[{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"day":"11","OA_type":"gold","external_id":{"pmid":["41381452"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-05-20T08:10:18Z","publisher":"Springer Nature","ddc":["570"],"has_accepted_license":"1","author":[{"full_name":"Artan, Murat","last_name":"Artan","orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat"},{"id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","first_name":"Hanna","full_name":"Schön, Hanna","last_name":"Schön"},{"last_name":"De Bono","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"_id":"20929","APC_amount":"7068 EUR","file_date_updated":"2026-01-05T10:58:28Z","oa":1,"corr_author":"1","quality_controlled":"1","PlanS_conform":"1","DOAJ_listed":"1","publication_status":"published","article_number":"11355","publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"title":"Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins","intvolume":"        16","year":"2025","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, and the Mass Spec Facility at the Max Perutz Labs, notably WeiQiang Chen and Markus Hartl, for invaluable discussions and comments on mass spec analyses of worm samples. All LC-MS/MS analyses were performed on instruments of the Vienna BioCenter Core Facilities (VBCF). Microscopy was supported by the Scientific Services Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF). We are grateful to Dr. Geraldine Seydoux (Johns Hopkins University) for worm strains and plasmids, and Dr. Seung-Jae V. Lee (KAIST) for RNAi clones. We are grateful to Ekaterina Lashmanova for designing the daf-16::TbID::mNG::3xFLAG knock-in construct and for her outstanding support in the lab. This work was supported by a Wellcome Investigator Award (209504/A/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","type":"journal_article","publication":"Nature Communications","date_published":"2025-12-11T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","doi":"10.1038/s41467-025-66409-0","citation":{"ieee":"M. Artan, H. Schön, and M. de Bono, “Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ista":"Artan M, Schön H, de Bono M. 2025. Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. Nature Communications. 16, 11355.","mla":"Artan, Murat, et al. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory Proteins.” <i>Nature Communications</i>, vol. 16, 11355, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-66409-0\">10.1038/s41467-025-66409-0</a>.","apa":"Artan, M., Schön, H., &#38; de Bono, M. (2025). Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-66409-0\">https://doi.org/10.1038/s41467-025-66409-0</a>","chicago":"Artan, Murat, Hanna Schön, and Mario de Bono. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory Proteins.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-66409-0\">https://doi.org/10.1038/s41467-025-66409-0</a>.","ama":"Artan M, Schön H, de Bono M. Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-66409-0\">10.1038/s41467-025-66409-0</a>","short":"M. Artan, H. Schön, M. de Bono, Nature Communications 16 (2025)."},"acknowledged_ssus":[{"_id":"Bio"}],"OA_place":"publisher","file":[{"file_name":"2025_NatureComm_Artan.pdf","file_size":1642352,"date_updated":"2026-01-05T10:58:28Z","content_type":"application/pdf","checksum":"748e2e003b878b85b6048d51621d6aae","success":1,"file_id":"20941","relation":"main_file","creator":"dernst","date_created":"2026-01-05T10:58:28Z","access_level":"open_access"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"article_type":"original","date_created":"2026-01-04T23:01:34Z","department":[{"_id":"MaDe"}],"month":"12","abstract":[{"text":"Insulin/insulin-like growth factor signaling inhibits FOXO transcription factors to control development, homeostasis, and aging. Here, we use proximity labeling to identify proteins interacting with the C. elegans FOXO DAF-16. We show that in well-fed, unstressed animals harboring active insulin signaling, DAF-16 forms a complex with the PAR-1/MARK serine/threonine kinase, a key regulator of cell polarity. PAR-1 inhibits DAF-16 accumulation and promotes DAF-16 phosphorylation at S249, at a conserved motif that PAR-1/human MARK2 phosphorylates in vitro. DAF-2 insulin-like receptor signaling stimulates DAF-16 S249 phosphorylation, suggesting DAF-2 activates PAR-1. DAF-2 also promotes PAR-1 expression by inhibiting DAF-16. PAR-1 knockdown, or DAF-16 S249A, prolong lifespan, whereas phosphomimetic DAF-16 S249D suppresses the longevity of daf-2 mutants. At low insulin signaling, DAF-16 proximity labeling highlights transcription factors, chromatin regulators, and DNA repair proteins. One interactor, the zinc finger/homeobox protein ZFH-2/ZFHX3, forms a complex with DAF-16 and prolongs lifespan. Our work provides entry points for hypothesis-driven studies of FOXO function and longevity.","lang":"eng"}],"volume":16,"article_processing_charge":"Yes","status":"public"},{"intvolume":"       704","year":"2025","acknowledgement":"We thank the referee for their suggestions and comments, which helped us improve the quality and clarity of the paper. JLGM and EV acknowledge the support from the Spanish Ministry of Science and Innovation/State Agency of Research (MCIN/AEI) under the grant PID2021-127289-NB-I00. ST acknowledges the funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. AJM acknowledges support from the Swedish National Space Agency (Career Grant 2023-00146) and from the Swedish Research Council (Project Grant 2022-04043). JLGM also sincerely thanks AMP for his careful final reading of this manuscript. