41557-026-02155-0\">10.1038/s41557-026-02155-0</a>","mla":"Becker, Lea Marie, et al. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” <i>Nature Chemistry</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41557-026-02155-0\">10.1038/s41557-026-02155-0</a>.","chicago":"Becker, Lea Marie, Haohao Fu, Benjamin Tatman, Matthias Dreydoppel, Anna Kapitonova, Daniel Balazs, Ulrich Weininger, Sylvain Engilberge, Christophe Chipot, and Paul Schanda. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” <i>Nature Chemistry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41557-026-02155-0\">https://doi.org/10.1038/s41557-026-02155-0</a>.","short":"L.M. Becker, H. Fu, B. Tatman, M. Dreydoppel, A. Kapitonova, D. Balazs, U. Weininger, S. Engilberge, C. Chipot, P. Schanda, Nature Chemistry (2026).","ista":"Becker LM, Fu H, Tatman B, Dreydoppel M, Kapitonova A, Balazs D, Weininger U, Engilberge S, Chipot C, Schanda P. 2026. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry."},"date_published":"2026-06-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","corr_author":"1","department":[{"_id":"PaSc"},{"_id":"LifeSc"}],"publisher":"Springer Nature","date_created":"2026-06-21T22:03:01Z","quality_controlled":"1","date_updated":"2026-07-20T09:49:12Z","oa_version":"Published Version","_id":"22105","month":"06","project":[{"grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41557-026-02155-0","open_access":"1"}],"doi":"10.1038/s41557-026-02155-0","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","PlanS_conform":"1","type":"journal_article","related_material":{"record":[{"status":"public","relation":"research_data","id":"20641"},{"status":"public","id":"21145","relation":"research_data"},{"relation":"dissertation_contains","id":"22334","status":"public"}]},"supplementarymaterial":"yes"},{"OA_place":"publisher","oa":1,"OA_type":"gold","article_processing_charge":"Yes","issue":"1","author":[{"full_name":"Becker, Lea Marie","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"last_name":"Toscano","id":"334a5e40-8747-11f0-b671-ba1f5154b4b4","first_name":"Giorgia","full_name":"Toscano, Giorgia"},{"first_name":"Anna","full_name":"Kapitonova, Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova"},{"first_name":"Rajkumar","full_name":"Singh, Rajkumar","last_name":"Singh","id":"a3089acd-6806-11ee-bacc-f0c7d500ad20"},{"full_name":"Guillerm, Undina","first_name":"Undina","last_name":"Guillerm","id":"bb74f472-ae54-11eb-9835-bc9c22fb1183"},{"last_name":"Lichtenecker","full_name":"Lichtenecker, Roman J.","first_name":"Roman J."},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul"}],"day":"16","ddc":["540"],"abstract":[{"text":"The advantageous characteristics attributed to the 19F nucleus have made it a popular target for nuclear magnetic resonance (NMR) once again in recent years. Aside from solution NMR, an increasing number of studies have been conducted applying solid-state magic-angle spinning (MAS) NMR to fluorine-labelled samples. Here, the high chemical shift anisotropy and strong dipolar couplings can be utilised to get structural insights into proteins and measure long distances. Despite increasing popularity and promising benefits, the sensitivity of biomolecular 19F MAS NMR often suffers from slow longitudinal T1 relaxation and therefore long recycle delays. In this work, we expand paramagnetic doping, an approach commonly used to reduce proton T1 relaxation times, to 19F-labelled biological samples. We study the effect of Gd(DTPA) and Gd(DTPA-BMA) on 19F T1 and T2, and 13C T1 and T2 relaxation in a [5-19F13C]-tryptophan-labelled protein via 19F-detected MAS NMR experiments. The observed paramagnetic relaxation enhancement substantially reduces measurement times of 19F MAS NMR experiments without compromising resolution. Additionally, we report the chemical shift assignments of all four fluorotryptophan signals in the 12×39 kDa-large protein TET2 using a mutagenesis approach.","lang":"eng"}],"title":"Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants","publication_status":"published","page":"29-37","acknowledgement":"We thank Ben P. Tatman for insightful discussions. This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility. We thank Prof. Tobias Madl (Medical University Graz) for a sample of Omniscan. Lea M. Becker is the recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01).","publication":"Magnetic Resonance","publication_identifier":{"eissn":["2699-0016"]},"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"external_id":{"pmid":["42057802"]},"pmid":1,"language":[{"iso":"eng"}],"year":"2026","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","PlanS_conform":"1","type":"journal_article","related_material":{"record":[{"id":"22334","relation":"dissertation_contains","status":"public"}]},"_id":"21777","month":"04","oa_version":"Published Version","date_created":"2026-05-03T22:01:36Z","quality_controlled":"1","volume":7,"date_updated":"2026-07-20T09:49:12Z","scopus_import":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/mr-7-29-2026"}],"doi":"10.5194/mr-7-29-2026","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"publisher":"Copernicus Publications","date_published":"2026-04-16T00:00:00Z","citation":{"ama":"Becker LM, Toscano G, Kapitonova A, et al. Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants. <i>Magnetic Resonance</i>. 2026;7(1):29-37. doi:<a href=\"https://doi.org/10.5194/mr-7-29-2026\">10.5194/mr-7-29-2026</a>","ieee":"L. M. Becker <i>et al.</i>, “Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants,” <i>Magnetic Resonance</i>, vol. 7, no. 1. Copernicus Publications, pp. 29–37, 2026.","apa":"Becker, L. M., Toscano, G., Kapitonova, A., Singh, R., Guillerm, U., Lichtenecker, R. J., &#38; Schanda, P. (2026). Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-7-29-2026\">https://doi.org/10.5194/mr-7-29-2026</a>","ista":"Becker LM, Toscano G, Kapitonova A, Singh R, Guillerm U, Lichtenecker RJ, Schanda P. 2026. Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants. Magnetic Resonance. 7(1), 29–37.","short":"L.M. Becker, G. Toscano, A. Kapitonova, R. Singh, U. Guillerm, R.J. Lichtenecker, P. Schanda, Magnetic Resonance 7 (2026) 29–37.","chicago":"Becker, Lea Marie, Giorgia Toscano, Anna Kapitonova, Rajkumar Singh, Undina Guillerm, Roman J. Lichtenecker, and Paul Schanda. “Accelerated 19F Biomolecular Magic-Angle Spinning NMR with Paramagnetic Dopants.” <i>Magnetic Resonance</i>. Copernicus Publications, 2026. <a href=\"https://doi.org/10.5194/mr-7-29-2026\">https://doi.org/10.5194/mr-7-29-2026</a>.","mla":"Becker, Lea Marie, et al. “Accelerated 19F Biomolecular Magic-Angle Spinning NMR with Paramagnetic Dopants.” <i>Magnetic Resonance</i>, vol. 7, no. 1, Copernicus Publications, 2026, pp. 29–37, doi:<a href=\"https://doi.org/10.5194/mr-7-29-2026\">10.5194/mr-7-29-2026</a>."},"intvolume":"         7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","corr_author":"1","status":"public"},{"department":[{"_id":"LaEr"}],"article_number":"2607.05848","arxiv":1,"corr_author":"1","status":"public","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-07-07T00:00:00Z","citation":{"ista":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. 2607.05848.","mla":"Lee, Jaehun, and László Erdös. <i>Mesoscopic Eigenvalue Statistics for Correlated Random Matrices</i>. 2607.05848, doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>.","chicago":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices,” n.d. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>.","short":"J. Lee, L. Erdös, (n.d.).","ama":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>","apa":"Lee, J., &#38; Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>","ieee":"J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices.” ."},"keyword":["Central limit theorem","universality","matrix Dyson equation","multi-resolvent local law"],"type":"preprint","doi":"10.48550/arXiv.2607.05848","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2607.05848","open_access":"1"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"_id":"22359","oa_version":"Preprint","month":"07","date_created":"2026-07-18T08:59:02Z","date_updated":"2026-07-20T10:55:10Z","das_tickbox":"1","year":"2026","external_id":{"arxiv":["2607.05848"]},"language":[{"iso":"eng"}],"author":[{"first_name":"Jaehun","full_name":"Lee, Jaehun","id":"96155047-f36a-11ef-b766-8b5ae7cecd49","last_name":"Lee"},{"full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603"}],"day":"07","OA_type":"green","article_processing_charge":"No","OA_place":"repository","oa":1,"acknowledgement":"Supported by ERC Advanced Grant “RMTBeyond” No. 101020331","publication_status":"submitted","title":"Mesoscopic eigenvalue statistics for correlated random matrices","abstract":[{"text":"We prove a mesoscopic central limit theorem for linear eigenvalue statistics of correlated Hermitian random matrices. The class considered here includes Wigner and Wigner-type matrices, as well as models whose entry correlations decay polynomially in the distance between index pairs. The proof combines a multivariate cumulant expansion with multi-resolvent local laws and a detailed analysis of the resulting variance kernel on the