[{"intvolume":"     16087","alternative_title":["LNCS"],"citation":{"ista":"Cano Cordoba F, Henzinger TA, Kueffner K. 2025. Algorithmic fairness: A runtime perspective. 25th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 16087, 1–21.","short":"F. Cano Cordoba, T.A. Henzinger, K. Kueffner, in:, 25th International Conference on Runtime Verification, Springer Nature, 2025, pp. 1–21.","chicago":"Cano Cordoba, Filip, Thomas A Henzinger, and Konstantin Kueffner. “Algorithmic Fairness: A Runtime Perspective.” In <i>25th International Conference on Runtime Verification</i>, 16087:1–21. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">https://doi.org/10.1007/978-3-032-05435-7_1</a>.","mla":"Cano Cordoba, Filip, et al. “Algorithmic Fairness: A Runtime Perspective.” <i>25th International Conference on Runtime Verification</i>, vol. 16087, Springer Nature, 2025, pp. 1–21, doi:<a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">10.1007/978-3-032-05435-7_1</a>.","ieee":"F. Cano Cordoba, T. A. Henzinger, and K. Kueffner, “Algorithmic fairness: A runtime perspective,” in <i>25th International Conference on Runtime Verification</i>, Graz, Austria, 2025, vol. 16087, pp. 1–21.","ama":"Cano Cordoba F, Henzinger TA, Kueffner K. Algorithmic fairness: A runtime perspective. In: <i>25th International Conference on Runtime Verification</i>. Vol 16087. Springer Nature; 2025:1-21. doi:<a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">10.1007/978-3-032-05435-7_1</a>","apa":"Cano Cordoba, F., Henzinger, T. A., &#38; Kueffner, K. (2025). Algorithmic fairness: A runtime perspective. In <i>25th International Conference on Runtime Verification</i> (Vol. 16087, pp. 1–21). Graz, Austria: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-032-05435-7_1\">https://doi.org/10.1007/978-3-032-05435-7_1</a>"},"status":"public","quality_controlled":"1","ec_funded":1,"OA_place":"repository","year":"2025","OA_type":"green","related_material":{"record":[{"relation":"dissertation_contains","id":"22808","status":"public"}]},"conference":{"end_date":"2025-09-19","name":"RV: Runtime Verification","location":"Graz, Austria","start_date":"2025-09-15"},"publisher":"Springer Nature","language":[{"iso":"eng"}],"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"date_created":"2026-01-29T16:01:41Z","oa_version":"Preprint","date_updated":"2026-09-18T07:41:29Z","title":"Algorithmic fairness: A runtime perspective","external_id":{"arxiv":["2507.20711"]},"corr_author":"1","date_published":"2025-09-13T00:00:00Z","doi":"10.1007/978-3-032-05435-7_1","fulldoi":"https://doi.org/10.1007/978-3-032-05435-7_1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2507.20711","open_access":"1"}],"publication":"25th International Conference on Runtime Verification","article_processing_charge":"No","oa":1,"department":[{"_id":"ToHe"}],"publication_status":"published","month":"09","day":"13","_id":"21090","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","author":[{"id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","full_name":"Cano Cordoba, Filip","orcid":"0000-0002-0783-904X","first_name":"Filip","last_name":"Cano Cordoba"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"orcid":"0000-0001-8974-2542","full_name":"Kueffner, Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin","last_name":"Kueffner"}],"arxiv":1,"type":"conference","abstract":[{"lang":"eng","text":"Fairness in AI is traditionally studied as a static property evaluated once, over a fixed dataset. However, real-world AI systems operate sequentially, with outcomes and environments evolving over time. This paper proposes a framework for analysing fairness as a runtime property. Using a minimal yet expressive model based on sequences of coin tosses with possibly evolving biases, we study the problems of monitoring and enforcing fairness expressed in either toss outcomes or coin biases. Since there is no one-size-fits-all solution for either problem, we provide a summary of monitoring and enforcement strategies, parametrised by environment dynamics, prediction horizon, and confidence thresholds. For both problems, we present general results under simple or minimal assumptions. We survey existing solutions for the monitoring problem for Markovian and additive dynamics, and existing solutions for the enforcement problem in static settings with known dynamics."}],"volume":16087,"page":"1-21","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783032054357"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","abstract":[{"text":"Differentially private gradient descent (DP-GD) is a popular algorithm to train deep learning models with provable guarantees on the privacy of the training data. In the last decade, the problem of understanding its performance cost with respect to standard GD has received remarkable attention from the research community, which formally derived upper bounds on the excess population risk  RP  in different learning settings. However, existing bounds typically degrade with over-parameterization, i.e., as the number of parameters  p  gets larger than the number of training samples  n  -- a regime which is ubiquitous in current deep-learning practice. As a result, the lack of theoretical insights leaves practitioners without clear guidance, leading some to reduce the effective number of trainable parameters to improve performance, while others use larger models to achieve better results through scale. In this work, we show that in the popular random features model with quadratic loss, for any sufficiently large  p , privacy can be obtained for free, i.e.,  |RP|=o(1) , not only when the privacy parameter  ε  has constant order, but also in the strongly private setting  ε=o(1) . This challenges the common wisdom that over-parameterization inherently hinders performance in private learning.","lang":"eng"}],"arxiv":1,"acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) Grant number COE 12. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The authors were also supported by the 2019 Lopez-Loreta prize, and Simone Bombari was supported by a Google PhD fellowship. We thank Diyuan Wu, Edwige Cyffers, Francesco Pedrotti, Inbar Seroussi, Nikita P. Kalinin, Pietro Pelliconi, Roodabeh Safavi, Yizhe Zhu, and Zhichao Wang for helpful discussions.","_id":"19627","author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","full_name":"Bombari, Simone","first_name":"Simone","last_name":"Bombari"},{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"volume":122,"file_date_updated":"2025-05-05T07:27:54Z","file":[{"file_name":"2025_PNAS_Bombari.pdf","relation":"main_file","success":1,"file_id":"19648","checksum":"1ac6f78e368d35a0cafb4d2d9bd63443","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-05-05T07:27:54Z","file_size":2328320,"date_created":"2025-05-05T07:27:54Z"}],"oa":1,"article_type":"original","article_number":"e2423072122","fulldoi":"https://doi.org/10.1073/pnas.2423072122","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences","isi":1,"day":"15","month":"04","has_accepted_license":"1","department":[{"_id":"MaMo"}],"publication_status":"published","issue":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"22857","relation":"dissertation_contains","status":"public"}]},"external_id":{"arxiv":["2410.14787"],"pmid":["40215275"],"isi":["001471214000001"]},"APC_amount":"2754,32 EUR","title":"Privacy for free in the overparameterized regime","corr_author":"1","doi":"10.1073/pnas.2423072122","date_published":"2025-04-15T00:00:00Z","date_created":"2025-04-27T22:02:13Z","oa_version":"Published Version","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust LLMs","_id":"92099302-16d5-11f0-9cad-f9a785f54fbd"},{"name":"Bilateral Artificial Intelligence (Mondelli)","_id":"74caaef7-b034-11f1-8f2d-e0e993bb422e","grant_number":"COE12"}],"date_updated":"2026-09-21T13:07:01Z","pmid":1,"ddc":["000"],"citation":{"ama":"Bombari S, Mondelli M. Privacy for free in the overparameterized regime. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(15). doi:<a href=\"https://doi.org/10.1073/pnas.2423072122\">10.1073/pnas.2423072122</a>","apa":"Bombari, S., &#38; Mondelli, M. (2025). Privacy for free in the overparameterized regime. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2423072122\">https://doi.org/10.1073/pnas.2423072122</a>","short":"S. Bombari, M. Mondelli, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"Bombari, Simone, and Marco Mondelli. “Privacy for Free in the Overparameterized Regime.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2423072122\">https://doi.org/10.1073/pnas.2423072122</a>.","ieee":"S. Bombari and M. Mondelli, “Privacy for free in the overparameterized regime,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15. National Academy of Sciences, 2025.","mla":"Bombari, Simone, and Marco Mondelli. “Privacy for Free in the Overparameterized Regime.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15, e2423072122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2423072122\">10.1073/pnas.2423072122</a>.","ista":"Bombari S, Mondelli M. 2025. Privacy for free in the overparameterized regime. Proceedings of the National Academy of Sciences. 122(15), e2423072122."},"intvolume":"       122","OA_type":"hybrid","OA_place":"publisher","year":"2025","quality_controlled":"1","status":"public"},{"article_processing_charge":"No","publication":"Proceedings of the 42nd International Conference on Machine Learning","file_date_updated":"2026-02-19T08:04:38Z","file":[{"checksum":"d4ba4f7717b362ca38878f45e57bd643","creator":"dernst","date_created":"2026-02-19T08:04:38Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-02-19T08:04:38Z","file_size":887526,"file_name":"2025_ICML_Bombari.pdf","relation":"main_file","file_id":"21335","success":1}],"oa":1,"publication_status":"published","department":[{"_id":"MaMo"}],"day":"30","month":"07","has_accepted_license":"1","arxiv":1,"acknowledgement":"Marco Mondelli is funded by the European Union (ERC, INF2, project number 101161364). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. Simone Bombari is supported by a Google PhD fellowship. The authors would like to thank GuanWen Qiu for helpful discussions.","_id":"21324","author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","full_name":"Bombari, Simone","first_name":"Simone","last_name":"Bombari"},{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"type":"conference","abstract":[{"text":"Learning models have been shown to rely on spurious correlations between non-predictive features and the associated labels in the training data, with negative implications on robustness, bias and fairness. In this work, we provide a statistical characterization of this phenomenon for high-dimensional regression, when the data contains a predictive core feature x and a spurious feature y. Specifically, we quantify the amount of spurious correlations C learned via linear regression, in terms of the data covariance and the strength λ of the ridge regularization. As a consequence, we first capture the simplicity of y through the spectrum of its covariance, and its correlation with x through the Schur complement of the full data covariance. Next, we prove a trade-off between C and the in-distribution test loss L, by showing that the value of λ that minimizes L lies in an interval where C is increasing. Finally, we investigate the effects of over-parameterization via the random features model, by showing its equivalence to regularized linear regression. Our theoretical results are supported by numerical experiments on Gaussian, Color-MNIST, and CIFAR-10 datasets.","lang":"eng"}],"page":"4839-4873","publication_identifier":{"eissn":["2640-3498"]},"volume":267,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       267","alternative_title":["PMLR"],"citation":{"ista":"Bombari S, Mondelli M. 2025. Spurious correlations in high dimensional regression: The roles of regularization, simplicity bias and over-parameterization. Proceedings of the 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 4839–4873.","ieee":"S. Bombari and M. Mondelli, “Spurious correlations in high dimensional regression: The roles of regularization, simplicity bias and over-parameterization,” in <i>Proceedings of the 42nd International Conference on Machine Learning</i>, Vancouver, Canada, 2025, vol. 267, pp. 4839–4873.","mla":"Bombari, Simone, and Marco Mondelli. “Spurious Correlations in High Dimensional Regression: The Roles of Regularization, Simplicity Bias and over-Parameterization.” <i>Proceedings of the 42nd International Conference on Machine Learning</i>, vol. 267, ML Research Press, 2025, pp. 4839–73.","chicago":"Bombari, Simone, and Marco Mondelli. “Spurious Correlations in High Dimensional Regression: The Roles of Regularization, Simplicity Bias and over-Parameterization.” In <i>Proceedings of the 42nd International Conference on Machine Learning</i>, 267:4839–73. ML Research Press, 2025.","short":"S. Bombari, M. Mondelli, in:, Proceedings of the 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 4839–4873.","apa":"Bombari, S., &#38; Mondelli, M. (2025). Spurious correlations in high dimensional regression: The roles of regularization, simplicity bias and over-parameterization. In <i>Proceedings of the 42nd International Conference on Machine Learning</i> (Vol. 267, pp. 4839–4873). Vancouver, Canada: ML Research Press.","ama":"Bombari S, Mondelli M. Spurious correlations in high dimensional regression: The roles of regularization, simplicity bias and over-parameterization. In: <i>Proceedings of the 42nd International Conference on Machine Learning</i>. Vol 267. ML Research Press; 2025:4839-4873."