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. We acknowledge the use of the public data products from RAVE (https://www.rave-survey.org), GALAH (https://galah-survey.org), APOGEE ((https://www.sdss.org) and LAMOST (http://www.lamost.org) surveys. This research has also made use of the SIMBAD database and the VizieR catalogue access tool, operated at CDS, Strasbourg, France, as well as the NASA Astrophysics Data System Bibliographic Services and the arXiv pre-print server operated by Cornell University. Computational analyses in this work relied extensively on the NumPy and SciPy libraries for numerical computing, matplotlib and seaborn for data visualization, and the Gala package for Galactic dynamics. This work also made use of Astropy, a community-developed core PYTHON package and an ecosystem of tools and resources for astronomy. We thank the developers and maintainers of these open-source resources for their invaluable contributions to the astronomical community.","arxiv":1,"article_number":"A237","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"title":"A kinematic history of stellar encounters with Beta Pictoris","doi":"10.1051/0004-6361/202555940","type":"journal_article","date_published":"2025-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Astronomy & Astrophysics","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"date_created":"2026-01-04T23:01:34Z","article_type":"original","citation":{"short":"J.L. Gragera-Más, S. Torres Rodriguez, A.J. Mustill, E. Villaver, Astronomy &#38; Astrophysics 704 (2025).","ama":"Gragera-Más JL, Torres Rodriguez S, Mustill AJ, Villaver E. A kinematic history of stellar encounters with Beta Pictoris. <i>Astronomy &#38; Astrophysics</i>. 2025;704. doi:<a href=\"https://doi.org/10.1051/0004-6361/202555940\">10.1051/0004-6361/202555940</a>","ieee":"J. L. Gragera-Más, S. Torres Rodriguez, A. J. Mustill, and E. Villaver, “A kinematic history of stellar encounters with Beta Pictoris,” <i>Astronomy &#38; Astrophysics</i>, vol. 704. EDP Sciences, 2025.","ista":"Gragera-Más JL, Torres Rodriguez S, Mustill AJ, Villaver E. 2025. A kinematic history of stellar encounters with Beta Pictoris. Astronomy &#38; Astrophysics. 704, A237.","chicago":"Gragera-Más, J. L., Santiago Torres Rodriguez, A. J. Mustill, and E. Villaver. “A Kinematic History of Stellar Encounters with Beta Pictoris.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202555940\">https://doi.org/10.1051/0004-6361/202555940</a>.","apa":"Gragera-Más, J. L., Torres Rodriguez, S., Mustill, A. J., &#38; Villaver, E. (2025). A kinematic history of stellar encounters with Beta Pictoris. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202555940\">https://doi.org/10.1051/0004-6361/202555940</a>","mla":"Gragera-Más, J. L., et al. “A Kinematic History of Stellar Encounters with Beta Pictoris.” <i>Astronomy &#38; Astrophysics</i>, vol. 704, A237, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202555940\">10.1051/0004-6361/202555940</a>."},"OA_place":"publisher","file":[{"relation":"main_file","date_created":"2026-01-05T11:06:16Z","creator":"dernst","file_id":"20942","access_level":"open_access","date_updated":"2026-01-05T11:06:16Z","file_name":"2025_AstronomyAstrophysics_GrageraMas.pdf","file_size":11021467,"content_type":"application/pdf","success":1,"checksum":"2fb4d5a1603043aa7931a31f2c180877"}],"oa_version":"Published Version","status":"public","department":[{"_id":"LiBu"}],"volume":704,"month":"12","abstract":[{"text":"Context. Beta Pictoris is an A-type star that hosts a complex planetary system with two massive gas giants and a prominent debris disc. Variable absorption lines in its stellar spectrum have been interpreted as signatures of exocomets – comet-like bodies transiting the star. Stellar flybys can gravitationally perturb objects in the outer comet reservoir, altering their orbits and potentially injecting them into the inner system, thereby triggering exocomet showers.\r\nAims. We assessed the contribution of stellar flybys to the observed exocomet activity by reconstructing the stellar encounter history of β Pictoris in the past and future.\r\nMethods. We used Gaia DR3 data, supplemented with radial velocities from complementary spectroscopic surveys, to compile a catalogue of stars currently within 80 pc of β Pictoris. Their orbits were integrated backwards and forwards in time in an axisymmetric Galactic potential (via the GALA package) to identify encounters within 2 pc of the system.