operator-level.","lang":"eng"}]},{"OA_place":"repository","oa":1,"article_processing_charge":"No","OA_type":"green","issue":"4","day":"15","author":[{"last_name":"Bao","first_name":"Zhigang","full_name":"Bao, Zhigang"},{"first_name":"Jaehun","full_name":"Lee, Jaehun","last_name":"Lee","id":"96155047-f36a-11ef-b766-8b5ae7cecd49"},{"full_name":"Xu, Xiaocong","first_name":"Xiaocong","last_name":"Xu"}],"abstract":[{"text":"In this paper, we consider the rectangular random matrix\r\nX =(xij ) ∈ RN×n whose entries are iid with tail P(|xij | >\r\nt) ∼ t−α for some α> 0. We consider the regime N(n)/n →\r\na > 1 as n tends to infinity. Our main interest lies in the right\r\nsingular vector corresponding to the smallest singular value,\r\nwhich we will refer to as the ``bottom singular vector'', denoted\r\nby 𝔲. In this paper, we prove the following phase transition\r\nregarding the localization length of 𝔲: when α< 2 the\r\nlocalization length is O(n/ log n); when α> 2 the localization\r\nlength is of order n. Similar results hold for all right singular\r\nvectors around the smallest singular value. The variational\r\ndefinition of the bottom singular vector suggests that the\r\nmechanism for this localization-delocalization transition when\r\nα goes across 2 is intrinsically different from the one for the\r\ntop singular vector when α goes across 4","lang":"eng"}],"title":"Phase transition for the bottom singular vector of rectangular random matrices","extern":"1","publication_status":"published","publication":"Journal of Functional Analysis","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2409.01819"]},"article_type":"original","year":"2026","type":"journal_article","date_created":"2026-07-18T10:32:41Z","volume":290,"quality_controlled":"1","date_updated":"2026-07-20T11:01:15Z","_id":"22360","month":"02","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2409.01819"}],"doi":"10.1016/j.jfa.2025.111266","publisher":"Elsevier","date_published":"2026-02-15T00:00:00Z","citation":{"ista":"Bao Z, Lee J, Xu X. 2026. Phase transition for the bottom singular vector of rectangular random matrices. Journal of Functional Analysis. 290(4), 111266.","mla":"Bao, Zhigang, et al. “Phase Transition for the Bottom Singular Vector of Rectangular Random Matrices.” <i>Journal of Functional Analysis</i>, vol. 290, no. 4, 111266, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.jfa.2025.111266\">10.1016/j.jfa.2025.111266</a>.","chicago":"Bao, Zhigang, Jaehun Lee, and Xiaocong Xu. “Phase Transition for the Bottom Singular Vector of Rectangular Random Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.jfa.2025.111266\">https://doi.org/10.1016/j.jfa.2025.111266</a>.","short":"Z. Bao, J. Lee, X. Xu, Journal of Functional Analysis 290 (2026).","ama":"Bao Z, Lee J, Xu X. Phase transition for the bottom singular vector of rectangular random matrices. <i>Journal of Functional Analysis</i>. 2026;290(4). doi:<a href=\"https://doi.org/10.1016/j.jfa.2025.111266\">10.1016/j.jfa.2025.111266</a>","apa":"Bao, Z., Lee, J., &#38; Xu, X. (2026). Phase transition for the bottom singular vector of rectangular random matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2025.111266\">https://doi.org/10.1016/j.jfa.2025.111266</a>","ieee":"Z. Bao, J. Lee, and X. Xu, “Phase transition for the bottom singular vector of rectangular random matrices,” <i>Journal of Functional Analysis</i>, vol. 290, no. 4. Elsevier, 2026."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       290","status":"public","article_number":"111266","arxiv":1},{"scopus_import":"1","date_created":"2026-07-19T22:01:46Z","quality_controlled":"1","volume":1006,"date_updated":"2026-07-20T13:31:18Z","_id":"22362","oa_version":"Published Version","month":"07","doi":"10.3847/1538-4357/ae7bfa","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","has_accepted_license":"1","supplementarymaterial":"no","DOAJ_listed":"1","intvolume":"      1006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wang F, Champagne JB, Huang J, Yang J, Hennawi JF, Fan X, Zhang H, Costa T, Decarli R, Habouzit M, Sun F, Bañados E, Jin X, Kakiichi K, Meyer RA, Wu Y, Belladitta S, Blecha L, Bosman SEI, Cai Z, Connor T, Davies FB, Eilers AC, Haiman Z, Jun HD, Li M, Li Z, Liu W, Lupi A, Lyu J, Mazzucchelli C, Onoue M, Pizzati E, Pudoka M, Rojas-Ruiz S, Schindler JT, Shen Y, Tee WL, Trakhtenbrot B, Trebitsch M, Vestergaard M, Volonteri M, Walter F, Zhang H, Zou S. 2026. ASPIRE: The environments and dark matter halos of luminous quasars in the epoch of reionization. Astrophysical Journal. 1006(1), 39.","short":"F. Wang, J.B. Champagne, J. Huang, J. Yang, J.F. Hennawi, X. Fan, H. Zhang, T. Costa, R. Decarli, M. Habouzit, F. Sun, E. Bañados, X. Jin, K. Kakiichi, R.A. Meyer, Y. Wu, S. Belladitta, L. Blecha, S.E.I. Bosman, Z. Cai, T. Connor, F.B. Davies, A.C. Eilers, Z. Haiman, H.D. Jun, M. Li, Z. Li, W. Liu, A. Lupi, J. Lyu, C. Mazzucchelli, M. Onoue, E. Pizzati, M. Pudoka, S. Rojas-Ruiz, J.T. Schindler, Y. Shen, W.L. Tee, B. Trakhtenbrot, M. Trebitsch, M. Vestergaard, M. Volonteri, F. Walter, H. Zhang, S. Zou, Astrophysical Journal 1006 (2026).","chicago":"Wang, Feige, Jaclyn B. Champagne, Jiamu Huang, Jinyi Yang, Joseph F. Hennawi, Xiaohui Fan, Haowen Zhang, et al. “ASPIRE: The Environments and Dark Matter Halos of Luminous Quasars in the Epoch of Reionization.” <i>Astrophysical Journal</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/1538-4357/ae7bfa\">https://doi.org/10.3847/1538-4357/ae7bfa</a>.","mla":"Wang, Feige, et al. “ASPIRE: The Environments and Dark Matter Halos of Luminous Quasars in the Epoch of Reionization.” <i>Astrophysical Journal</i>, vol. 1006, no. 1, 39, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae7bfa\">10.3847/1538-4357/ae7bfa</a>.","ama":"Wang F, Champagne JB, Huang J, et al. ASPIRE: The environments and dark matter halos of luminous quasars in the epoch of reionization. <i>Astrophysical Journal</i>. 2026;1006(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae7bfa\">10.3847/1538-4357/ae7bfa</a>","ieee":"F. Wang <i>et al.</i>, “ASPIRE: The environments and dark matter halos of luminous quasars in the epoch of reionization,” <i>Astrophysical Journal</i>, vol. 1006, no. 1. IOP Publishing, 2026.","apa":"Wang, F., Champagne, J. B., Huang, J., Yang, J., Hennawi, J. F., Fan, X., … Zou, S. (2026). ASPIRE: The environments and dark matter halos of luminous quasars in the epoch of reionization. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae7bfa\">https://doi.org/10.3847/1538-4357/ae7bfa</a>"},"date_published":"2026-07-20T00:00:00Z","article_number":"39","arxiv":1,"status":"public","department":[{"_id":"ZoHa"}],"file_date_updated":"2026-07-20T13:19:42Z","publisher":"IOP Publishing","title":"ASPIRE: The environments and dark matter halos of luminous quasars in the epoch of reionization","abstract":[{"lang":"eng","text":"We present a systematic study of the environments of 25 luminous quasars at z > 6.5 from the ASPIRE program.\r\nUsing JWST/NIRCam wide-field slitless spectroscopy data, we identified 487 galaxies at 5.3 ≲ z ≲ 7.0 exhibiting\r\n[O III] emission. Among these, 122 [O III] emitters lie within |Δvlos| < 1000 km s\r\n−1 of the quasars, corresponding\r\nto a ∼9.4-fold enhancement relative to the average galaxy density at other redshifts. Furthermore, we identified 16\r\n[C II]-emitting galaxies at the quasar redshifts from Atacama Large Millimeter/submillimeter Array (ALMA) mosaic observations. A cross-correlation function analysis between quasars and [O III]+[C II] emitters yields a\r\ncross-correlation length of r 8.68 h cMpc 0\r\nQG\r\n0.55 = +0.51 1\r\nand an autocorrelation of r 15.76 h cMpc 0\r\nQQ\r\n2.70 = +2.48 1 ,\r\nindicating that z ∼ 7 quasars reside in dark matter halos with\r\nMhalo 1012.27 0.26 M 0.21\r\n= +\r\nand have a quasar lifetime of\r\ntQ 10 yr 7.05 1.01\r\n0.95\r\n= +\r\n. Notably, the number of [O III]-emitting galaxies at quasar redshifts varies significantly from\r\nfield to field, ranging from 0 to 20, highlighting a diverse quasar environment. Remarkably, seven quasars trace\r\nsignificant galaxy overdensities (i.e., protoclusters), with δgal > 5 within a volume of V ∼ 500 cMpc3\r\n. We also\r\nfind that |Δvlos| increases rapidly toward smaller galaxy–quasar separations in protocluster fields, consistent with\r\ngalaxy kinematics around extremely massive halos in cosmological simulations. By combining JWST and ALMA\r\ndata, we reveal the complex and diverse environments of these early quasars, providing robust evidence that the\r\nearliest luminous quasars are effective tracers of galaxy overdensities, albeit with substantial field-to-field\r\nvariation."}],"acknowledgement":"F.W. acknowledges support from NSF award AST-2513040. J.B.C. acknowledges funding from the JWST Arizona/Steward Postdoc in Early galaxies and Reionization (JASPER) Scholar contract at the University of Arizona. M.H. acknowledges support from the Swiss SNSF Starting Grant (grant no. 218032). S.E.I.B. is supported by the Deutsche Forschungsgemeinschaft (DFG) under Emmy Noether grant No. BO 5771/1-1. J.-T.S. is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—project No. 518006966. A.L. acknowledges support from PRIN MUR 2022935STW. C.M. acknowledges support from Fondecyt Iniciacion grant 11240336 and the ANID BASAL project FB210003. R.A.M. acknowledges support from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. B.T. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 950533) and from the Excellence Cluster ORIGINS, which is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2094—390783311. M.V. gratefully acknowledges financial support from the Independent Research Fund Denmark via grant Nos. DFF 8021-00130 and 3103-00146 and from the Carlsberg Foundation (grant CF23-0417).