},"status":"public","quality_controlled":"1","OA_type":"gold","year":"2025","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"22857","relation":"dissertation_contains"}]},"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2025-07-19","start_date":"2025-07-13","location":"Vancouver, Canada"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"publisher":"ML Research Press","date_created":"2026-02-18T11:58:00Z","oa_version":"Published Version","project":[{"name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","grant_number":"101161364"},{"_id":"92099302-16d5-11f0-9cad-f9a785f54fbd","name":"Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust LLMs"}],"date_updated":"2026-09-21T13:07:01Z","ddc":["000"],"external_id":{"arxiv":["2502.01347"]},"corr_author":"1","title":"Spurious correlations in high dimensional regression: The roles of regularization, simplicity bias and over-parameterization","date_published":"2025-07-30T00:00:00Z"},{"has_accepted_license":"1","day":"19","month":"09","issue":"38","publication_status":"published","department":[{"_id":"FlSc"}],"oa":1,"file":[{"success":1,"file_id":"20372","relation":"main_file","file_name":"2025_ScienceAdvance_Carpentier.pdf","date_created":"2025-09-23T07:57:51Z","date_updated":"2025-09-23T07:57:51Z","file_size":3599137,"access_level":"open_access","content_type":"application/pdf","checksum":"4e2407bdabf8d53f399eb8a20d86218e","creator":"dernst"}],"file_date_updated":"2025-09-23T07:57:51Z","article_number":"eadw4124","article_type":"original","scopus_import":"1","fulldoi":"https://doi.org/10.1126/sciadv.adw4124","publication":"Science Advances","isi":1,"article_processing_charge":"Yes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":11,"publication_identifier":{"eissn":["2375-2548"]},"type":"journal_article","abstract":[{"text":"The Huntingtin protein (HTT), named for its role in Huntington’s disease, has been best understood as a scaffolding protein that promotes vesicle transport by molecular motors along microtubules. Here, we show that HTT also interacts with the actin cytoskeleton, and its loss of function disturbs the morphology and function of the axonal growth cone. We demonstrate that HTT organizes F-actin into bundles. Cryo–electron tomography (cryo-ET) and subtomogram averaging (STA) structural analyses reveal that HTT’s N-terminal HEAT and Bridge domains wrap around F-actin, while the C-terminal HEAT domain is displaced; furthermore, HTT dimerizes via the N-HEAT domain to bridge parallel actin filaments separated by ~20 nanometers. Our study provides the structural basis for understanding how HTT interacts with and organizes the actin cytoskeleton.","lang":"eng"}],"_id":"20370","acknowledgement":"We thank C. Cuveillier, J. Delaroche, T. Ferraro, and A. Zanchi for help with TIRF experiments, electron microscopy preparation, data analysis, and cell cultures, respectively; A. Antkowiak, C. Bosc, C. Fassier, A. Fourest-Lieuvin, and V. Brandt for helpful discussions. We acknowledge the contribution of the Photonic Imaging Center of Grenoble Institute Neuroscience which is part of the ISdV core facility and certified by the IBiSA label and ICM.Quant (RRID:SCR_026393) core facility of the Paris Brain Institute (ICM); the AniRA lentivector production facility from the CELPHEDIA Infrastructure and SFR Biosciences (UAR3444/CNRS, US8/Inserm, ENS de Lyon, UCBL); the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp, A. Schloegl and S. Elefante); and the Electron Microscopy Facility (EMF, V.V. Hodirnau). The software programs used for the processing were supported by SBGrid (www.sbgrid.org). This work was supported by the Agence Nationale pour la Recherche (AXYON: ANR-18-CE16-0009-01, S.H.), Austrian Science Fund (FWF) grants (P33367, F.K.M.S.; E435, J.M.H.), ChanZuckerberg Initiative (CZI) grant (DAF2021-234754, F.K.M.S.), Hereditary Disease Foundation Research Grant (HDF 990846, M.C.), European Union (ERC: ActinID 101076260, F.K.M.S.), Fondation pour la Recherche Médicale (FRM: équipe labellisée DEQ202203014675, S.H.; PhD fellowship, FDT202001010865, R.C.), Korea Health Industry Development Institute (KHIDI) (Korea-Switzerland global research support grant: RS-2023-00266300, J.-J.S.), National Research Foundation (NRF) of Korea (Korea-Austria collaborative grant NRF-2019K1A3A1A181160, J.-J.S. and F.K.M.S.; NRF-2020R1A2B5B03001517 and RS-2024-00333346 and RS-2024-00436173, J.-J.S.; 2021R1C1C1006700, D.K.).","PlanS_conform":"1","author":[{"last_name":"Carpentier","first_name":"Rémi","full_name":"Carpentier, Rémi"},{"first_name":"Jaesung","last_name":"Kim","full_name":"Kim, Jaesung"},{"first_name":"Mariacristina","last_name":"Capizzi","full_name":"Capizzi, Mariacristina"},{"first_name":"Hyeongju","last_name":"Kim","full_name":"Kim, Hyeongju"},{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler"},{"first_name":"Jesse","last_name":"Hansen","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","orcid":"0000-0001-7967-2085"},{"full_name":"Kim, Min Jeong","first_name":"Min Jeong","last_name":"Kim"},{"first_name":"Eric","last_name":"Denarier","full_name":"Denarier, Eric"},{"full_name":"Blot, Béatrice","last_name":"Blot","first_name":"Béatrice"},{"full_name":"Degennaro, Marine","last_name":"Degennaro","first_name":"Marine"},{"first_name":"Sophia","last_name":"Labou","full_name":"Labou, Sophia"},{"first_name":"Isabelle","last_name":"Arnal","full_name":"Arnal, Isabelle"},{"full_name":"Marcaida, Maria J.","first_name":"Maria J.","last_name":"Marcaida"},{"full_name":"Peraro, Matteo Dal","first_name":"Matteo Dal","last_name":"Peraro"},{"last_name":"Kim","first_name":"Doory","full_name":"Kim, Doory"},{"first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"first_name":"Ji-Joon","last_name":"Song","full_name":"Song, Ji-Joon"},{"full_name":"Humbert, Sandrine","last_name":"Humbert","first_name":"Sandrine"}],"OA_place":"publisher","year":"2025","OA_type":"gold","quality_controlled":"1","status":"public","citation":{"ista":"Carpentier R, Kim J, Capizzi M, Kim H, Fäßler F, Hansen J, Kim MJ, Denarier E, Blot B, Degennaro M, Labou S, Arnal I, Marcaida MJ, Peraro MD, Kim D, Schur FK, Song J-J, Humbert S. 2025. Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. Science Advances. 11(38), eadw4124.","mla":"Carpentier, Rémi, et al. “Structure of the Huntingtin F-Actin Complex Reveals Its Role in Cytoskeleton Organization.” <i>Science Advances</i>, vol. 11, no. 38, eadw4124, AAAS, 2025, doi:<a href=\"https://doi.org/10.1126/sciadv.adw4124\">10.1126/sciadv.adw4124</a>.","ieee":"R. Carpentier <i>et al.</i>, “Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization,” <i>Science Advances</i>, vol. 11, no. 38. AAAS, 2025.","chicago":"Carpentier, Rémi, Jaesung Kim, Mariacristina Capizzi, Hyeongju Kim, Florian Fäßler, Jesse Hansen, Min Jeong Kim, et al. “Structure of the Huntingtin F-Actin Complex Reveals Its Role in Cytoskeleton Organization.” <i>Science Advances</i>. AAAS, 2025. <a href=\"https://doi.org/10.1126/sciadv.adw4124\">https://doi.org/10.1126/sciadv.adw4124</a>.","short":"R. Carpentier, J. Kim, M. Capizzi, H. Kim, F. Fäßler, J. Hansen, M.J. Kim, E. Denarier, B. Blot, M. Degennaro, S. Labou, I. Arnal, M.J. Marcaida, M.D. Peraro, D. Kim, F.K. Schur, J.-J. Song, S. Humbert, Science Advances 11 (2025).","apa":"Carpentier, R., Kim, J., Capizzi, M., Kim, H., Fäßler, F., Hansen, J., … Humbert, S. (2025). Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adw4124\">https://doi.org/10.1126/sciadv.adw4124</a>","ama":"Carpentier R, Kim J, Capizzi M, et al. Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization. <i>Science Advances</i>. 2025;11(38). doi:<a href=\"https://doi.org/10.1126/sciadv.adw4124\">10.1126/sciadv.adw4124</a>"},"intvolume":"        11","DOAJ_listed":"1","external_id":{"isi":["001575751700013"],"pmid":["40971423"]},"title":"Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization","corr_author":"1","APC_amount":"1395,61 EUR","date_published":"2025-09-19T00:00:00Z","doi":"10.1126/sciadv.adw4124","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"grant_number":"CZI01","name":"CryoMinflux-guided in-situ molecular census and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308"},{"grant_number":"101076260","name":"A molecular atlas of Actin filament IDentities in the cell motility machinery","_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"oa_version":"Published Version","date_created":"2025-09-22T08:00:52Z","ddc":["570"],"pmid":1,"date_updated":"2026-09-24T08:17:37Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"AAAS","language":[{"iso":"eng"}]},{"date_updated":"2026-09-24T10:13:38Z","ddc":["530"],"oa_version":"Published Version","date_created":"2025-09-10T05:41:30Z","project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"doi":"10.1103/qvls-7s3q","date_published":"2025-07-17T00:00:00Z","external_id":{"isi":["001537333100001"],"arxiv":["2408.07829 "]},"corr_author":"1","title":"Dual relaxation oscillations in a Josephson-junction array","related_material":{"record":[{"relation":"earlier_version","id":"18057","status":"public"}]},"publisher":"American Physical Society","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ec_funded":1,"quality_controlled":"1","status":"public","OA_type":"hybrid","year":"2025","OA_place":"publisher","intvolume":"        24","citation":{"ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson-junction array. <i>Physical Review Applied</i>. 2025;24. doi:<a href=\"https://doi.org/10.1103/qvls-7s3q\">10.1103/qvls-7s3q</a>","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (2025). Dual relaxation oscillations in a Josephson-junction array. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/qvls-7s3q\">https://doi.org/10.1103/qvls-7s3q</a>","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson-Junction Array.” <i>Physical Review Applied</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/qvls-7s3q\">https://doi.org/10.1103/qvls-7s3q</a>.","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, Physical Review Applied 24 (2025).","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson-junction array,” <i>Physical Review Applied</i>, vol. 24. American Physical Society, 2025.","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson-Junction Array.” <i>Physical Review Applied</i>, vol. 24, 014035, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/qvls-7s3q\">10.1103/qvls-7s3q</a>.","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. 2025. Dual relaxation oscillations in a Josephson-junction array. Physical Review Applied. 24, 014035."