\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program #2078 and can be accessed via doi:10.17909/vt74-kd84. Support for program #2078 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. We acknowledge the strong support provided by the program coordinator Weston Eck and instrument reviewers Norbert Pirzkal and Stephanie La Massa.","publication_status":"published","article_processing_charge":"Yes","OA_type":"gold","OA_place":"publisher","oa":1,"ddc":["520"],"day":"20","author":[{"last_name":"Wang","full_name":"Wang, Feige","first_name":"Feige"},{"last_name":"Champagne","first_name":"Jaclyn B.","full_name":"Champagne, Jaclyn B."},{"first_name":"Jiamu","full_name":"Huang, Jiamu","last_name":"Huang"},{"last_name":"Yang","first_name":"Jinyi","full_name":"Yang, Jinyi"},{"last_name":"Hennawi","first_name":"Joseph F.","full_name":"Hennawi, Joseph F."},{"full_name":"Fan, Xiaohui","first_name":"Xiaohui","last_name":"Fan"},{"first_name":"Haowen","full_name":"Zhang, Haowen","last_name":"Zhang"},{"full_name":"Costa, Tiago","first_name":"Tiago","last_name":"Costa"},{"first_name":"Roberto","full_name":"Decarli, Roberto","last_name":"Decarli"},{"full_name":"Habouzit, Melanie","first_name":"Melanie","last_name":"Habouzit"},{"full_name":"Sun, Fengwu","first_name":"Fengwu","last_name":"Sun"},{"full_name":"Bañados, Eduardo","first_name":"Eduardo","last_name":"Bañados"},{"last_name":"Jin","first_name":"Xiangyu","full_name":"Jin, Xiangyu"},{"last_name":"Kakiichi","first_name":"Koki","full_name":"Kakiichi, Koki"},{"full_name":"Meyer, Romain A.","first_name":"Romain A.","last_name":"Meyer"},{"last_name":"Wu","full_name":"Wu, Yunjing","first_name":"Yunjing"},{"first_name":"Silvia","full_name":"Belladitta, Silvia","last_name":"Belladitta"},{"last_name":"Blecha","full_name":"Blecha, Laura","first_name":"Laura"},{"last_name":"Bosman","full_name":"Bosman, Sarah E.I.","first_name":"Sarah E.I."},{"full_name":"Cai, Zheng","first_name":"Zheng","last_name":"Cai"},{"last_name":"Connor","full_name":"Connor, Thomas","first_name":"Thomas"},{"last_name":"Davies","full_name":"Davies, Frederick B.","first_name":"Frederick B."},{"first_name":"Anna Christina","full_name":"Eilers, Anna Christina","last_name":"Eilers"},{"orcid":"0000-0003-3633-5403","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman","first_name":"Zoltán","full_name":"Haiman, Zoltán"},{"first_name":"Hyunsung D.","full_name":"Jun, Hyunsung D.","last_name":"Jun"},{"first_name":"Mingyu","full_name":"Li, Mingyu","last_name":"Li"},{"first_name":"Zihao","full_name":"Li, Zihao","last_name":"Li"},{"first_name":"Weizhe","full_name":"Liu, Weizhe","last_name":"Liu"},{"last_name":"Lupi","first_name":"Alessandro","full_name":"Lupi, Alessandro"},{"last_name":"Lyu","first_name":"Jianwei","full_name":"Lyu, Jianwei"},{"first_name":"Chiara","full_name":"Mazzucchelli, Chiara","last_name":"Mazzucchelli"},{"last_name":"Onoue","first_name":"Masafusa","full_name":"Onoue, Masafusa"},{"full_name":"Pizzati, Elia","first_name":"Elia","last_name":"Pizzati"},{"last_name":"Pudoka","first_name":"Maria","full_name":"Pudoka, Maria"},{"last_name":"Rojas-Ruiz","full_name":"Rojas-Ruiz, Sofía","first_name":"Sofía"},{"full_name":"Schindler, Jan Torge","first_name":"Jan Torge","last_name":"Schindler"},{"last_name":"Shen","full_name":"Shen, Yue","first_name":"Yue"},{"full_name":"Tee, Wei Leong","first_name":"Wei Leong","last_name":"Tee"},{"full_name":"Trakhtenbrot, Benny","first_name":"Benny","last_name":"Trakhtenbrot"},{"full_name":"Trebitsch, Maxime","first_name":"Maxime","last_name":"Trebitsch"},{"last_name":"Vestergaard","first_name":"Marianne","full_name":"Vestergaard, Marianne"},{"last_name":"Volonteri","full_name":"Volonteri, Marta","first_name":"Marta"},{"full_name":"Walter, Fabian","first_name":"Fabian","last_name":"Walter"},{"first_name":"Huanian","full_name":"Zhang, Huanian","last_name":"Zhang"},{"first_name":"Siwei","full_name":"Zou, Siwei","last_name":"Zou"}],"issue":"1","language":[{"iso":"eng"}],"dataavailabilitystatement":"This paper makes use of the following ALMA data: ADS/JAO.ALMA#2022.1.01077.L. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.\r\n\r\nFacility: JWST - James Webb Space Telescope (NIRCam).\r\n\r\nSoftware: astropy (Astropy Collaboration et al. 2018), Matplotlib (J. D. Hunter 2007), Numpy (C. R. Harris et al. 2020), Photutils (L. Bradley et al. 2022), Scipy (P. Virtanen et al. 2020), Source Extractor (E. Bertin & S. Arnouts 1996).","external_id":{"arxiv":["2602.04979"]},"researchdata_availability":"no","article_type":"original","year":"2026","publication":"Astrophysical Journal","file":[{"file_size":6884305,"date_updated":"2026-07-20T13:19:42Z","date_created":"2026-07-20T13:19:42Z","creator":"dernst","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"22377","relation":"main_file","file_name":"2026_AstrophysicalJour_Wang.pdf","checksum":"dd561fc00841217c227687e42d499ff0"}],"das_tickbox":"1","publication_identifier":{"eissn":["15384357"],"issn":["0004637X"]}},{"status":"public","article_number":"226","arxiv":1,"citation":{"ama":"Venditti A, Graziani L, Schneider R, et al. Catching the nebular needle in a polluted haystack: Line-emission signatures from population III-forming pockets around massive galaxies at the end of reionization. <i>The Astrophysical Journal</i>. 2026;1005(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae7b2c\">10.3847/1538-4357/ae7b2c</a>","apa":"Venditti, A., Graziani, L., Schneider, R., Bromm, V., Muñoz, J. B., Di Cesare, C., … Chisholm, J. (2026). Catching the nebular needle in a polluted haystack: Line-emission signatures from population III-forming pockets around massive galaxies at the end of reionization. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae7b2c\">https://doi.org/10.3847/1538-4357/ae7b2c</a>","ieee":"A. Venditti <i>et al.</i>, “Catching the nebular needle in a polluted haystack: Line-emission signatures from population III-forming pockets around massive galaxies at the end of reionization,” <i>The Astrophysical Journal</i>, vol. 1005, no. 2. IOP Publishing, 2026.","ista":"Venditti A, Graziani L, Schneider R, Bromm V, Muñoz JB, Di Cesare C, Valiante R, Calabrò A, Maiolino R, Finkelstein SL, Parente M, Saggini M, Chisholm J. 2026. Catching the nebular needle in a polluted haystack: Line-emission signatures from population III-forming pockets around massive galaxies at the end of reionization. The Astrophysical Journal. 1005(2), 226.","mla":"Venditti, Alessandra, et al. “Catching the Nebular Needle in a Polluted Haystack: Line-Emission Signatures from Population III-Forming Pockets around Massive Galaxies at the End of Reionization.” <i>The Astrophysical Journal</i>, vol. 1005, no. 2, 226, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae7b2c\">10.3847/1538-4357/ae7b2c</a>.","chicago":"Venditti, Alessandra, Luca Graziani, Raffaella Schneider, Volker Bromm, Julian B. Muñoz, Claudia Di Cesare, Rosa Valiante, et al. “Catching the Nebular Needle in a Polluted Haystack: Line-Emission Signatures from Population III-Forming Pockets around Massive Galaxies at the End of Reionization.” <i>The Astrophysical Journal</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/1538-4357/ae7b2c\">https://doi.org/10.3847/1538-4357/ae7b2c</a>.","short":"A. Venditti, L. Graziani, R. Schneider, V. Bromm, J.B. Muñoz, C. Di Cesare, R. Valiante, A. Calabrò, R. Maiolino, S.L. Finkelstein, M. Parente, M. Saggini, J. Chisholm, The Astrophysical Journal 1005 (2026)."},"date_published":"2026-07-10T00:00:00Z","DOAJ_listed":"1","intvolume":"      1005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing","department":[{"_id":"JoMa"}],"file_date_updated":"2026-07-20T13:05:27Z","doi":"10.3847/1538-4357/ae7b2c","quality_controlled":"1","date_updated":"2026-07-20T13:07:08Z","date_created":"2026-07-19T22:01:46Z","volume":1005,"oa_version":"Published Version","_id":"22364","month":"07","project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224"}],"scopus_import":"1","supplementarymaterial":"yes","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","has_accepted_license":"1","type":"journal_article","article_type":"original","year":"2026","researchdata_availability":"no","language":[{"iso":"eng"}],"dataavailabilitystatement":"Software: dustyGadget (L. Graziani et al. 2020), BPASSv2.2.134 (J. J. Eldridge et al. 2017; E. R. Stanway & J. J. Eldridge 2018), Yggdrasil35 (E. Zackrisson et al. 2011), Cloudy22.0136 (G. J. Ferland et al. 2017), NumPy37 (S. van der Walt et al. 2011; C. R. Harris et al. 2020), matplotlib38 (J. D. Hunter 2007), SciPy39 (Jones et al. 2001; P. Virtanen et al. 2020).","external_id":{"arxiv":["2603.27582"]},"das_tickbox":"1","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"file":[{"access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"date_created":"2026-07-20T13:05:27Z","date_updated":"2026-07-20T13:05:27Z","file_size":2267572,"checksum":"e783c9c10cf773482ac2f3b340ad130b","file_name":"2026_AstrophysicalJour_Venditti.pdf","relation":"main_file","file_id":"22375"}],"publication":"The Astrophysical Journal","publication_status":"published","acknowledgement":"We thank Elka Rusta and Stefania Salvadori for providing predictions of the He II line luminosities from the NEFERTITI model. A.V. acknowledges funding from the Cosmic Frontier Center and the University of Texas at Austin’s College of Natural Sciences. A.V., L.G., and R.S. acknowledge support from the PRIN 2022 MUR project 2022CB3PJ3—First Light And Galaxy aSsembly (FLAGS) funded by the European Union—Next Generation EU. J.B.M. was supported by NSF Grants AST-2307354 and AST-2408637, and by the NSF-Simons AI Institute for Cosmic Origins. This research was also supported in part by grant NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP). R.V. acknowledges support from PRIN MUR “2022935STW” funded by European Union-Next Generation EU, Missione 4 Componente 2 CUP C53D23000950006 and from Bando Ricerca Fondamentale INAF 2023, Theory Grant “Theoretical models for Black Holes Archaeology.\" C.D.C. acknowledges support from the European Union (ERC, AGENTS, 101076224).","abstract":[{"text":"Finding the first generation of (Population III or Pop III) stars is one of the most ambitious and exciting challenges of astrophysics. JWST opened concrete prospects for their detection during the Epoch of Reionization, where increasing evidence suggests that residual Pop III formation may persist, even within pristine pockets of high-mass halos, due to inhomogeneous enrichment. However, the identification of Pop III stars within globally enriched environments will be challenging. We investigate the detectability of a subdominant Pop III component in/around massive (M⋆ ≳ 10^9 M⊙) galaxies at z ≈ 6.5–9 from the dustyGadget cosmological simulation suite, and the confusion arising from second-generation (Pop II) stars in their surroundings. We find that young (≲1 Myr), massive (MIII ∼ 6 × 10^5 M⊙) Pop III clusters forming within these galaxy environments are responsible for strong HeII1640 line emission (LHeII1640 ≳ 10^41 erg ^s−1), which would be detectable with ≈10(50) hr of medium-resolution observations with NIRSpec/IFU at z ≈ 6(10). These bright luminosities cannot be produced by standard Pop II populations alone. On the other hand, the dominant Pop II component within massive “hybrid” Pop III hosts powers strong metal line emission (L[OIII]5007 ≳ 10^42 erg s^−1), indicating that the detection of metal lines alone cannot exclude the presence of Pop IIIs in high-z galaxy environments. We further discuss candidate selection strategies based on Lyα, Hα, and Hβ emission, and how spatially resolved observations may enable the detection of isolated, pristine pockets in the outskirts of massive halos.","lang":"eng"}],"title":"Catching the nebular needle in a polluted haystack: Line-emission signatures from population III-forming pockets around massive galaxies at the end of reionization","issue":"2","ddc":["520"],"day":"10","author":[{"first_name":"Alessandra","full_name":"Venditti, Alessandra","last_name":"Venditti"},{"last_name":"Graziani","first_name":"Luca","full_name":"Graziani, Luca"},{"last_name":"Schneider","full_name":"Schneider, Raffaella","first_name":"Raffaella"},{"full_name":"Bromm, Volker","first_name":"Volker","last_name":"Bromm"},{"full_name":"Muñoz, Julian B.","first_name":"Julian B.","last_name":"Muñoz"},{"id":"2d002343-372f-11ef-98ec-a164d20427cb","last_name":"Di Cesare","full_name":"Di Cesare, Claudia","first_name":"Claudia"},{"full_name":"Valiante, Rosa","first_name":"Rosa","last_name":"Valiante"},{"full_name":"Calabrò, Antonello","first_name":"Antonello","last_name":"Calabrò"},{"full_name":"Maiolino, Roberto","first_name":"Roberto","last_name":"Maiolino"},{"full_name":"Finkelstein, Steven L.","first_name":"Steven L.","last_name":"Finkelstein"},{"first_name":"Massimiliano","full_name":"Parente, Massimiliano","last_name":"Parente"},{"first_name":"Matteo","full_name":"Saggini, Matteo","last_name":"Saggini"},{"full_name":"Chisholm, John","first_name":"John","last_name":"Chisholm"}],"oa":1,"OA_place":"publisher","article_processing_charge":"Yes","OA_type":"gold"},{"title":"All the massive galaxy overdensities during reionisation: JWST rest-frame optical selection reveals young, chemically evolved galaxies embedded in dense, neutral gas at z > 5","abstract":[{"lang":"eng","text":"The high-redshift progenitors of present-day galaxy clusters are believed to substantially contribute to the global star formation rate density and drive the large-scale reionisation of the Universe. Here we present a blind and unbiased search for and characterisation of galaxy overdensities during the reionisation epoch at redshifts z ∼ 5.5 − 7 based on rest-frame optical JWST/NIRCam grism spectroscopy of the Abell 2744 lensing field as part of the JWST All the Little Things (ALT) survey. Using a physically motivated, cosmological inference friends-of-friends (FoF) algorithm, we identified six galaxy overdensities, including five robust systems at z = 5.66–6.77. They are all characterised by total halo masses of Mhalo ≳ 1011 M⊙, inferred from a range of proxies. We find that the galaxy members in these overdense environments are on average less massive though equally metal-rich, and generally comprised of younger stellar populations, as indicated by their bluer spectral slopes and less prominent Balmer breaks compared to field galaxies at similar redshifts. Further, we use this novel rest-frame optical selection of galaxy proto-clusters to infer the fraction and 3D distribution of strong Lyman-α emitters (LAEs) and damped Lyman-α absorbers (DLAs) in the overdensity environments. We find that two out of the six galaxy overdensities have excess H I absorption compared to the field average, while the other four are consistent within their large scatter in density. These results present the first direct observational constraints on the tomography of the dense, neutral gas reservoirs in large-scale galaxy overdensities at z > 5 and highlight the limitations of pre-JWST searches for reionisation-era galaxy overdensities relying on the detection of strong LAEs alone."}],"acknowledgement":"We would like to thank the anonymous referee for their positive and constructive report and all the observers world-wide for their substantial effort in securing all the public JWST data that were essential for this work. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140. KEH acknowledges support from the Independent Research Fund Denmark (DFF) under grant 5251-00009B and co-funding by the European Union (ERC, HEAVYMETAL, 101071865). Views and opinions expressed are, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. We used the following software for this work: Python, and the scientific Python ecosystem, in particular NumPy (Harris et al. 2020), SciPy (including cKDTree) (Virtanen et al. 2021), Matplotlib (Hunter 2007), and Astropy (Astropy Collaboration 2013, 2018, 2022).","publication_status":"published","article_processing_charge":"No","OA_type":"diamond","OA_place":"publisher","oa":1,"day":"01","ddc":["520"],"author":[{"full_name":"Terp, Chamilla","first_name":"Chamilla","last_name":"Terp"},{"last_name":"Heintz","first_name":"Kasper E.","full_name":"Heintz, Kasper E."},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"full_name":"Naidu, Rohan P.","first_name":"Rohan P.","last_name":"Naidu"},{"first_name":"Pascal A.","full_name":"Oesch, Pascal A.","last_name":"Oesch"},{"full_name":"Witten, Callum","first_name":"Callum","last_name":"Witten"},{"last_name":"Kashino","full_name":"Kashino, Daichi","first_name":"Daichi"},{"first_name":"Clara L.","full_name":"Pollock, Clara L.","last_name":"Pollock"},{"id":"2d002343-372f-11ef-98ec-a164d20427cb","last_name":"Di Cesare","full_name":"Di Cesare, Claudia","first_name":"Claudia"},{"id":"018f0249-0e87-11f0-b167-cbce08fbd541","last_name":"Torralba Torregrosa","orcid":"0000-0001-5586-6950","full_name":"Torralba Torregrosa, Alberto","first_name":"Alberto"}],"language":[{"iso":"eng"}],"dataavailabilitystatement":"The specific observations analysed in this work can be accessed via https://doi.org/10.5281/zenodo.13871850","researchdata_availability":"yes","article_type":"original","year":"2026","publication":"Astronomy & Astrophysics","file":[{"file_size":6156048,"date_created":"2026-07-20T13:41:19Z","date_updated":"2026-07-20T13:41:19Z","success":1,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"22378","file_name":"2026_AstronomyAstrophysics_Terp.pdf","checksum":"0a63db666cfac8e4e6271b75419a26f2"}],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"das_tickbox":"1","scopus_import":"1","quality_controlled":"1","date_updated":"2026-07-20T13:42:20Z","date_created":"2026-07-19T22:01:47Z","volume":710,"oa_version":"Published Version","_id":"22369","month":"06","doi":"10.1051/0004-6361/202659436","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","PlanS_conform":"1","supplementarymaterial":"yes","intvolume":"       710","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Terp C, Heintz KE, Matthee JJ, Naidu RP, Oesch PA, Witten C, Kashino D, Pollock CL, Di Cesare C, Torralba Torregrosa A. 2026. All the massive galaxy overdensities during reionisation: JWST rest-frame optical selection reveals young, chemically evolved galaxies embedded in dense, neutral gas at z &#62; 5. Astronomy &#38; Astrophysics. 710, A290.","chicago":"Terp, Chamilla, Kasper E. Heintz, Jorryt J Matthee, Rohan P. Naidu, Pascal A. Oesch, Callum Witten, Daichi Kashino, Clara L. Pollock, Claudia Di Cesare, and Alberto Torralba Torregrosa. “All the Massive Galaxy Overdensities during Reionisation: JWST Rest-Frame Optical Selection Reveals Young, Chemically Evolved Galaxies Embedded in Dense, Neutral Gas at z &#62; 5.