},"publication_identifier":{"issn":["2331-7019"]},"volume":24,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"acknowledgement":"We gratefully acknowledge support from the Miba Machine Shop and the Nanofabrictation Facility at IST Austria. This work was supported by the Austrian FWF under Grant No. P33692-N (S.M., J.S., and A.P.H.), the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS Foundation research grant (A.P.H.).","_id":"20324","PlanS_conform":"1","author":[{"orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","first_name":"Soham"},{"first_name":"Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","full_name":"Lancheros Naranjo, Diego A"},{"first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P"}],"abstract":[{"lang":"eng","text":"We report relaxation oscillations in a one-dimensional array of Josephson junctions, wherein the array dynamically switches between low-current and high-current states. The oscillations are current-voltage dual to those ordinarily observed in single junctions. The current-voltage dual circuit quantitatively accounts for temporal dynamics of the array, including the dependence on biasing conditions. Injection locking of the oscillations results in well-developed current plateaux. A thermal model explains the self-consistent reduction of the superconducting gap due to overheating of the array in the high-current state. Our work suggests that overheating determines the switching from the high-current state to the low-current state."}],"type":"journal_article","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"publication_status":"published","day":"17","month":"07","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Physical Review Applied","isi":1,"scopus_import":"1","fulldoi":"https://doi.org/10.1103/qvls-7s3q","article_type":"original","article_number":"014035","file_date_updated":"2025-09-10T07:29:06Z","file":[{"relation":"main_file","file_name":"2025_PhysReviewAppl_Mukhopadhyay.pdf","file_id":"20335","success":1,"checksum":"6cc3c9beeb7c0a88ee0a072c9a32b78b","creator":"dernst","date_created":"2025-09-10T07:29:06Z","file_size":1370466,"date_updated":"2025-09-10T07:29:06Z","content_type":"application/pdf","access_level":"open_access"}],"oa":1},{"abstract":[{"lang":"eng","text":"Sex-linked and autosomal loci experience different selective pressures and evolutionary dynamics. X (or Z) chromosomes are often hemizygous in males (or females), as Y (or W) chromosomes often degenerate. Such hemizygous regions can be under greater efficacy of selection, as recessive mutations are immediately exposed to selection in the heterogametic sex leading to faster adaptation and faster divergence on the X chromosome (the so-called Faster-X or Faster-Z effect). However, in young nonrecombining regions, Y/W chromosomes often have many functional genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on the X/Z by the Y/W homolog is expected to drive slower adaptation for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect has been studied extensively, much less is known empirically about the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage of published population genomic data in the female-heterogametic human parasite Schistosoma japonicum to characterize the gene content and diversity levels of the diploid and hemizygous regions of the Z chromosome. We used different metrics of selective pressures acting on genes to test for differences in the efficacy of selection in hemizygous and diploid Z regions, relative to autosomes. We found consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly pronounced for female-biased genes on the diploid Z, as predicted by recent theoretical work."}],"type":"journal_article","author":[{"full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"_id":"19370","acknowledgement":"The authors would like to thank three anonymous reviewers for comments and suggestions. We are also grateful to Christelle Fraïsse, Marwan Elkrewi, and Filip Ruzicka for the help in this project.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":17,"publication_identifier":{"eissn":["1759-6653"]},"article_number":"evaf021","article_type":"original","oa":1,"file":[{"success":1,"file_id":"19378","relation":"main_file","file_name":"2025_GBE_Mrnjavac.pdf","date_created":"2025-03-10T08:25:59Z","file_size":768371,"date_updated":"2025-03-10T08:25:59Z","content_type":"application/pdf","access_level":"open_access","checksum":"e3aa993e3d6dad10cb806c243fa57408","creator":"dernst"}],"file_date_updated":"2025-03-10T08:25:59Z","publication":"Genome Biology and Evolution","isi":1,"article_processing_charge":"Yes","scopus_import":"1","fulldoi":"https://doi.org/10.1093/gbe/evaf021","has_accepted_license":"1","month":"02","day":"01","issue":"2","publication_status":"published","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"publisher":"Oxford University Press","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"relation":"earlier_version","id":"18549","status":"public"}],"link":[{"url":"https://git.ista.ac.at/amrnjava/schistosomes_slower_z","relation":"software"}]},"date_published":"2025-02-01T00:00:00Z","doi":"10.1093/gbe/evaf021","external_id":{"pmid":["39913672"],"isi":["001423671400001"]},"corr_author":"1","title":"Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum","ddc":["570"],"pmid":1,"date_updated":"2026-09-24T11:18:17Z","date_created":"2025-03-09T23:01:27Z","oa_version":"Published Version","citation":{"ista":"Mrnjavac A, Vicoso B. 2025. Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum. Genome Biology and Evolution. 17(2), evaf021.","ieee":"A. Mrnjavac and B. Vicoso, “Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum,” <i>Genome Biology and Evolution</i>, vol. 17, no. 2. Oxford University Press, 2025.","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on a Young Z Chromosome Region of Schistosoma Japonicum.” <i>Genome Biology and Evolution</i>, vol. 17, no. 2, evaf021, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/gbe/evaf021\">10.1093/gbe/evaf021</a>.","short":"A. Mrnjavac, B. Vicoso, Genome Biology and Evolution 17 (2025).","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on a Young Z Chromosome Region of Schistosoma Japonicum.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/gbe/evaf021\">https://doi.org/10.1093/gbe/evaf021</a>.","apa":"Mrnjavac, A., &#38; Vicoso, B. (2025). Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evaf021\">https://doi.org/10.1093/gbe/evaf021</a>","ama":"Mrnjavac A, Vicoso B. Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum. <i>Genome Biology and Evolution</i>. 2025;17(2). doi:<a href=\"https://doi.org/10.1093/gbe/evaf021\">10.1093/gbe/evaf021</a>"},"intvolume":"        17","OA_place":"publisher","year":"2025","OA_type":"gold","status":"public","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ, (or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion membership down to F322W2 ∼ 27. We identified an intriguing feature at the very low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24 and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent discontinuity in the slope of the main sequence. A similar discontinuity is seen in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset of absorption. We therefore hypothesize that the cluster hosts disproportionately more oxygen-poor stars near the bottom of the main sequence compared to the upper main sequence and the red giant branch. Our results show no strong or conclusive evidence of a rise in the brown dwarf luminosity function at faint magnitudes, in contrast to previous findings likely affected by faint red background galaxies. In our analysis, we accounted for this contamination by using proper motion membership."}],"type":"journal_article","arxiv":1,"acknowledgement":"We dedicate this paper to the memory of our colleague Prof. Harvey Richer (⋆ April 1944 —† 13 November 2023), a highly accomplished astronomer and expert in stellar populations and in particular within globular clusters, who passed away during this project. Harvey grew up in Montreal and was at least the second star man to graduate from his high school, having been preceded by William Shatner by more than a decade. He worked at the University of British Columbia for most of his career, and his focus was the late stages of stellar evolution, in particular carbon stars and white dwarfs. We thank the referee for his valuable suggestions and comments, which helped improve the paper, as well as for his prompt revision.","_id":"18866","author":[{"last_name":"Scalco","first_name":"M.","full_name":"Scalco, M."},{"full_name":"Gerasimov, R.","last_name":"Gerasimov","first_name":"R."},{"full_name":"Bedin, L. R.","first_name":"L. R.","last_name":"Bedin"},{"full_name":"Vesperini, E.","last_name":"Vesperini","first_name":"E."},{"full_name":"Correnti, M.","last_name":"Correnti","first_name":"M."},{"full_name":"Nardiello, D.","last_name":"Nardiello","first_name":"D."},{"full_name":"Burgasser, A.","last_name":"Burgasser","first_name":"A."},{"full_name":"Richer, H.","first_name":"H.","last_name":"Richer"},{"id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","full_name":"Caiazzo, Ilaria","orcid":"0000-0002-4770-5388","last_name":"Caiazzo","first_name":"Ilaria"},{"first_name":"J.","last_name":"Heyl","full_name":"Heyl, J."},{"full_name":"Libralato, M.","last_name":"Libralato","first_name":"M."},{"last_name":"Anderson","first_name":"J.","full_name":"Anderson, J."},{"full_name":"Griggio, M.","last_name":"Griggio","first_name":"M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"volume":694,"article_type":"original","article_number":"A68","file_date_updated":"2025-04-16T07:13:31Z","file":[{"date_created":"2025-04-16T07:13:31Z","access_level":"open_access","content_type":"application/pdf","file_size":18080704,"date_updated":"2025-04-16T07:13:31Z","checksum":"db765ce222df60a1e7c19da1968906a8","creator":"dernst","success":1,"file_id":"19569","file_name":"2025_AstronomyAstrophysics_Scalco.pdf","relation":"main_file"}],"oa":1,"article_processing_charge":"Yes","publication":"Astronomy & Astrophysics","isi":1,"fulldoi":"https://doi.org/10.1051/0004-6361/202452907","scopus_import":"1","day":"04","month":"02","has_accepted_license":"1","department":[{"_id":"IlCa"}],"publication_status":"published","publisher":"EDP Sciences","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1051/0004-6361/202452907","date_published":"2025-02-04T00:00:00Z","external_id":{"isi":["001414753300007"],"arxiv":["2501.04446"]},"title":"JWST photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence at the star--brown dwarf transition","date_updated":"2026-09-24T13:45:58Z","ddc":["520"],"oa_version":"Published Version","date_created":"2025-01-21T15:29:36Z","citation":{"ista":"Scalco M, Gerasimov R, Bedin LR, Vesperini E, Correnti M, Nardiello D, Burgasser A, Richer H, Caiazzo I, Heyl J, Libralato M, Anderson J, Griggio M. 2025. JWST photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence at the star--brown dwarf transition. Astronomy &#38; Astrophysics. 694, A68.","ama":"Scalco M, Gerasimov R, Bedin LR, et al. JWST photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence at the star--brown dwarf transition. <i>Astronomy &#38; Astrophysics</i>. 2025;694. doi:<a href=\"https://doi.org/10.1051/0004-6361/202452907\">10.1051/0004-6361/202452907</a>","apa":"Scalco, M., Gerasimov, R., Bedin, L. R., Vesperini, E., Correnti, M., Nardiello, D., … Griggio, M. (2025). JWST photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence at the star--brown dwarf transition. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202452907\">https://doi.org/10.1051/0004-6361/202452907</a>","chicago":"Scalco, M., R. Gerasimov, L. R. Bedin, E. Vesperini, M. Correnti, D. Nardiello, A. Burgasser, et al. “JWST Photometry and Astrometry of 47 Tucanæ. Discontinuity in the Stellar Sequence at the Star--Brown Dwarf Transition.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202452907\">https://doi.org/10.1051/0004-6361/202452907</a>.","short":"M. Scalco, R. Gerasimov, L.R. Bedin, E. Vesperini, M. Correnti, D. Nardiello, A. Burgasser, H. Richer, I. Caiazzo, J. Heyl, M. Libralato, J. Anderson, M. Griggio, Astronomy &#38; Astrophysics 694 (2025).","mla":"Scalco, M., et al. “JWST Photometry and Astrometry of 47 Tucanæ. Discontinuity in the Stellar Sequence at the Star--Brown Dwarf Transition.” <i>Astronomy &#38; Astrophysics</i>, vol. 694, A68, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202452907\">10.1051/0004-6361/202452907</a>.","ieee":"M. Scalco <i>et al.</i>, “JWST photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence at the star--brown dwarf transition,” <i>Astronomy &#38; Astrophysics</i>, vol. 694. EDP Sciences, 2025."},"intvolume":"       694","OA_type":"diamond","OA_place":"publisher","year":"2025","quality_controlled":"1","status":"public"},{"publisher":"Oxford University Press","language":[{"iso":"eng"}],"das_tickbox":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1093/genetics/iyae191","date_published":"2025-02-01T00:00:00Z","title":"Linking molecular mechanisms to their evolutionary consequences: a primer","external_id":{"isi":["001379194200001"],"pmid":["39601269"]},"corr_author":"1","date_updated":"2026-10-01T08:30:12Z","pmid":1,"ddc":["570"],"oa_version":"Published Version","date_created":"2025-01-29T08:21:35Z","citation":{"ista":"Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.","apa":"Grah, R., Guet, C. C., Tkačik, G., &#38; Lagator, M. (2025). Linking molecular mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyae191\">https://doi.org/10.1093/genetics/iyae191</a>","ama":"Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. 2025;229(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyae191\">10.1093/genetics/iyae191</a>","ieee":"R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms to their evolutionary consequences: a primer,” <i>Genetics</i>, vol. 229, no. 2. Oxford University Press, 2025.","mla":"Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>, vol. 229, no. 2, iyae191, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyae191\">10.1093/genetics/iyae191</a>.","short":"R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025).","chicago":"Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyae191\">https://doi.org/10.1093/genetics/iyae191</a>."},"intvolume":"       229","OA_type":"hybrid","year":"2025","OA_place":"publisher","quality_controlled":"1","status":"public","abstract":[{"lang":"eng","text":"A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties—the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation—can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes."}],"type":"journal_article","supplementarymaterial":"yes","author":[{"first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato"}],"_id":"18936","acknowledgement":"The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions that helped improve our work.\r\nFunding for this work was provided by the Wellcome Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society Research Grant (RG\\R2\\232522) to M.L.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1943-2631"]},"volume":229,"article_type":"original","article_number":"iyae191","file":[{"file_id":"19580","success":1,"relation":"main_file","file_name":"2025_Genetics_Grah.pdf","file_size":1511688,"date_updated":"2025-04-16T09:41:04Z","content_type":"application/pdf","access_level":"open_access","date_created":"2025-04-16T09:41:04Z","checksum":"f730e416795969449ef49d97b82ac494","creator":"dernst"}],"file_date_updated":"2025-04-16T09:41:04Z","oa":1,"article_processing_charge":"Yes (in subscription journal)","isi":1,"publication":"Genetics","fulldoi":"https://doi.org/10.1093/genetics/iyae191","scopus_import":"1","month":"02","day":"01","researchdata_availability":"upon request","has_accepted_license":"1","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"issue":"2","dataavailabilitystatement":"Strains and plasmids are available upon request. All experimental raw data can be found in Supplementary Data 1. All code underpinning this work is available at https://github.com/Lagator-Group/Linking-Molecular-Mechanisms-to-their-Evolutionary-consequence-a-primer or upon request.  Supplemental material available at GENETICS online"},{"citation":{"mla":"Agasthya, Lokahith N., et al. “Moist Convective Scaling: Insights from an Idealised Model.” <i>Quarterly Journal of the Royal Meteorological Society</i>, vol. 151, no. 766, e4902, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/qj.4902\">10.1002/qj.4902</a>.","ieee":"L. N. Agasthya, C. J. Muller, and M. Cheve, “Moist convective scaling: Insights from an idealised model,” <i>Quarterly Journal of the Royal Meteorological Society</i>, vol. 151, no. 766. Wiley, 2025.","chicago":"Agasthya, Lokahith N, Caroline J Muller, and Mathis Cheve. “Moist Convective Scaling: Insights from an Idealised Model.” <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/qj.4902\">https://doi.org/10.1002/qj.4902</a>.","short":"L.N. Agasthya, C.J. Muller, M. Cheve, Quarterly Journal of the Royal Meteorological Society 151 (2025).","apa":"Agasthya, L. N., Muller, C. J., &#38; Cheve, M. (2025). Moist convective scaling: Insights from an idealised model. <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley. <a href=\"https://doi.org/10.1002/qj.4902\">https://doi.org/10.1002/qj.4902</a>","ama":"Agasthya LN, Muller CJ, Cheve M. Moist convective scaling: Insights from an idealised model. <i>Quarterly Journal of the Royal Meteorological Society</i>. 2025;151(766). doi:<a href=\"https://doi.org/10.1002/qj.4902\">10.1002/qj.4902</a>","ista":"Agasthya LN, Muller CJ, Cheve M. 2025. Moist convective scaling: Insights from an idealised model. Quarterly Journal of the Royal Meteorological Society. 151(766), e4902."},"intvolume":"       151","year":"2025","OA_place":"publisher","OA_type":"hybrid","status":"public","quality_controlled":"1","ec_funded":1,"das_tickbox":"1","publisher":"Wiley","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2025-01-01T00:00:00Z","doi":"10.1002/qj.4902","external_id":{"isi":["001363135200001"]},"corr_author":"1","title":"Moist convective scaling: Insights from an idealised model","ddc":["550"],"date_updated":"2026-10-01T09:23:20Z","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"date_created":"2024-12-01T23:01:54Z","oa_version":"Published Version","article_number":"e4902","article_type":"original","oa":1,"file_date_updated":"2025-07-03T06:46:27Z","file":[{"creator":"dernst","checksum":"2b4968f1c794da56d1eb7b856a406de7","date_created":"2025-07-03T06:46:27Z","date_updated":"2025-07-03T06:46:27Z","file_size":5924105,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2025_QuartJRMS_Agasthya.pdf","success":1,"file_id":"19958"}],"publication":"Quarterly Journal of the Royal Meteorological Society","isi":1,"article_processing_charge":"Yes (via OA deal)","fulldoi":"https://doi.org/10.1002/qj.4902","scopus_import":"1","has_accepted_license":"1","researchdata_availability":"upon request","month":"01","day":"01","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author, Lokahith Agasthya, upon reasonable request.","issue":"766","publication_status":"published","department":[{"_id":"CaMu"}],"abstract":[{"text":"The response of clouds and moist-convective processes to heat loss to space by long-wave radiative cooling is an important feedback in the Earth's atmosphere. It is known that moist convection increases roughly in equilibrium with radiative cooling, an assumption often made in simplified models of the tropical atmosphere. In this study, we use an idealised two-dimensional model of the atmosphere introduced by Vallis et. al. and incorporate a bulk-cooling term, which is an idealisation of radiative cooling in the atmosphere. We comment briefly on the static stability of the system to dry and moist convection and characteris its moist convective response to changes in the bulk cooling. We find that, while the clear-sky regions of the model respond directly to the change in the cooling term, the regions dominated by moist convective plumes are insensitive to changes in cooling. Similar to previous findings from cloud-resolving models, we too find in our idealised setting that the majority of the increase in convection occurs via an increase in the areal coverage of convection, rather than its intensity. We argue that these small-scale convective processes are an upper bound on how quickly convective intensity can change to stay in equilibrium with radiative cooling.","lang":"eng"}],"type":"journal_article","supplementarymaterial":"yes","acknowledgement":"The authors gratefully acknowledge the help of Julian Renaud and Alzbeta “Bety” Pechacova. Julian went through the relevant literature on the topic in the initial stages of the study in a very thorough manner and allowed the authors to understand the various types of idealised models that have been studied and the various approaches used. Bety ran simulations and performed analysis of the outputs of several simulations, which were crucial to bringing the article to its final form.\r\n\r\nThe authors also acknowledge the input of Prof. Martin Singh (Monash University, Australia) and discussions with Gregory Dritschel, Prof. Steven Tobias, and Prof. Douglas Parker (Leeds University, United Kingdom).\r\n\r\nThis project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101034413. C. Muller gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","_id":"18605","author":[{"id":"cd100965-0804-11ed-9c55-f4878ff4e877","full_name":"Agasthya, Lokahith N","last_name":"Agasthya","first_name":"Lokahith N"},{"last_name":"Muller","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"},{"first_name":"Mathis","last_name":"Cheve","id":"c2cdb722-b15c-11ef-9e63-db902a30b40d","full_name":"Cheve, Mathis"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":151,"publication_identifier":{"issn":["0035-9009"],"eissn":["1477-870X"]},"acknowledged_ssus":[{"_id":"ScienComp"}]},{"supplementarymaterial":"no","arxiv":1,"_id":"12662","author":[{"id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","full_name":"Súkeník, Peter","first_name":"Peter","last_name":"Súkeník"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","PlanS_conform":"1","abstract":[{"text":"Modern machine learning tasks often require considering not just one but multiple objectives. For example, besides the prediction quality, this could be the efficiency, robustness or fairness of the learned models, or any of their combinations. Multi-objective learning offers a natural framework for handling such problems without having to commit to early trade-offs. Surprisingly, statistical learning theory so far offers almost no insight into the generalization properties of multi-objective learning. In this work, we make first steps to fill this gap: We establish foundational generalization bounds for the multi-objective setting as well as generalization and excess bounds for learning with scalarizations. We also provide the first theoretical analysis of the relation between the Pareto-optimal sets of the true objectives and the Pareto-optimal sets of their empirical approximations from training data. In particular, we show a surprising asymmetry: All Pareto-optimal solutions can be approximated by empirically Pareto-optimal ones, but not vice versa.","lang":"eng"}],"type":"journal_article","page":"24669–24683","publication_identifier":{"eissn":["1433-3058"],"issn":["0941-0643"]},"volume":37,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","publication":"Neural Computing and Applications","fulldoi":"https://doi.org/10.1007/s00521-024-10616-1","scopus_import":"1","article_type":"original","file":[{"creator":"dernst","checksum":"61ad4591aee16b1e02daf6c164321a42","date_created":"2025-12-30T06:39:11Z","file_size":500213,"date_updated":"2025-12-30T06:39:11Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2025_NeuralCompApplic_Sukenik.pdf","file_id":"20877","success":1}],"file_date_updated":"2025-12-30T06:39:11Z","oa":1,"department":[{"_id":"ChLa"}],"publication_status":"published","dataavailabilitystatement":"Our manuscript does not include or refer to any data sources.","day":"01","month":"10","researchdata_availability":"not applicable","has_accepted_license":"1","language":[{"iso":"eng"}],"publisher":"Springer Nature","das_tickbox":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-10-01T09:29:43Z","ddc":["004"],"date_created":"2023-02-20T08:23:06Z","oa_version":"Published Version","doi":"10.1007/s00521-024-10616-1","date_published":"2025-10-01T00:00:00Z","title":"Generalization in multi-objective machine learning","external_id":{"arxiv":["2208.13499"]},"corr_author":"1","intvolume":"        37","citation":{"ista":"Súkeník P, Lampert C. 2025. Generalization in multi-objective machine learning. Neural Computing and Applications. 