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202659436\">https://doi.org/10.1051/0004-6361/202659436</a>.","short":"C. Terp, K.E. Heintz, J.J. Matthee, R.P. Naidu, P.A. Oesch, C. Witten, D. Kashino, C.L. Pollock, C. Di Cesare, A. Torralba Torregrosa, Astronomy &#38; Astrophysics 710 (2026).","mla":"Terp, Chamilla, et al. “All the Massive Galaxy Overdensities during Reionisation: JWST Rest-Frame Optical Selection Reveals Young, Chemically Evolved Galaxies Embedded in Dense, Neutral Gas at z &#62; 5.” <i>Astronomy &#38; Astrophysics</i>, vol. 710, A290, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202659436\">10.1051/0004-6361/202659436</a>.","ama":"Terp C, Heintz KE, Matthee JJ, et al. All the massive galaxy overdensities during reionisation: JWST rest-frame optical selection reveals young, chemically evolved galaxies embedded in dense, neutral gas at z &#62; 5. <i>Astronomy &#38; Astrophysics</i>. 2026;710. doi:<a href=\"https://doi.org/10.1051/0004-6361/202659436\">10.1051/0004-6361/202659436</a>","ieee":"C. Terp <i>et al.</i>, “All the massive galaxy overdensities during reionisation: JWST rest-frame optical selection reveals young, chemically evolved galaxies embedded in dense, neutral gas at z &#62; 5,” <i>Astronomy &#38; Astrophysics</i>, vol. 710. EDP Sciences, 2026.","apa":"Terp, C., Heintz, K. E., Matthee, J. J., Naidu, R. P., Oesch, P. A., Witten, C., … Torralba Torregrosa, A. (2026). All the massive galaxy overdensities during reionisation: JWST rest-frame optical selection reveals young, chemically evolved galaxies embedded in dense, neutral gas at z &#62; 5. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202659436\">https://doi.org/10.1051/0004-6361/202659436</a>"},"date_published":"2026-06-01T00:00:00Z","article_number":"A290","status":"public","department":[{"_id":"JoMa"}],"file_date_updated":"2026-07-20T13:41:19Z","publisher":"EDP Sciences"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       123","citation":{"apa":"Zoller, B., Benichou, A., Gregor, T., &#38; Tkačik, G. (2026). Invariant nonequilibrium dynamics in gene regulation optimize information flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2524855123\">https://doi.org/10.1073/pnas.2524855123</a>","ieee":"B. Zoller, A. Benichou, T. Gregor, and G. Tkačik, “Invariant nonequilibrium dynamics in gene regulation optimize information flow,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 123, no. 28. National Academy of Sciences, 2026.","ama":"Zoller B, Benichou A, Gregor T, Tkačik G. Invariant nonequilibrium dynamics in gene regulation optimize information flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2026;123(28). doi:<a href=\"https://doi.org/10.1073/pnas.2524855123\">10.1073/pnas.2524855123</a>","mla":"Zoller, Benjamin, et al. “Invariant Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 123, no. 28, e2524855123, National Academy of Sciences, 2026, doi:<a href=\"https://doi.org/10.1073/pnas.2524855123\">10.1073/pnas.2524855123</a>.","chicago":"Zoller, Benjamin, Alexis Benichou, Thomas Gregor, and Gašper Tkačik. “Invariant Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2026. <a href=\"https://doi.org/10.1073/pnas.2524855123\">https://doi.org/10.1073/pnas.2524855123</a>.","short":"B. Zoller, A. Benichou, T. Gregor, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 123 (2026).","ista":"Zoller B, Benichou A, Gregor T, Tkačik G. 2026. Invariant nonequilibrium dynamics in gene regulation optimize information flow. Proceedings of the National Academy of Sciences of the United States of America. 123(28), e2524855123."},"date_published":"2026-07-14T00:00:00Z","article_number":"e2524855123","status":"public","corr_author":"1","file_date_updated":"2026-07-20T13:12:47Z","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","scopus_import":"1","project":[{"grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"oa_version":"Published Version","_id":"22363","month":"07","quality_controlled":"1","volume":123,"date_updated":"2026-07-20T13:15:11Z","date_created":"2026-07-19T22:01:46Z","doi":"10.1073/pnas.2524855123","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"has_accepted_license":"1","supplementarymaterial":"yes","dataavailabilitystatement":"Software code data have been deposited in Institute Pasteur GitHub (https://gitlab.pasteur.fr/tglab/invariantpromoterdynamicspaper) (51).","external_id":{"pmid":["42406962"]},"pmid":1,"language":[{"iso":"eng"}],"researchdata_availability":"yes","year":"2026","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":24580098,"date_created":"2026-07-20T13:12:47Z","date_updated":"2026-07-20T13:12:47Z","success":1,"creator":"dernst","checksum":"f4d82dd706ff1629db68d71190288350","relation":"main_file","file_id":"22376","file_name":"2026_PNAS_Zoller.pdf"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"das_tickbox":"1","title":"Invariant nonequilibrium dynamics in gene regulation optimize information flow","abstract":[{"text":"Eukaryotic gene regulation relies on stochastic yet controlled promoter switching, in which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies have revealed a surprising invariance of the “switching correlation time” (TC)—the characteristic decay time of the autocorrelation function of promoter activity fluctuations—across gene expression levels in multiple genes and organisms. A biophysically plausible explanation for this invariance has so far been lacking. Here, we show that this empirical constraint imposes stringent requirements on minimal yet realistic models of transcriptional regulation. Specifically, reproducing TC–invariance requires regulatory architectures with at least four internal states and nonequilibrium dynamics that break detailed balance. Using Bayesian inference on Drosophila gap gene expression data, we demonstrate that such models i) quantitatively reproduce the observed TC–invariance, ii) remain robust to parameter perturbations, and iii) maximize information transmission from transcription factor concentration to gene expression. Remarkably, the TC-invariant modulation strategy we identify as optimal closely parallels contemporary control-theoretic results on the modulation of stochastic switching systems. Taken together, our results suggest that eukaryotic transcriptional regulation operates in a nonequilibrium regime to balance precision, reaction-rate limitations, and energy dissipation, thereby achieving near-optimal information transmission under fundamental physical constraints.","lang":"eng"}],"acknowledgement":"This work was supported by the French NationalResearch Agency (ANR-20-CE12-0028 “ChroDynE” and ANR-23-CE13-0021“GastruCyp” and ANR-10 LABX-73 “Revive;” all T.G.), and by funding from theEuropean Research Council (ERC-2023-SyG, “Dynatrans,” 101118866, T.G. andG.T.). This work was also supported in part by the U.S. NSF, through the Centerfor the Physics of Biological Function (PHY-1734030, T.G.), and by NIH GrantsR01GM097275, U01DA047730, and U01DK127429 (T.G.)","publication_status":"published","OA_type":"hybrid","article_processing_charge":"Yes","oa":1,"OA_place":"publisher","author":[{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"full_name":"Benichou, Alexis","first_name":"Alexis","last_name":"Benichou","id":"3a67230c-5fc0-11ef-a673-de9a2ffadafe"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper"}],"day":"14","ddc":["570"],"issue":"28"},{"department":[{"_id":"MiLe"}],"publisher":"AAAS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       393","citation":{"apa":"Petrov, P. N., Zhang, J. T., Remis, J., Axelrod, J. J., Cheng, H., Cooper, E. S., … Müller, H. (2026). Laser phase plate improves structure determination of small proteins by cryo-EM. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aeh0665\">https://doi.org/10.1126/science.aeh0665</a>","ieee":"P. N. Petrov <i>et al.</i>, “Laser phase plate improves structure determination of small proteins by cryo-EM,” <i>Science</i>, vol. 393, no. 6807. AAAS, pp. 195–196, 2026.","ama":"Petrov PN, Zhang JT, Remis J, et al. Laser phase plate improves structure determination of small proteins by cryo-EM. <i>Science</i>. 2026;393(6807):195-196. doi:<a href=\"https://doi.org/10.1126/science.aeh0665\">10.1126/science.aeh0665</a>","mla":"Petrov, Petar N., et al. “Laser Phase Plate Improves Structure Determination of Small Proteins by Cryo-EM.” <i>Science</i>, vol. 393, no. 6807, AAAS, 2026, pp. 195–96, doi:<a href=\"https://doi.org/10.1126/science.aeh0665\">10.1126/science.aeh0665</a>.","short":"P.N. Petrov, J.T. Zhang, J. Remis, J.J. Axelrod, H. Cheng, E.S. Cooper, I.K. Hicklin, S. Sandhaus, C. Schnurr, R.M. Glaeser, H. Müller, Science 393 (2026) 195–196.","chicago":"Petrov, Petar N, Jessie T. Zhang, Jonathan Remis, Jeremy J. Axelrod, Hang Cheng, Eric S. Cooper, Ian K. Hicklin, et al. “Laser Phase Plate Improves Structure Determination of Small Proteins by Cryo-EM.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.aeh0665\">https://doi.org/10.1126/science.aeh0665</a>.","ista":"Petrov PN, Zhang JT, Remis J, Axelrod JJ, Cheng H, Cooper ES, Hicklin IK, Sandhaus S, Schnurr C, Glaeser RM, Müller H. 2026. Laser phase plate improves structure determination of small proteins by cryo-EM. Science. 393(6807), 195–196."