37, 24669–24683.","ama":"Súkeník P, Lampert C. Generalization in multi-objective machine learning. <i>Neural Computing and Applications</i>. 2025;37:24669–24683. doi:<a href=\"https://doi.org/10.1007/s00521-024-10616-1\">10.1007/s00521-024-10616-1</a>","apa":"Súkeník, P., &#38; Lampert, C. (2025). Generalization in multi-objective machine learning. <i>Neural Computing and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00521-024-10616-1\">https://doi.org/10.1007/s00521-024-10616-1</a>","short":"P. Súkeník, C. Lampert, Neural Computing and Applications 37 (2025) 24669–24683.","chicago":"Súkeník, Peter, and Christoph Lampert. “Generalization in Multi-Objective Machine Learning.” <i>Neural Computing and Applications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00521-024-10616-1\">https://doi.org/10.1007/s00521-024-10616-1</a>.","mla":"Súkeník, Peter, and Christoph Lampert. “Generalization in Multi-Objective Machine Learning.” <i>Neural Computing and Applications</i>, vol. 37, Springer Nature, 2025, pp. 24669–24683, doi:<a href=\"https://doi.org/10.1007/s00521-024-10616-1\">10.1007/s00521-024-10616-1</a>.","ieee":"P. Súkeník and C. Lampert, “Generalization in multi-objective machine learning,” <i>Neural Computing and Applications</i>, vol. 37. Springer Nature, pp. 24669–24683, 2025."},"status":"public","quality_controlled":"1","OA_type":"hybrid","OA_place":"publisher","year":"2025"},{"date_created":"2025-01-29T13:33:47Z","oa_version":"None","project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"}],"pmid":1,"date_updated":"2026-10-01T11:03:02Z","corr_author":"1","external_id":{"isi":["001456660400001"],"pmid":["38951023"]},"title":"Tissue active matter: Integrating mechanics and signaling into dynamical models","doi":"10.1101/cshperspect.a041653","date_published":"2025-04-01T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press","language":[{"iso":"eng"}],"das_tickbox":"0","ec_funded":1,"status":"public","quality_controlled":"1","OA_type":"closed access","year":"2025","intvolume":"        17","citation":{"apa":"Brückner, D., &#38; Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>","ama":"Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>","ieee":"D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.","mla":"Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>.","chicago":"Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2025. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>.","short":"D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025).","ista":"Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653."},"publication_identifier":{"issn":["1943-0264"]},"volume":17,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18960","acknowledgement":"We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288.","author":[{"orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","first_name":"David","last_name":"Brückner"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"}],"supplementarymaterial":"no","type":"journal_article","abstract":[{"lang":"eng","text":"The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter."}],"department":[{"_id":"EdHa"}],"publication_status":"published","issue":"4","day":"01","month":"04","researchdata_availability":"no","scopus_import":"1","fulldoi":"https://doi.org/10.1101/cshperspect.a041653","article_processing_charge":"No","isi":1,"publication":"Cold Spring Harbor Perspectives in Biology","article_type":"original","article_number":"a041653"},{"abstract":[{"lang":"eng","text":"Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct."}],"type":"journal_article","supplementarymaterial":"yes","author":[{"first_name":"Martin","last_name":"Obr","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Percipalle","first_name":"Mathias","id":"4986e21c-eb97-11eb-a6c2-a4ef0b629971","full_name":"Percipalle, Mathias"},{"last_name":"Chernikova","first_name":"Darya","full_name":"Chernikova, Darya","id":"7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0"},{"full_name":"Yang, Huixin","first_name":"Huixin","last_name":"Yang"},{"first_name":"Andreas","last_name":"Thader","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pinke","first_name":"Gergely","full_name":"Pinke, Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Porley","first_name":"Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","full_name":"Porley, Dario J"},{"full_name":"Mansky, Louis M.","first_name":"Louis M.","last_name":"Mansky"},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur"}],"_id":"17884","acknowledgement":"This work was funded by the Institute of Science and Technology Austria (ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This research was also supported by the scientific service units of ISTA through resources provided by Scientific Computing, the Life Science Facility, and the EM Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775 and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P. was supported by the DOC doctoral fellowship program of the Austrian Academy of Sciences. R.A.D was supported by the National Institute of Allergy and Infectious Diseases (grant R01AI147890). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Specifically, we also want to thank A. Schlögl for computational support and J. Hansen and V. Vogt for critical comments on the manuscript. We also thank the other members of the Schur lab for helpful discussions and experimental advice.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":32,"page":"268-276","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_type":"original","oa":1,"file_date_updated":"2025-04-23T07:02:33Z","file":[{"checksum":"c641ad94afb28917b20425db676fc3ee","creator":"dernst","date_created":"2025-04-23T07:02:33Z","file_size":13724041,"date_updated":"2025-04-23T07:02:33Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2025_NatureStrucBio_Obr.pdf","file_id":"19608","success":1}],"publication":"Nature Structural & Molecular Biology","isi":1,"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41594-024-01390-8","has_accepted_license":"1","researchdata_availability":"yes","day":"01","month":"02","dataavailabilitystatement":"The EM density maps and models for the immature HTLV-1 CA-NTD lattice and representative tomograms were deposited to the EM Data Bank under accession codes EMD-17929, EMD-17930, EMD-17931, EMD-17932, EMD-17933, EMD-17934, EMD-17935, EMD-17936, EMD-17937, EMD-17938, EMD-17939, EMD-17940, EMD-17941, EMD-17942 and EMD-17943 and the PDB under accession codes 8PU6, 8PU7, 8PU8, 8PU9, 8PUA, 8PUB, 8PUC, 8PUD, 8PUE, 8PUF, 8PUG and 8PUH. PDB 1QRJ was used as starting model to derive a refined model of the HTLV-1 CA-NTD. The models used to generate Fig. 3 and Extended Data Fig. 3 were PDB 5L93 (HIV-1), PDB 5A9E (RSV), PDB 6HWI (M-PMV) and PDB 6HWW (MLV). The UniProt codes for the protein sequences used for generating Extended Data Fig. 9 were P03345 (GAG_HTL1A), P03346 (GAG_HTLV2), Q0R5R4 (GAG_HTL32), P25058 (GAG_BLVAU), P04585 (POL_HV1H2), P15832 (GAG_HV2D2), P16087 (GAG_FIVPE), P69732 (GAG_EIAVY), P03322 (GAG_RSVP), P0C776 (GAG_ALVA), P07567 (GAG_MPMV), P31622 (GAG_JSRV), P10258 (GAG_MMTVB), P03355 (POL_MLVMS), P10262 (GAG_FLV) and Q9TTC2 (GAG_KORV). Source data are provided with this paper.","publication_status":"published","department":[{"_id":"FlSc"},{"_id":"LeSa"}],"das_tickbox":"1","oaworkid":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2025-02-01T00:00:00Z","doi":"10.1038/s41594-024-01390-8","external_id":{"oaworkid":["W4402316284"],"pmid":["39242978"],"isi":["001306564000001"]},"title":"Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice","APC_amount":"12348 EUR","corr_author":"1","ddc":["570"],"pmid":1,"date_updated":"2026-10-01T11:23:34Z","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"},{"_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","grant_number":"25762"}],"date_created":"2024-09-08T10:29:06Z","oa_version":"Published Version","citation":{"chicago":"Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick, and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>.","short":"M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural &#38; Molecular Biology 32 (2025) 268–276.","ieee":"M. Obr <i>et al.</i>, “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 268–276, 2025.","mla":"Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 268–76, doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>.","ama":"Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:268-276. doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>","apa":"Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., … Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>","ista":"Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural &#38; Molecular Biology. 32, 268–276."},"intvolume":"        32","year":"2025","OA_place":"publisher","OA_type":"hybrid","quality_controlled":"1","status":"public"},{"OA_type":"gold","year":"2025","OA_place":"publisher","quality_controlled":"1","status":"public","citation":{"ista":"Yao D, Rancati D, Cadei R, Fumero M, Locatello F. 2025. Unifying causal representation learning with the invariance principle. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Yao D, Rancati D, Cadei R, Fumero M, Locatello F. Unifying causal representation learning with the invariance principle. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025.","apa":"Yao, D., Rancati, D., Cadei, R., Fumero, M., &#38; Locatello, F. (2025). Unifying causal representation learning with the invariance principle. In <i>13th International Conference on Learning Representations</i>. Singapore: ICLR.","chicago":"Yao, Dingling, Dario Rancati, Riccardo Cadei, Marco Fumero, and Francesco Locatello. “Unifying Causal Representation Learning with the Invariance Principle.” In <i>13th International Conference on Learning Representations</i>. ICLR, 2025.","short":"D. Yao, D. Rancati, R. Cadei, M. Fumero, F. Locatello, in:, 13th International Conference on Learning Representations, ICLR, 2025.","mla":"Yao, Dingling, et al. “Unifying Causal Representation Learning with the Invariance Principle.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025.","ieee":"D. Yao, D. Rancati, R. Cadei, M. Fumero, and F. Locatello, “Unifying causal representation learning with the invariance principle,” in <i>13th International Conference on Learning Representations</i>, Singapore, 2025."},"date_published":"2025-01-22T00:00:00Z","corr_author":"1","title":"Unifying causal representation learning with the invariance principle","external_id":{"arxiv":["2409.02772"]},"date_updated":"2026-10-02T08:49:53Z","ddc":["000"],"date_created":"2025-02-05T09:23:25Z","oa_version":"Published Version","language":[{"iso":"eng"}],"publisher":"ICLR","das_tickbox":"0","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"start_date":"2025-04-24","location":"Singapore","name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28"},"month":"01","day":"22","has_accepted_license":"1","researchdata_availability":"no","publication_status":"published","department":[{"_id":"FrLo"}],"file_date_updated":"2026-01-27T12:43:25Z","file":[{"relation":"main_file","file_name":"4356_Unifying_Causal_Represent (1).pdf","success":1,"file_id":"21048","checksum":"c4b5a4a644228c6d1b0283e1368bce9e","creator":"flocatel","file_size":877014,"date_updated":"2026-01-27T12:43:25Z","content_type":"application/pdf","access_level":"open_access","date_created":"2026-01-27T12:43:25Z"}],"oa":1,"article_processing_charge":"No","publication":"13th International Conference on Learning Representations","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Causal representation learning aims at recovering latent causal variables from high-dimensional observations to solve causal downstream tasks, such as predicting the effect of new interventions or more robust classification. A plethora of methods have been developed, each tackling carefully crafted problem settings that lead to different types of identifiability. The folklore is that these different settings are important, as they are often linked to different rungs of Pearl's causal hierarchy, although not all neatly fit. Our main contribution is to show that many existing causal representation learning approaches methodologically align the representation to known data symmetries. Identification of the variables is guided by equivalence classes across different \"data pockets\" that are not necessarily causal. This result suggests important implications, allowing us to unify many existing approaches in a single method that can mix and match different assumptions, including non-causal ones, based on the invariances relevant to our application. It also significantly benefits applicability, which we demonstrate by improving treatment effect estimation on real-world high-dimensional ecological data. Overall, this paper clarifies the role of causality assumptions in the discovery of causal variables and shifts the focus to preserving data symmetries.","lang":"eng"}],"type":"conference","supplementarymaterial":"no","arxiv":1,"_id":"19010","acknowledgement":"We thank Jiaqi Zhang, Francesco Montagna, David Lopez-Paz, Kartik Ahuja, Thomas Kipf, Sara\r\nMagliacane, Julius von Kügelgen, Kun Zhang, and Bernhard Schölkopf for extremely helpful discussion. Riccardo Cadei was supported by a Google Research Scholar Award to Francesco Locatello. We acknowledge the Third Bellairs Workshop on Causal Representation Learning held at the Bellairs Research Institute, February 9/16, 2024, and a debate on the difference between interventions and counterfactuals in disentanglement and CRL that took place during Dhanya Sridhar’s lecture, which motivated us to significantly broaden the scope of the paper. We thank Dhanya and all participants of the workshop.","author":[{"full_name":"Yao, Dingling","id":"d3e02e50-48a8-11ee-8f62-c108061797fa","last_name":"Yao","first_name":"Dingling"},{"first_name":"Dario","last_name":"Rancati","id":"feb58f2e-72ef-11ef-b75a-8f0894539cd0","full_name":"Rancati, Dario"},{"first_name":"Riccardo","last_name":"Cadei","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b","full_name":"Cadei, Riccardo"},{"full_name":"Fumero, Marco","id":"1c1593eb-393f-11ef-bb8e-ab4f1e979650","last_name":"Fumero","first_name":"Marco"},{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"}]},{"oa":1,"file_date_updated":"2025-07-03T06:55:20Z","file":[{"date_created":"2025-07-03T06:55:20Z","date_updated":"2025-07-03T06:55:20Z","file_size":133201290,"content_type":"application/pdf","access_level":"open_access","checksum":"ebc99d7108e728f46db0a009292675ef","creator":"dernst","file_id":"19959","success":1,"relation":"main_file","file_name":"2025_Nature_Tavakoli.pdf"}],"article_type":"original","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41586-025-08985-1","publication":"Nature","isi":1,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"12","month":"06","department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"GaNo"}],"publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner."}],"_id":"19704","acknowledgement":"We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).","PlanS_conform":"1","author":[{"first_name":"Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"full_name":"Januszewski, Michał","first_name":"Michał","last_name":"Januszewski"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","full_name":"Vistunou, Vitali","first_name":"Vitali","last_name":"Vistunou"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas"},{"orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob","first_name":"Jakob","last_name":"Vorlaufer"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger"},{"full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira","first_name":"Bárbara"},{"full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"},{"last_name":"Jain","first_name":"Viren","full_name":"Jain, Viren"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"volume":642,"page":"398-410","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"citation":{"ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp. 398–410, doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>.","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410, 2025.","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>."},"intvolume":"       642","year":"2025","OA_place":"publisher","OA_type":"hybrid","quality_controlled":"1","status":"public","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"publisher":"Springer Nature","related_material":{"record":[{"id":"18697","relation":"research_data","status":"public"},{"status":"public","id":"18677","relation":"earlier_version"}],"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/"}]},"title":"Light-microscopy-based connectomic reconstruction of mammalian brain tissue","external_id":{"pmid":["40335689"],"isi":["001483477000001"]},"corr_author":"1","date_published":"2025-06-12T00:00:00Z","doi":"10.1038/s41586-025-08985-1","project":[{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"date_created":"2025-05-18T22:02:51Z","oa_version":"Published Version","ddc":["570"],"date_updated":"2026-10-02T09:59:44Z","pmid":1},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"95","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","abstract":[{"text":"\tThis thesis is organized into two parts, each comprising two chapters: Chapter 1 and 2 offer models for the evolution of vaccine resistance in response to diverse vaccination strategies. Chapter 3 and 4 review the statistics of records, their connection to models of innovation and an application to the cultural evolution of sports.\r\n\tIn chapter 1 we present a modelling study from 2021 on the evolution of SARS-CoV-2. At that time the vaccine-resistant Omicron variant had not yet evolved. In our model we consider a population that is becoming vaccinated over time, while a pathogen is spreading in the population and eventually becoming resistant to the vaccine. We explore effective pharmaceutical and non-pharmaceutical interventions to prevent the emergence of vaccine resistance. \r\n\tIn chapter 2 we model a particular set of complex vaccination strategies, mosaic and pyramid vaccination, where an immunologically diverse portfolio of vaccines is considered. We find that a bet-hatching strategy, in which vaccine types are distributed in the population, is effective at hindering the evolution of vaccine resistance if mutation rates are high. \r\n\tIn chapter 3 we switch gears and present a review on the statistics of records. We highlight similarities and analogies to other models in the fields of statistical physics, evolution and innovation. This offers interesting complimentary perspectives on well-known models. \r\n\tIn chapter 4 we apply models of record statistics and innovation to study cultural evolution in sport. We propose a model of sport evolution that combines deterministic improvements in performance and stochastic bursts of improvements due to innovation. ","lang":"eng"}],"doi_confirm":"1","_id":"20811","author":[{"last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon"}],"month":"12","day":"15","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GaTk"},{"_id":"FyKo"}],"file":[{"file_id":"20831","success":1,"file_name":"2025_Rella_Simon_Thesis.pdf","relation":"main_file","date_created":"2025-12-16T21:49:52Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2025-12-16T21:49:52Z","file_size":29019662,"checksum":"a0bd7a585720e60df284101b8afdf6bb","creator":"srella"},{"file_name":"2025_Rella_Simon_Thesis_Sourcefiles.zip","relation":"source_file","file_id":"20832","checksum":"b8b3a90932ae1d96d307838710f46e32","creator":"srella","date_created":"2025-12-16T21:52:19Z","content_type":"application/zip","access_level":"open_access","date_updated":"2025-12-16T21:52:19Z","file_size":42094025}],"file_date_updated":"2025-12-16T21:52:19Z","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-20811","article_processing_charge":"No","corr_author":"1","title":"Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation","doi":"10.15479/AT-ISTA-20811","date_published":"2025-12-15T00:00:00Z","date_created":"2025-12-12T14:39:56Z","oa_version":"Published Version","date_updated":"2026-10-02T10:12:19Z","supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"}],"ddc":["616","576","614","519"],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"part_of_dissertation","id":"9905","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18307"}]},"degree_awarded":"PhD","OA_place":"publisher","year":"2025","status":"public","citation":{"short":"S. Rella, Adaptive Processes in Biology and Culture: Models of Evolving Vaccine Resistance and the Record Statistics of Innovation, Institute of Science and Technology Austria, 2025.","chicago":"Rella, Simon. “Adaptive Processes in Biology and Culture: Models of Evolving Vaccine Resistance and the Record Statistics of Innovation.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20811\">https://doi.org/10.15479/AT-ISTA-20811</a>.","mla":"Rella, Simon. <i>Adaptive Processes in Biology and Culture: Models of Evolving Vaccine Resistance and the Record Statistics of Innovation</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20811\">10.15479/AT-ISTA-20811</a>.","ieee":"S. Rella, “Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation,” Institute of Science and Technology Austria, 2025.","ama":"Rella S. Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20811\">10.15479/AT-ISTA-20811</a>","apa":"Rella, S. (2025). <i>Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20811\">https://doi.org/10.15479/AT-ISTA-20811</a>","ista":"Rella S. 2025. Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"]},{"citation":{"apa":"Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (2025). Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-57252-4\">https://doi.org/10.1038/s41467-025-57252-4</a>","ama":"Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-57252-4\">10.1038/s41467-025-57252-4</a>","mla":"Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” <i>Nature Communications</i>, vol. 16, 2103, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-57252-4\">10.1038/s41467-025-57252-4</a>.","ieee":"M. Janik <i>et al.</i>, “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","short":"M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A. Garzón Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, Nature Communications 16 (2025).","chicago":"Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-57252-4\">https://doi.org/10.1038/s41467-025-57252-4</a>.","ista":"Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Garzón Manjón A, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. 2025. Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors. Nature Communications. 16, 2103."