},"date_published":"2026-07-09T00:00:00Z","status":"public","type":"journal_article","has_accepted_license":"1","supplementarymaterial":"yes","scopus_import":"1","oa_version":"None","_id":"22365","month":"07","volume":393,"quality_controlled":"1","date_updated":"2026-07-20T12:58:46Z","date_created":"2026-07-19T22:01:46Z","doi":"10.1126/science.aeh0665","publication":"Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"das_tickbox":"1","dataavailabilitystatement":"The datasets are publicly available in the Electron Microscopy Public Image Archive [A1: EMPIAR-13528 (on), EMPIAR-13527 (off); A2: EMPIAR-13529 (on), EMPIAR-13526 (off); A3: EMPIAR-13530 (on), EMPIAR-13525 (off); H1: EMPIAR-13535 (on), EMPIAR-13533 (off); H2: EMPIAR-13534 (on), EMPIAR-13532 (off); H3: EMPIAR-13537 (on), EMPIAR-13531 (off)]. The final reconstructed maps are deposited in the Electron Microscopy Data Bank [A1: EMD-76790 (on), EMD-76791 (off); A2: EMD-76792 (on), EMD-76793 (off); A3: EMD-76794 (on), EMD-76797 (off); H1: EMD-76802 (on), EMD-76804 (off); H2: EMD-76805 (on), EMD-76806 (off); H3: EMD-76807 (on), EMD-76809 (off)]. The initial structures in Fig. 3 are deposited at EMD-76810 (on) and EMD-76811 (off). Code for converting EER movies to binned TIF format with proper accounting for electron dose is deposited in Zenodo (47) and available on GitHub at https://github.com/matterwaves/eer2tiff/releases/tag/v0.1.0. All specimen preparation materials are commercially available.","pmid":1,"external_id":{"pmid":["42275466"]},"language":[{"iso":"eng"}],"researchdata_availability":"yes","year":"2026","article_type":"original","OA_type":"closed access","article_processing_charge":"No","author":[{"id":"b1d6732d-8cb6-11f0-baab-bd460ee3a287","last_name":"Petrov","first_name":"Petar N","full_name":"Petrov, Petar N"},{"last_name":"Zhang","first_name":"Jessie T.","full_name":"Zhang, Jessie T."},{"full_name":"Remis, Jonathan","first_name":"Jonathan","last_name":"Remis"},{"last_name":"Axelrod","first_name":"Jeremy J.","full_name":"Axelrod, Jeremy J."},{"last_name":"Cheng","full_name":"Cheng, Hang","first_name":"Hang"},{"last_name":"Cooper","first_name":"Eric S.","full_name":"Cooper, Eric S."},{"last_name":"Hicklin","full_name":"Hicklin, Ian K.","first_name":"Ian K."},{"first_name":"Shahar","full_name":"Sandhaus, Shahar","last_name":"Sandhaus"},{"first_name":"Cooper","full_name":"Schnurr, Cooper","last_name":"Schnurr"},{"last_name":"Glaeser","full_name":"Glaeser, Robert M.","first_name":"Robert M."},{"last_name":"Müller","first_name":"Holger","full_name":"Müller, Holger"}],"ddc":["570"],"day":"09","issue":"6807","title":"Laser phase plate improves structure determination of small proteins by cryo-EM","abstract":[{"lang":"eng","text":"Phase plates can, in principle, overcome the poor image contrast in cryo–electron microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. However, previous designs have been unstable and compromised the high-resolution signal and have thus been unable to surpass results achieved by standard cryo-EM. Here, we show that the laser phase plate (LPP), installed in a modern, custom Titan Krios microscope, enhances the resolution in single-particle reconstruction of small proteins by improving specimen-motion correction and recovery of information from the early frames, as well as particle visualization, three-dimensional classification, and alignment. These advances use standard defocus ranges and reconstruction procedures but open the door to LPP-tailored protocols, offering further improvements by leveraging the LPP demonstrated here."}],"acknowledgement":"The authors thank O. Schwartz and S. Scheres for helpful remarks and discussions; D. Agard, B. Carragher, C. Potter, and P. Olshin for close collaboration; A. Singh, L. Maisenbacher, S. Strasser, and I. Pope for help with mirror inspection; J. Fang, E. Nogales, and J. Hurley for sharing their lab space and assisting with sample preparation; B. Buijsse, W. Hagen, B. Jiang, and T. Coyle at Thermo Fisher Scientific for the design of the custom transfer optics and technical support; G. Long and T. Gutierrez at the UC Berkeley Physics R&D Machine Shop for machining cavity components and tooling. This work was supported by the following: Chan Zuckerberg Initiative award numbers 2021-234606 and 2025-367757, National Institutes of Health grant R01GM126011, Gordon and Betty Moore Foundation grant 9366, Lawrence Berkeley National Laboratory Directed Research and Development Program grant 25-111, and Cooperative Research and Development Agreement award AWD00004352 (to H.M.); National Institutes of Health fellowship F32GM149186 (to P.N.P.).","publication_status":"published","page":"195-196"},{"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) [doi: 10.55776/P34743, 10.55776/Y782, 10.55776/P35197 and 10.55776/J4981]. For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission.","publication_status":"epub_ahead","title":"A probabilistic view on the adapted Wasserstein distance","abstract":[{"text":"Causal optimal transport and adapted Wasserstein distance have applications in different fields from optimization to mathematical finance and machine learning. The goal of this article is to provide equivalent formulations of these concepts in classic probabilistic language. In particular, we prove a Skorokhod representation theorem for adapted weak convergence, reformulate the equivalence of stochastic processes using Markovian lifts, and give an expression for the adapted Wasserstein distance based on representing processes on a common stochastic basis.","lang":"eng"}],"day":"10","ddc":["500"],"author":[{"last_name":"Beiglböck","first_name":"Mathias","full_name":"Beiglböck, Mathias"},{"first_name":"Susanne","full_name":"Pflügl, Susanne","last_name":"Pflügl","id":"8da18bd3-8437-11f1-a311-c814b8b76424"},{"first_name":"Stefan","full_name":"Schrott, Stefan","last_name":"Schrott"}],"article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","OA_place":"publisher","oa":1,"article_type":"original","year":"2026","language":[{"iso":"eng"}],"external_id":{"arxiv":["2406.19810"]},"das_tickbox":"1","publication_identifier":{"issn":["0304-4149"]},"publication":"Stochastic Processes and their Applications","doi":"10.1016/j.spa.2026.105032","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.spa.2026.105032"}],"scopus_import":"1","date_created":"2026-07-19T22:01:45Z","quality_controlled":"1","volume":201,"date_updated":"2026-07-20T12:46:53Z","month":"07","_id":"22361","oa_version":"Published Version","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","has_accepted_license":"1","article_number":"105032","arxiv":1,"status":"public","intvolume":"       201","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-07-10T00:00:00Z","citation":{"ista":"Beiglböck M, Pflügl S, Schrott S. 2026. A probabilistic view on the adapted Wasserstein distance. Stochastic Processes and their Applications. 201, 105032.","mla":"Beiglböck, Mathias, et al. “A Probabilistic View on the Adapted Wasserstein Distance.” <i>Stochastic Processes and Their Applications</i>, vol. 201, 105032, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.spa.2026.105032\">10.1016/j.spa.2026.105032</a>.","chicago":"Beiglböck, Mathias, Susanne Pflügl, and Stefan Schrott. “A Probabilistic View on the Adapted Wasserstein Distance.” <i>Stochastic Processes and Their Applications</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.spa.2026.105032\">https://doi.org/10.1016/j.spa.2026.105032</a>.","short":"M. Beiglböck, S. Pflügl, S. Schrott, Stochastic Processes and Their Applications 201 (2026).","ama":"Beiglböck M, Pflügl S, Schrott S. A probabilistic view on the adapted Wasserstein distance. <i>Stochastic Processes and their Applications</i>. 2026;201. doi:<a href=\"https://doi.org/10.1016/j.spa.2026.105032\">10.1016/j.spa.2026.105032</a>","apa":"Beiglböck, M., Pflügl, S., &#38; Schrott, S. (2026). A probabilistic view on the adapted Wasserstein distance. <i>Stochastic Processes and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.spa.2026.105032\">https://doi.org/10.1016/j.spa.2026.105032</a>","ieee":"M. Beiglböck, S. Pflügl, and S. Schrott, “A probabilistic view on the adapted Wasserstein distance,” <i>Stochastic Processes and their Applications</i>, vol. 201. Elsevier, 2026."},"publisher":"Elsevier","department":[{"_id":"JaMa"}]},{"department":[{"_id":"FlSc"}],"publisher":"Springer Nature","citation":{"ama":"Lin TC, Coles CH, Alfadil E, et al. An intrinsic cytoskeletal oscillator establishes neuronal polarity. <i>Nature</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41586-026-10755-6\">10.1038/s41586-026-10755-6</a>","ieee":"T. C. Lin <i>et al.</i>, “An intrinsic cytoskeletal oscillator establishes neuronal polarity,” <i>Nature</i>. Springer Nature, 2026.","apa":"Lin, T. C., Coles, C. H., Alfadil, E., Fäßler, F., Husch, A., Dupraz, S., … Bradke, F. (2026). An intrinsic cytoskeletal oscillator establishes neuronal polarity. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-026-10755-6\">https://doi.org/10.1038/s41586-026-10755-6</a>","ista":"Lin TC, Coles CH, Alfadil E, Fäßler F, Husch A, Dupraz S, Pietralla T, Narita A, Schelski M, Flynn KC, Stern S, Möhl C, Hilton BJ, Vauti F, Arnold HH, Schur FK, Bradke F. 2026. An intrinsic cytoskeletal oscillator establishes neuronal polarity. Nature.","short":"T.C. Lin, C.H. Coles, E. Alfadil, F. Fäßler, A. Husch, S. Dupraz, T. Pietralla, A. Narita, M. Schelski, K.C. Flynn, S. Stern, C. Möhl, B.J. Hilton, F. Vauti, H.H. Arnold, F.K. Schur, F. Bradke, Nature (2026).","chicago":"Lin, Tien Chen, Charlotte H. Coles, Eissa Alfadil, Florian Fäßler, Andreas Husch, Sebastian Dupraz, Thorben Pietralla, et al. “An Intrinsic Cytoskeletal Oscillator Establishes Neuronal Polarity.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-026-10755-6\">https://doi.org/10.1038/s41586-026-10755-6</a>.","mla":"Lin, Tien Chen, et al. “An Intrinsic Cytoskeletal Oscillator Establishes Neuronal Polarity.” <i>Nature</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41586-026-10755-6\">10.1038/s41586-026-10755-6</a>."},"date_published":"2026-07-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"PlanS_conform":"1","has_accepted_license":"1","type":"journal_article","supplementarymaterial":"yes","quality_controlled":"1","date_created":"2026-07-19T22:01:48Z","date_updated":"2026-07-20T14:18:10Z","_id":"22372","oa_version":"Published Version","month":"07","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41586-026-10755-6","open_access":"1"}],"doi":"10.1038/s41586-026-10755-6","publication":"Nature","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"das_tickbox":"1","researchdata_availability":"yes","language":[{"iso":"eng"}],"dataavailabilitystatement":"The raw data of the representative images have been deposited into Zenodo (https://doi.org/10.5281/zenodo.20118606)99. Owing to the large file size of the raw image data and the processed data used in the analyses that generated the graphs, we archived the image files in the read-only file archive at the DZNE institute. We provide raw data files upon request. The request can be directed to and will be fulfilled by the lead contact F.B. Source data are provided with this paper. The custom ImageJ macro used for generating kymographs, extracting neurite tip positions and protein intensities is available at GitHub (https://github.com/darkbreaker0/IJ_NeuriteGrowthScript) and Zenodo (https://doi.org/10.5281/zenodo.20118606)99. The custom R and Python scripts used in the study are available at GitHub (https://github.com/darkbreaker0/Arp3_neuronal_polarization_2026) and Zenodo (https://doi.org/10.5281/zenodo.20118606)99. The code used for polarity determination of the actin filament in tomograms is available at Zenodo (https://doi.org/10.5281/zenodo.20081075)93.","external_id":{"pmid":["42420447"]},"pmid":1,"article_type":"original","year":"2026","oa":1,"OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","ddc":["570"],"day":"08","author":[{"first_name":"Tien Chen","full_name":"Lin, Tien Chen","last_name":"Lin"},{"full_name":"Coles, Charlotte H.","first_name":"Charlotte H.","last_name":"Coles"},{"first_name":"Eissa","full_name":"Alfadil, Eissa","last_name":"Alfadil"},{"full_name":"Fäßler, Florian","first_name":"Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","full_name":"Husch, Andreas","last_name":"Husch"},{"first_name":"Sebastian","full_name":"Dupraz, Sebastian","last_name":"Dupraz"},{"first_name":"Thorben","full_name":"Pietralla, Thorben","last_name":"Pietralla"},{"full_name":"Narita, Akihiro","first_name":"Akihiro","last_name":"Narita"},{"full_name":"Schelski, Max","first_name":"Max","last_name":"Schelski"},{"last_name":"Flynn","first_name":"Kevin C.","full_name":"Flynn, Kevin C."},{"full_name":"Stern, Sina","first_name":"Sina","last_name":"Stern"},{"last_name":"Möhl","full_name":"Möhl, Christoph","first_name":"Christoph"},{"last_name":"Hilton","first_name":"Brett J.","full_name":"Hilton, Brett J."},{"last_name":"Vauti","full_name":"Vauti, Franz","first_name":"Franz"},{"first_name":"Hans Henning","full_name":"Arnold, Hans Henning","last_name":"Arnold"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km","full_name":"Schur, Florian Km"},{"first_name":"Frank","full_name":"Bradke, Frank","last_name":"Bradke"}],"abstract":[{"text":"Neurons acquire polarity by specifying one neurite as the axon, whereas the others become dendrites. But how this fundamental asymmetry is established remains unclear1. Neuronal polarization has been thought to rely primarily on growth cones that sense external cues2. Here we show that growth cones alone do not direct this process and that the soma acts as a central organizer of neuronal polarization. Using live imaging and genetic loss-of-function approaches in vivo, combined with optogenetic control and local cytoskeletal perturbations in cultured neurons, we uncover a soma-initiated oscillatory program that primes axon selection. Periodic actin branching that depends on the actin-related protein 2/3 (ARP2/3) complex at the soma remodels a global actomyosin network, thereby generating an actin wave that retracts neurites before propagating into a single neurite tip. Exposure to this wave relaxes local actomyosin contractility, which drives a transient microtubule-based protrusion and biases this neurite towards axon fate. As the cell exits this oscillatory stage, this neurite can overcome global inhibition and extend independently of ARP2/3, whereas actomyosin activity suppresses axon formation in the remaining neurites so that they subsequently become dendrites. This soma-driven mechanism ensures the emergence of a single axon independent of environmental cues and underpins the unidirectional information flow in neuronal circuits.","lang":"eng"}],"title":"An intrinsic cytoskeletal oscillator establishes neuronal polarity","publication_status":"epub_ahead","acknowledgement":"We thank O. Gruss, E. Handley, H. Herzel, A. Kania, A. Koseska, E. Kiermaier, D. Manstein, C. Niessen, K. Rottner, J. Schiweck, G. Tavosanis, D. Wachten, R. Wedlich-Söldner and W. Witke for critically reading and discussing the manuscript; C. Günter and V. Štimac for feedback on data presentation; B. Randel, J. Benner, L. Meyn and A.-T. Pham for technical assistance; L. M. Neußer, K. Herz, K. Van-De-Kamp and M. Diwo for their support on mice maintenance; H. Fried, I. Koenig, S. Filser and Y. Fu for their technical support on experimental setup; and M. Aghabeig for writing the Fiji macro scripts. C.H.C. was a Human Frontier Science Program Long-term Postdoctoral Fellow (LT000100/2013). F.B. is supported by the Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), the International Foundation for Research in Paraplegia, Wings for Life, ERANET AXON REPAIR, ERANET RATER SCI and the Chan–Zuckerberg Initiative (CZI). F.B. is also funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)–Project-ID 227953431–SFB 1089, SFB 1690 as well as SFB 1158 and SPP 2395. F.B. is a member of the excellence cluster ImmunoSensation2 (EXC2151–390873048) and the iBehave NRW network. F.B. is a recipient of the Roger de Spoelberch Prize. F.K.M.S. acknowledges support from Austrian Science Fund (FWF): P33367. A.N. is supported by JSPS KAKENHI (grant numbers 18H02410 and 21H02440). Open access funding provided by Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) in der Helmholtz-Gemeinschaft."},{"file_date_updated":"2026-07-20T14:00:33Z","department":[{"_id":"GradSch"},{"_id":"VaKa"}],"publisher":"Institute of Science and Technology Austria","date_published":"2026-07-11T00:00:00Z","citation":{"ista":"Li Y. 2026. Spectral rigidity and nonrigidity of dynamical systems. Institute of Science and Technology Austria.","chicago":"Li, Yunzhe. “Spectral Rigidity and Nonrigidity of Dynamical Systems.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22255\">https://doi.org/10.15479/AT-ISTA-22255</a>.","short":"Y. Li, Spectral Rigidity and Nonrigidity of Dynamical Systems, Institute of Science and Technology Austria, 2026.","mla":"Li, Yunzhe. <i>Spectral Rigidity and Nonrigidity of Dynamical Systems</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22255\">10.15479/AT-ISTA-22255</a>.","ama":"Li Y. Spectral rigidity and nonrigidity of dynamical systems. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22255\">10.15479/AT-ISTA-22255</a>","ieee":"Y. Li, “Spectral rigidity and nonrigidity of dynamical systems,” Institute of Science and Technology Austria, 2026.","apa":"Li, Y. (2026). <i>Spectral rigidity and nonrigidity of dynamical systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22255\">https://doi.org/10.15479/AT-ISTA-22255</a>"},"doi_confirm":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","corr_author":"1","ec_funded":1,"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"dissertation","related_material":{"record":[{"status":"public","id":"22340","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"22341","status":"public"}]},"_id":"22255","month":"07","oa_version":"Published Version","date_created":"2026-07-08T12:44:31Z","date_updated":"2026-07-20T14:58:23Z","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","grant_number":"885707"}],"doi":"10.15479/AT-ISTA-22255","publication_identifier":{"issn":["2663-337X"]},"file":[{"checksum":"8201cb5a427656a41828ecde8a85c04b","relation":"main_file","file_id":"22337","file_name":"2026_Li_Yunzhe_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-07-14T10:48:45Z","date_created":"2026-07-14T10:48:45Z","file_size":1260717,"creator":"yli"},{"access_level":"closed","content_type":"application/x-zip-compressed","creator":"yli","file_size":418752,"date_updated":"2026-07-20T14:00:33Z","date_created":"2026-07-14T11:07:18Z","checksum":"19ee8461ed77f5b7980fc9461f778b6f","file_name":"2026_Li_Yunzhe_Thesis.zip","relation":"source_file","file_id":"22339"}],"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"language":[{"iso":"eng"}],"year":"2026","degree_awarded":"PhD","oa":1,"OA_place":"publisher","article_processing_charge":"No","supervisor":[{"first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"author":[{"first_name":"Yunzhe","full_name":"Li, Yunzhe","last_name":"Li","id":"41cb05d3-f128-11eb-9611-e4e2b3cfba31"}],"day":"11","ddc":["515"],"abstract":[{"text":"This thesis studies spectral rigidity and nonrigidity phenomena in dynamical systems. The central question is whether a dynamical system can be determined, up to a natural conjugacy, from its spectrum. We consider three related spectra: the length spectrum, the action spectrum, and the Lyapunov spectrum.