},"DOAJ_listed":"1","intvolume":"        16","OA_place":"publisher","year":"2025","OA_type":"gold","status":"public","quality_controlled":"1","ec_funded":1,"language":[{"iso":"eng"}],"publisher":"Springer Nature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"18886","relation":"research_data","status":"public"},{"id":"18144","relation":"earlier_version","status":"public"}]},"date_published":"2025-03-01T00:00:00Z","doi":"10.1038/s41467-025-57252-4","title":"Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors","external_id":{"pmid":["40025007"],"isi":["001434774800001"],"arxiv":["2407.03079"]},"corr_author":"1","APC_amount":"7068 EUR","ddc":["530"],"date_updated":"2026-10-02T11:05:09Z","pmid":1,"project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology","grant_number":"101069515"},{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"date_created":"2025-03-16T23:01:23Z","oa_version":"Published Version","article_number":"2103","article_type":"original","oa":1,"file":[{"checksum":"a9383dd978ca2c50b7dded6c0bb2cd49","creator":"dernst","date_updated":"2025-03-17T10:53:32Z","file_size":6364878,"access_level":"open_access","content_type":"application/pdf","date_created":"2025-03-17T10:53:32Z","relation":"main_file","file_name":"2025_NatureComm_Janik.pdf","success":1,"file_id":"19415"}],"file_date_updated":"2025-03-17T10:53:32Z","isi":1,"publication":"Nature Communications","article_processing_charge":"Yes","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41467-025-57252-4","has_accepted_license":"1","day":"01","month":"03","publication_status":"published","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"M-Shop"}],"abstract":[{"text":"High kinetic inductance superconductors are gaining increasing interest for the realisation of qubits, amplifiers and detectors. Moreover, thanks to their high impedance, quantum buses made of such materials enable large zero-point fluctuations of the voltage, boosting the coupling rates to spin and charge qubits. However, fully exploiting the potential of disordered or granular superconductors is challenging, as their inductance and, therefore, impedance at high values are difficult to control. Here, we report a reproducible fabrication of granular aluminium resonators by developing a wireless ohmmeter, which allows in situ measurements during film deposition and, therefore, control of the kinetic inductance of granular aluminium films. Reproducible fabrication of circuits with impedances (inductances) exceeding 13 kΩ (1 nH per square) is now possible. By integrating a 7.9 kΩ resonator with a germanium double quantum dot, we demonstrate strong charge-photon coupling with a rate of gc/2π = 566 ± 2 MHz. This broadly applicable method opens the path for novel qubits and high-fidelity, long-distance two-qubit gates.","lang":"eng"}],"type":"journal_article","_id":"19401","author":[{"first_name":"Marian","last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","orcid":"0009-0003-9037-8831"},{"first_name":"Kevin Etienne Robert","last_name":"Roux","id":"53f93ea2-803f-11ed-ab7e-b283135794ef","full_name":"Roux, Kevin Etienne Robert"},{"full_name":"Borja Espinosa, Carla N","id":"18777c01-896a-11ed-bdf8-e4851dc07d16","last_name":"Borja Espinosa","first_name":"Carla N"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi","first_name":"Oliver"},{"id":"160D87FA-96B5-11E9-BF77-7626E6697425","full_name":"Baghdadi, Abdulhamid","first_name":"Abdulhamid","last_name":"Baghdadi"},{"id":"38756BB2-F248-11E8-B48F-1D18A9856A87","full_name":"Adletzberger, Thomas","first_name":"Thomas","last_name":"Adletzberger"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"last_name":"Garzón Manjón","first_name":"Alba","full_name":"Garzón Manjón, Alba"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"first_name":"Ioan M.","last_name":"Pop","full_name":"Pop, Ioan M."},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. We thank Simon Robson for proofreading the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the HORIZON-RIA 101069515 project. This research was funded in whole or in part by the Austrian Science Fund (FWF) https://doi.org/10.55776/P32235, https://doi.org/10.55776/I5060 and https://doi.org/10.55776/P36507. For Open Access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. M.J. acknowledges funding from FellowQUTE 2024-01. K.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. I.M.P. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission - NextGenerationEU (Regulation EU 2020/2094), through CSIC’s Quantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa programme from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD programme. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors acknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Centre at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM60.","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":16,"publication_identifier":{"eissn":["2041-1723"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"title":"Research data for publication 'Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors'","corr_author":"1","date_published":"2025-01-27T00:00:00Z","doi":"10.15479/AT:ISTA:18886","project":[{"grant_number":"101069515","name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices"},{"grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"}],"oa_version":"Published Version","date_created":"2025-01-27T09:48:44Z","ddc":["530"],"date_updated":"2026-10-02T11:05:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"19401"},{"status":"public","relation":"used_in_publication","id":"18144"}]},"OA_place":"repository","year":"2025","OA_type":"gold","status":"public","citation":{"ama":"Janik M. Research data for publication “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18886\">10.15479/AT:ISTA:18886</a>","apa":"Janik, M. (2025). Research data for publication “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18886\">https://doi.org/10.15479/AT:ISTA:18886</a>","chicago":"Janik, Marian. “Research Data for Publication ‘Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:18886\">https://doi.org/10.15479/AT:ISTA:18886</a>.","short":"M. Janik, (2025).","mla":"Janik, Marian. <i>Research Data for Publication “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18886\">10.15479/AT:ISTA:18886</a>.","ieee":"M. Janik, “Research data for publication ‘Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors.’” Institute of Science and Technology Austria, 2025.","ista":"Janik M. 2025. Research data for publication ‘Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18886\">10.15479/AT:ISTA:18886</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"contributor":[{"contributor_type":"researcher","last_name":"Roux","first_name":"Kevin Etienne Robert","id":"53f93ea2-803f-11ed-ab7e-b283135794ef"},{"contributor_type":"researcher","last_name":"Borja Espinosa","first_name":"Carla N","id":"18777c01-896a-11ed-bdf8-e4851dc07d16"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","contributor_type":"researcher","last_name":"Sagi","first_name":"Oliver"},{"contributor_type":"researcher","first_name":"Abdulhamid","last_name":"Baghdadi","id":"160D87FA-96B5-11E9-BF77-7626E6697425"},{"last_name":"Adletzberger","first_name":"Thomas","contributor_type":"researcher","id":"38756BB2-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","last_name":"Calcaterra","first_name":"Stefano"},{"contributor_type":"researcher","last_name":"Botifoll","first_name":"Marc"},{"last_name":"Manjón","first_name":"Alba Garzón","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Jordi","last_name":"Arbiol"},{"last_name":"Chrastina","first_name":"Daniel","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Isella","first_name":"Giovanni"},{"contributor_type":"researcher","last_name":"Pop","first_name":"Ioan M."},{"first_name":"Georgios","last_name":"Katsaros","contributor_type":"researcher","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","abstract":[{"text":"Research Data for publication 'Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors'","lang":"eng"}],"acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. We thank Simon Robson for proofreading the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the HORIZON-RIA 101069515 project. This research was funded in whole or in part by the Austrian Science Fund (FWF) DOI:10.55776/P32235, DOI:10.55776/I5060 and DOI:10.55776/P36507. For Open Access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. M.J. acknowledges funding from FellowQUTE 2024-01. I.M.P. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG – German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC's Quantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors acknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM.","_id":"18886","author":[{"last_name":"Janik","first_name":"Marian","orcid":"0009-0003-9037-8831","full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","month":"01","day":"27","department":[{"_id":"GeKa"},{"_id":"GradSch"}],"oa":1,"file":[{"relation":"main_file","file_name":"readme.txt","success":1,"file_id":"18893","checksum":"977dffed4bec3c7d6315aa1cbd19e8a7","creator":"arashid","date_updated":"2025-01-27T11:27:30Z","file_size":1017,"content_type":"text/plain","access_level":"open_access","date_created":"2025-01-27T11:27:30Z"},{"file_name":"research_data.zip","relation":"main_file","success":1,"file_id":"18894","checksum":"7ab5e3e65ddf59bbf3622ace8a0cda1c","creator":"arashid","access_level":"open_access","content_type":"application/zip","file_size":33815056,"date_updated":"2025-01-27T11:27:35Z","date_created":"2025-01-27T11:27:35Z"}],"file_date_updated":"2025-01-27T11:27:35Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:18886","article_processing_charge":"No"},{"status":"public","ec_funded":1,"degree_awarded":"PhD","OA_place":"publisher","year":"2025","alternative_title":["ISTA Thesis"],"citation":{"ama":"Bhargava M. Design and control of deformable structures: From PCB lighting displays to elastomer robots. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20276\">10.15479/AT-ISTA-20276</a>","apa":"Bhargava, M. (2025). <i>Design and control of deformable structures: From PCB lighting displays to elastomer robots</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20276\">https://doi.org/10.15479/AT-ISTA-20276</a>","short":"M. Bhargava, Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots, Institute of Science and Technology Austria, 2025.","chicago":"Bhargava, Manas. “Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20276\">https://doi.org/10.15479/AT-ISTA-20276</a>.","mla":"Bhargava, Manas. <i>Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20276\">10.15479/AT-ISTA-20276</a>.","ieee":"M. Bhargava, “Design and control of deformable structures: From PCB lighting displays to elastomer robots,” Institute of Science and Technology Austria, 2025.","ista":"Bhargava M. 2025. Design and control of deformable structures: From PCB lighting displays to elastomer robots. Institute of Science and Technology Austria."},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767"}],"date_created":"2025-09-02T14:48:39Z","oa_version":"Published Version","ddc":["000"],"date_updated":"2026-10-02T11:13:08Z","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"corr_author":"1","title":"Design and control of deformable structures: From PCB lighting displays to elastomer robots","date_published":"2025-09-02T00:00:00Z","doi":"10.15479/AT-ISTA-20276","related_material":{"record":[{"id":"13049","relation":"part_of_dissertation","status":"public"},{"id":"20286","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18565","status":"public"}]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"publication_status":"published","has_accepted_license":"1","month":"09","day":"02","fulldoi":"https://doi.org/10.15479/AT-ISTA-20276","article_processing_charge":"No","oa":1,"file_date_updated":"2025-09-04T09:22:29Z","file":[{"relation":"main_file","file_name":"2025-Bhargava-Manas-Thesis.pdf","file_id":"20284","success":1,"checksum":"5baf8ca46c86a94fc8380ff1007aabd4","creator":"mbhargav","date_created":"2025-09-03T10:40:52Z","date_updated":"2025-09-03T10:40:52Z","file_size":161436245,"content_type":"application/pdf","access_level":"open_access"},{"date_updated":"2025-09-04T09:22:29Z","file_size":198831315,"access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2025-09-03T13:18:05Z","checksum":"66878fafbc0074f88ddd18f24a9fc647","creator":"mbhargav","file_id":"20285","relation":"source_file","file_name":"manas_phd_thesis_source_files.zip"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-065-7"]},"page":"96","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"Financial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design\r\nand Modeling that I gratefully acknowledge.\r\n","_id":"20276","author":[{"id":"FF8FA64C-AA6A-11E9-99AD-50D4E5697425","full_name":"Bhargava, Manas","orcid":"0009-0007-6138-6890","first_name":"Manas","last_name":"Bhargava"}],"doi_confirm":"1","type":"dissertation","abstract":[{"lang":"eng","text":"Complex 3D shapes can be created by morphing flat 2D configurations. Such deformations\r\neither preserve the intrinsic material geometry (e.g., folding paper) or modify it through\r\nlocalized contraction. Once transformed, the 3D shape can be further controlled to achieve a\r\ntarget functionality. A key challenge is to take the material specifications and the actuation\r\nprocess as input to automatically design the target 3D shape and its functionality. This thesis\r\npresents two novel computational pipelines for the design and control of shape-morphing\r\nstructures used to create functional prototypes.\r\nThe first pipeline borrows from the art of origami to fold paper into intricate shapes and\r\napplies this principle to make 3D lighting displays. We introduce, PCBend a computational\r\ndesign approach that covers a surface with individually addressable RGB LEDs, effectively\r\nforming a low-resolution surface by folding rigid printed circuit boards (PCBs). We optimize\r\ncut patterns on PCBs to act as hinges and co-design LED placement, circuit routing, and\r\nfabrication constraints to produce PCB blueprints. The PCBs are fabricated using automated\r\nstandard manufacturing services with LEDs embedded on them. Finally, the fabricated PCBs\r\nare cut along the contour and folded onto a 3D-printed support. The 3D lighting display is\r\nthen controlled to display complex surface light patterns.\r\nCreating 3D shapes through folding is only possible if their planar configuration, called ”unfolding” exists without any distortion or overlap. Existing methods often permit distortion\r\nor require multiple patches, which are unsuitable for fabrication pipelines that rely on folding\r\nnon-stretchable materials. We reinforce such fabrication pipelines by providing a geometric\r\nrelaxation to the problem, where the input shape is modified to admit overlap-free unfolding.\r\nThe second fabrication pipeline extends shape morphing to soft robotics by emulating nature’s\r\nblueprint of distributed actuation. Inspired by vertebrates, we build musculoskeletal robots\r\nusing modular active actuators, employing Liquid Crystal Elastomers (LCEs) as shrinkable\r\nartificial muscles integrated with 3D-printed bones. The chemical composition of LCEs is\r\naltered to enable untethered actuation through infrared radiation, allowing active control of\r\nindividual muscles and their corresponding bones. The combined motion of individual bones\r\ndefines the robot’s overall shape and functionality. Our proposed system significantly expands\r\nboth the design and control spaces of soft robots, which we harness using our computational\r\ndesign tools. We build several physical robots that exhibit complex shape morphing and varied\r\nterrain navigation, showcasing the versatility of our pipeline.\r\nThis thesis explores applications ranging from intricate light patterns displayed on 3D shapes\r\nformed by folding rigid PCBs to untethered robots that use contractile muscles to exhibit\r\nshape morphing and locomotion. Through these examples, the thesis highlights how computational design and distributed actuation, integrated with novel materials, can transform\r\npassive structures into functional prototypes."}]},{"type":"journal_article","abstract":[{"text":"We present a computational approach for unfolding 3D shapes isometrically into the plane as a single patch without overlapping triangles. This is a hard, sometimes impossible, problem, which existing methods are forced to soften by allowing for map distortions or multiple patches. Instead, we propose a geometric relaxation of the problem: We modify the input shape until it admits an overlap‐free unfolding. We achieve this by locally displacing vertices and collapsing edges, guided by the unfolding process. We validate our algorithm quantitatively and qualitatively on a large dataset of complex shapes and show its proficiency by fabricating real shapes from paper.","lang":"eng"}],"arxiv":1,"acknowledgement":"Researchers from INRIA received support from the DORNELL Inria Challenge. Silvia Sellán acknowledges support from NSERC Vanier Doctoral Scholarship and an MIT SoE Postdoctoral Fellowship for Engineering Excellence.","_id":"18565","author":[{"last_name":"Bhargava","first_name":"Manas","orcid":"0009-0007-6138-6890","full_name":"Bhargava, Manas","id":"FF8FA64C-AA6A-11E9-99AD-50D4E5697425"},{"first_name":"Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille"},{"full_name":"Freire, M.","first_name":"M.","last_name":"Freire"},{"first_name":"P. A.","last_name":"Hugron","full_name":"Hugron, P. A."},{"full_name":"Lefebvre, S.","last_name":"Lefebvre","first_name":"S."},{"full_name":"Sellán, S.","last_name":"Sellán","first_name":"S."},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"volume":44,"file_date_updated":"2025-04-16T09:06:45Z","file":[{"file_name":"Mesh_Simplification_For_Unfolding_cgf_submission_supplemental_video.mp4","relation":"main_file","success":1,"file_id":"18567","checksum":"34acdd9bfbe43f00eb6c7656afef3ac6","creator":"mbhargav","date_created":"2024-11-19T09:23:20Z","content_type":"video/mp4","access_level":"open_access","date_updated":"2024-11-19T09:23:20Z","file_size":36999751},{"file_name":"2025_CompGraphicsForum_Bhargava.pdf","relation":"main_file","success":1,"file_id":"19576","creator":"dernst","checksum":"efb06b01bae37f470954601bc004374d","date_created":"2025-04-16T09:06:45Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-04-16T09:06:45Z","file_size":5188265}],"oa":1,"article_type":"original","article_number":"e15269","scopus_import":"1","fulldoi":"https://doi.org/10.1111/cgf.15269","article_processing_charge":"Yes (via OA deal)","publication":"Computer Graphics Forum","isi":1,"month":"02","day":"01","researchdata_availability":"no","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"issue":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"publisher":"Wiley","das_tickbox":"0","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20276"}]},"corr_author":"1","external_id":{"isi":["001357046100001"],"arxiv":["2408.06944"]},"title":"Mesh simplification for unfolding","doi":"10.1111/cgf.15269","date_published":"2025-02-01T00:00:00Z","date_created":"2024-11-19T09:14:32Z","oa_version":"Published Version","keyword":["fabrication","single patch unfolding","mesh simplification"],"date_updated":"2026-10-02T11:13:08Z","ddc":["006"],"citation":{"ista":"Bhargava M, Schreck C, Freire M, Hugron PA, Lefebvre S, Sellán S, Bickel B. 2025. Mesh simplification for unfolding. Computer Graphics Forum. 44(1), e15269.","apa":"Bhargava, M., Schreck, C., Freire, M., Hugron, P. A., Lefebvre, S., Sellán, S., &#38; Bickel, B. (2025). Mesh simplification for unfolding. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.15269\">https://doi.org/10.1111/cgf.15269</a>","ama":"Bhargava M, Schreck C, Freire M, et al. Mesh simplification for unfolding. <i>Computer Graphics Forum</i>. 2025;44(1). doi:<a href=\"https://doi.org/10.1111/cgf.15269\">10.1111/cgf.15269</a>","ieee":"M. Bhargava <i>et al.</i>, “Mesh simplification for unfolding,” <i>Computer Graphics Forum</i>, vol. 44, no. 1. Wiley, 2025.","mla":"Bhargava, Manas, et al. “Mesh Simplification for Unfolding.” <i>Computer Graphics Forum</i>, vol. 44, no. 1, e15269, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/cgf.15269\">10.1111/cgf.15269</a>.","chicago":"Bhargava, Manas, Camille Schreck, M. Freire, P. A. Hugron, S. Lefebvre, S. Sellán, and Bernd Bickel. “Mesh Simplification for Unfolding.” <i>Computer Graphics Forum</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/cgf.15269\">https://doi.org/10.1111/cgf.15269</a>.","short":"M. Bhargava, C. Schreck, M. Freire, P.A. Hugron, S. Lefebvre, S. Sellán, B. Bickel, Computer Graphics Forum 44 (2025)."},"intvolume":"        44","OA_type":"hybrid","year":"2025","OA_place":"publisher","quality_controlled":"1","status":"public"},{"_id":"19759","author":[{"id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","first_name":"Bernd","last_name":"Prach"}],"doi_confirm":"1","abstract":[{"text":"Despite generating remarkable results in various computer vision tasks, deep learning comes\r\nwith some surprising shortcomings. For example, tiny perturbations, often imperceptible to\r\nthe human eye, can completely change the predictions of image classifiers. Despite a decade\r\nof research, the field has made limited progress in developing image classifiers that are both\r\naccurate and robust. This thesis aims to address this gap.\r\nAs our first contribution, we aim to simplify the process of training certifiably robust image\r\nclassifiers. We do this by designing a convolutional layer that does not require executing an\r\niterative procedure in every forward pass, but relies on an explicit bound instead. We also\r\npropose a loss function that allows optimizing for a particular margin more precisely.\r\nNext, we provide an overview and comparison of various methods that create robust image\r\nclassifiers by constraining the Lipschitz constant. This is important since generally longer\r\ntraining times and more parameters improve the performance of robust classifiers, making it\r\nchallenging to determine the most practical and effective methods from existing literature.\r\nIn 1-Lipschitz classification, the performance of current methods is still much worse than what\r\nwe expect on the simple tasks we consider. Therefore, we next investigate potential causes of\r\nthis shortcoming. We first consider the role of the activation function. We prove a theoretical\r\nshortcoming of the commonly used activation function, and provide an alternative without it.\r\nHowever this theoretical improvement does barely translate to the empirical performance of\r\nrobust classifiers, suggesting a different bottleneck.\r\nTherefore, in the final chapter, we study how the performance depends on the amount of\r\ntraining data. We prove that in the worst case, we might require far more data to train a\r\nrobust classifier compared to a normal one. We furthermore find that the amount of training\r\ndata is a key determinant of the performance current methods achieve on popular datasets.\r\nAdditionally, we show that linear subspaces exist with tiny data variance, and yet we can\r\nstill train very accurate classifiers after projecting into those subspaces. This shows that on\r\nthe datasets considered, enforcing robustness in classification makes the task strictly more\r\nchallenging.\r\n\r\n","lang":"eng"}],"publisher_comment":"In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink.  If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"page":"84","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/10.15479/at-ista-19759","oa":1,"file":[{"file_name":"ThesisFinal.pdf","relation":"main_file","file_id":"19829","checksum":"e5108e759014e2a9020c973c778fafc9","creator":"bprach","date_created":"2025-06-10T18:11:05Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2025-06-10T18:11:05Z","file_size":3578077},{"relation":"source_file","file_name":"ThesisFinal.zip","file_id":"19830","creator":"bprach","checksum":"51bf6c11fb6d8a9f8010b458c600a83f","file_size":74894357,"date_updated":"2025-06-10T18:14:03Z","content_type":"application/x-zip-compressed","access_level":"closed","date_created":"2025-06-10T18:14:03Z"}],"file_date_updated":"2025-06-10T18:14:03Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publication_status":"published","has_accepted_license":"1","month":"05","day":"30","related_material":{"record":[{"status":"public","id":"15039","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11839","status":"public"},{"id":"18874","relation":"part_of_dissertation","status":"public"},{"id":"17426","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","ddc":["000"],"supervisor":[{"first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"date_updated":"2026-10-02T11:16:04Z","date_created":"2025-05-28T16:20:48Z","oa_version":"Published Version","date_published":"2025-05-30T00:00:00Z","doi":"10.15479/10.15479/at-ista-19759","corr_author":"1","title":"Robust image classification with 1-Lipschitz networks","alternative_title":["ISTA Thesis"],"citation":{"ama":"Prach B. Robust image classification with 1-Lipschitz networks. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">10.15479/10.15479/at-ista-19759</a>","apa":"Prach, B. (2025). <i>Robust image classification with 1-Lipschitz networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">https://doi.org/10.15479/10.15479/at-ista-19759</a>","short":"B. Prach, Robust Image Classification with 1-Lipschitz Networks, Institute of Science and Technology Austria, 2025.","chicago":"Prach, Bernd. “Robust Image Classification with 1-Lipschitz Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">https://doi.org/10.15479/10.15479/at-ista-19759</a>.","mla":"Prach, Bernd. <i>Robust Image Classification with 1-Lipschitz Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/at-ista-19759\">10.15479/10.15479/at-ista-19759</a>.","ieee":"B. Prach, “Robust image classification with 1-Lipschitz networks,” Institute of Science and Technology Austria, 2025.","ista":"Prach B. 2025. Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria."},"status":"public","OA_place":"publisher","year":"2025","degree_awarded":"PhD"}]