\r\n\r\nThe first part of the thesis concerns Liouville metrics on the two-dimensional torus. It is a long-standing folklore conjecture that Liouville metrics are the only integrable metrics on the torus. We prove a length-spectral rigidity result for linear conformal deformations of Liouville metrics by exploiting the dynamical properties of the rational tori -- analogues of the resonant convex caustics in billiards. We also establish a complementary classification result showing that marked-length-isospectral Liouville metrics are characterized by rearrangements of the one-dimensional functions appearing in their conformal factors, generalizing a theorem of Abbondandolo-Mazzucchelli. In particular, the second result gives nonrigidity examples within the class of Liouville metrics.\r\n\r\nThe second part of the thesis studies the standard map from the viewpoint of action and Lyapunov spectra. We construct nontrivial deformations of the standard map which preserve the symplectic actions (respectively, the Lyapunov exponents) of infinitely many periodic orbits accumulating on an invariant curve. The proof combines a resonant normal form construction with Picard iteration schemes to obtain a sequence of periodic orbits accumulating on an invariant curve with a Liouville rotation number. Within the resonant normal forms we capture the dependence of these periodic orbits on the resonant Fourier coefficients of the dynamics on the invariant curve and, using the contraction mapping principle, obtain a suitable deformation achieving the prescribed spectral data associated with this sequence of orbits. The result can be viewed as a symplectic twist-map analogue of a length-spectral nonrigidity phenomenon for Riemannian manifolds and convex billiards, and it motivates the existence problem for similar 'partially length-isospectral' deformations of strictly convex billiard tables.\r\n","lang":"eng"}],"title":"Spectral rigidity and nonrigidity of dynamical systems","publication_status":"published","page":"131","acknowledgement":"The financial support of the ERC grant SPERIG #885707 is gratefully acknowledged.\r\n"},{"type":"journal_article","supplementarymaterial":"yes","month":"07","_id":"22371","oa_version":"Published Version","date_created":"2026-07-19T22:01:48Z","date_updated":"2026-07-20T14:28:59Z","quality_controlled":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s44319-026-00861-x"}],"doi":"10.1038/s44319-026-00861-x","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","citation":{"ieee":"P. G. Dehio <i>et al.</i>, “A conserved VPS34-PIKfyve-TRPML1-myosin II axis regulates the speed of amoeboid cell migration,” <i>EMBO Reports</i>. Springer Nature, 2026.","apa":"Dehio, P. G., Michard, C., Yam-Puc, J. C., Martí I Líndez, A. A., Jandke, A., Unterstab, G., … Hess, C. (2026). A conserved VPS34-PIKfyve-TRPML1-myosin II axis regulates the speed of amoeboid cell migration. <i>EMBO Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44319-026-00861-x\">https://doi.org/10.1038/s44319-026-00861-x</a>","ama":"Dehio PG, Michard C, Yam-Puc JC, et al. A conserved VPS34-PIKfyve-TRPML1-myosin II axis regulates the speed of amoeboid cell migration. <i>EMBO Reports</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s44319-026-00861-x\">10.1038/s44319-026-00861-x</a>","short":"P.G. Dehio, C. Michard, J.C. Yam-Puc, A.A. Martí I Líndez, A. Jandke, G. Unterstab, L. Fabre, L. Sauteur, M. Artinger, D.F. Legler, M.K. Sixt, T. Schaefer, M.P. Wymann, K. Okkenhaug, T. Soldati, M. Mehling, C. Hess, EMBO Reports (2026).","chicago":"Dehio, Philippe G, Céline Michard, Juan Carlos Yam-Puc, Adrià Arnau Martí I Líndez, Anett Jandke, Gunhild Unterstab, Lucien Fabre, et al. “A Conserved VPS34-PIKfyve-TRPML1-Myosin II Axis Regulates the Speed of Amoeboid Cell Migration.” <i>EMBO Reports</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s44319-026-00861-x\">https://doi.org/10.1038/s44319-026-00861-x</a>.","mla":"Dehio, Philippe G., et al. “A Conserved VPS34-PIKfyve-TRPML1-Myosin II Axis Regulates the Speed of Amoeboid Cell Migration.” <i>EMBO Reports</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s44319-026-00861-x\">10.1038/s44319-026-00861-x</a>.","ista":"Dehio PG, Michard C, Yam-Puc JC, Martí I Líndez AA, Jandke A, Unterstab G, Fabre L, Sauteur L, Artinger M, Legler DF, Sixt MK, Schaefer T, Wymann MP, Okkenhaug K, Soldati T, Mehling M, Hess C. 2026. A conserved VPS34-PIKfyve-TRPML1-myosin II axis regulates the speed of amoeboid cell migration. EMBO Reports."},"date_published":"2026-07-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","status":"public","OA_place":"publisher","oa":1,"OA_type":"gold","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Dehio, Philippe G","first_name":"Philippe G","last_name":"Dehio","id":"b769738e-a003-11ee-b1b8-9030316e0d59"},{"full_name":"Michard, Céline","first_name":"Céline","last_name":"Michard"},{"full_name":"Yam-Puc, Juan Carlos","first_name":"Juan Carlos","last_name":"Yam-Puc"},{"first_name":"Adrià Arnau","full_name":"Martí I Líndez, Adrià Arnau","last_name":"Martí I Líndez"},{"last_name":"Jandke","full_name":"Jandke, Anett","first_name":"Anett"},{"full_name":"Unterstab, Gunhild","first_name":"Gunhild","last_name":"Unterstab"},{"full_name":"Fabre, Lucien","first_name":"Lucien","last_name":"Fabre"},{"full_name":"Sauteur, Loïc","first_name":"Loïc","last_name":"Sauteur"},{"last_name":"Artinger","full_name":"Artinger, Marc","first_name":"Marc"},{"first_name":"Daniel F.","full_name":"Legler, Daniel F.","last_name":"Legler"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"full_name":"Schaefer, Thorsten","first_name":"Thorsten","last_name":"Schaefer"},{"last_name":"Wymann","first_name":"Matthias P.","full_name":"Wymann, Matthias P."},{"last_name":"Okkenhaug","first_name":"Klaus","full_name":"Okkenhaug, Klaus"},{"last_name":"Soldati","full_name":"Soldati, Thierry","first_name":"Thierry"},{"last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias","first_name":"Matthias"},{"full_name":"Hess, Christoph","first_name":"Christoph","last_name":"Hess"}],"day":"07","abstract":[{"lang":"eng","text":"Amoeboid cell migration is key to efficient T cell immunity. Spatial polarization of organelles within cells, including endo-lysosomes, is a prerequisite of migration. However, how ultrastructural polarization is linked to the signaling requirements governing T cell migration remains unknown. Here we show that signaling molecules generated by endo-lysosome-localized kinases regulate velocity of amoeboid migration. Specifically, imaging of T cells identifies accumulation of endo-lysosomes decorated with the lipid kinases VPS34–PIKfyve at the uropod of polarized cells. Activity of VPS34 and PIKfyve regulates speed, but not directedness, of migrating T cells. Mechanistically, PI(3,5)P2 generated by the sequential action of VPS34 and PIKfyve, mediates Ca2+ efflux from lysosomes via the mucolipin TRP cation channel 1 (TRPML1), thus controlling activity of myosin IIA and hence the generation of propulsive force through retrograde actin flow. The VPS34–PIKfyve kinases also regulate velocity of myeloid cells, as well as of the amoeba Dictyostelium discoideum – establishing the axis as an evolutionarily conserved speed control system of amoeboid cell migration."}],"title":"A conserved VPS34-PIKfyve-TRPML1-myosin II axis regulates the speed of amoeboid cell migration","publication_status":"epub_ahead","acknowledgement":"We thank the microscopy core facility of the Department of Biomedicine at the University and University Hospital of Basel for their technical support. This research was technically supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF) and the Lab Support Facility (LSF). CH was supported by the Swiss National Science Foundation (SNSF) (310030B_201277; 310030_192677; FZEB-0-180487), the ZBF Program Award 2025 (Hans Zäslin Bustany Foundation), and the Novartis Foundation for Medical-Biological Research (NFMBR) (#23A070). PD was supported by the Swiss Academy for Medical Sciences (SAMW) and SNSF (183980, 225441), the NFMBR (#23A070), AlumniMedizin Basel, and the Freiwillige Akademische Gesellschaft Basel. DFL was supported by the SNSF (220205). Open access funding provided by University of Basel.","publication":"EMBO Reports","das_tickbox":"1","publication_identifier":{"eissn":["1469-3178"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"researchdata_availability":"yes","dataavailabilitystatement":"The analysis workflow to quantify vesicle localization can be accessed on GitHub (https://github.com/loicsauteur/vesicle-analysis, version 0.1.1).\r\n\r\nThe source data of this paper are collected in the following database record: biostudies:S-SCDT-10_1038-S44319-026-00861-x.","external_id":{"pmid":["42414599"]},"pmid":1,"language":[{"iso":"eng"}],"year":"2026","article_type":"original"}]