\r\nResults. We identified 99 416 stars currently within 80 pc of β Pictoris with resolved kinematics. Among these, 49 stars (including the eight components of five binaries) encounter β Pictoris within 2 pc between –1.5 Myr and +2 Myr. For four of the binaries, the centre-of-mass trajectories also pass within 2 pc. We estimated the sample to be more than 60% complete within 0.5 Myr of today.\r\nConclusions. Despite β Pictoris being the eponym of its famous moving group, none of the identified encounters involved its moving group members; all are unrelated field stars. We found no encounter capable of shaping the observed disc structures, although stellar flybys may contribute to the long-term evolution of an Oort Cloud-like structure. Our catalogue constitutes the most complete reconstruction of the β Pictoris encounter history to date and provides a robust foundation for future dynamical simulations.","lang":"eng"}],"article_processing_charge":"No","external_id":{"arxiv":["2510.02509"]},"day":"01","OA_type":"diamond","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"date_updated":"2026-02-16T12:15:07Z","oa":1,"file_date_updated":"2026-01-05T11:06:16Z","publisher":"EDP Sciences","ddc":["520"],"has_accepted_license":"1","author":[{"full_name":"Gragera-Más, J. L.","last_name":"Gragera-Más","first_name":"J. L."},{"full_name":"Torres Rodriguez, Santiago","last_name":"Torres Rodriguez","orcid":"0000-0002-3150-8988","id":"a8df4360-4328-11ee-8f1a-e502d0c83fc2","first_name":"Santiago"},{"first_name":"A. J.","last_name":"Mustill","full_name":"Mustill, A. J."},{"first_name":"E.","last_name":"Villaver","full_name":"Villaver, E."}],"_id":"20930","DOAJ_listed":"1","publication_status":"published","PlanS_conform":"1","quality_controlled":"1"},{"author":[{"first_name":"J. S.G.","last_name":"Mombarg","full_name":"Mombarg, J. S.G."},{"first_name":"V.","full_name":"Vanlaer, V.","last_name":"Vanlaer"},{"id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","first_name":"Srijan B","last_name":"Das","orcid":"0000-0003-0896-7972","full_name":"Das, Srijan B"},{"full_name":"Rieutord, M.","last_name":"Rieutord","first_name":"M."},{"last_name":"Aerts","full_name":"Aerts, C.","first_name":"C."},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000","last_name":"Bugnet"},{"last_name":"Mathis","full_name":"Mathis, S.","first_name":"S."},{"last_name":"Reese","full_name":"Reese, D. R.","first_name":"D. R."},{"first_name":"J.","full_name":"Ballot, J.","last_name":"Ballot"}],"_id":"20931","ddc":["520"],"has_accepted_license":"1","publisher":"EDP Sciences","file_date_updated":"2026-01-05T08:36:28Z","oa":1,"PlanS_conform":"1","quality_controlled":"1","publication_status":"published","DOAJ_listed":"1","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"grant_number":"101165631","name":"Unveiling the mysteries of stellar dynamics: a pioneering journey in magnetoasteroseismology","_id":"914d8549-16d5-11f0-9cad-bbe6324c93a9"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2511.09617"]},"day":"19","OA_type":"diamond","date_updated":"2026-02-16T12:14:36Z","oa_version":"Published Version","file":[{"access_level":"open_access","creator":"dernst","date_created":"2026-01-05T08:36:28Z","relation":"main_file","file_id":"20937","success":1,"checksum":"d838b4783920c43b7cc866e9cf08b383","content_type":"application/pdf","file_size":2620909,"file_name":"2025_AstronomyAstrophysics_Mombarg.pdf","date_updated":"2026-01-05T08:36:28Z"}],"OA_place":"publisher","citation":{"apa":"Mombarg, J. S. G., Vanlaer, V., Das, S. B., Rieutord, M., Aerts, C., Bugnet, L. A., … Ballot, J. (2025). Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202557247\">https://doi.org/10.1051/0004-6361/202557247</a>","mla":"Mombarg, J. S. G., et al. “Is a 1D Perturbative Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators? Implications for Measurements of Rotation and Internal Magnetic Fields.” <i>Astronomy &#38; Astrophysics</i>, vol. 704, A336, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202557247\">10.1051/0004-6361/202557247</a>.","chicago":"Mombarg, J. S.G., V. Vanlaer, Srijan B Das, M. Rieutord, C. Aerts, Lisa Annabelle Bugnet, S. Mathis, D. R. Reese, and J. Ballot. “Is a 1D Perturbative Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators? Implications for Measurements of Rotation and Internal Magnetic Fields.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202557247\">https://doi.org/10.1051/0004-6361/202557247</a>.","ista":"Mombarg JSG, Vanlaer V, Das SB, Rieutord M, Aerts C, Bugnet LA, Mathis S, Reese DR, Ballot J. 2025. Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields. Astronomy &#38; Astrophysics. 704, A336.","ieee":"J. S. G. Mombarg <i>et al.</i>, “Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields,” <i>Astronomy &#38; Astrophysics</i>, vol. 704. EDP Sciences, 2025.","ama":"Mombarg JSG, Vanlaer V, Das SB, et al. Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields. <i>Astronomy &#38; Astrophysics</i>. 2025;704. doi:<a href=\"https://doi.org/10.1051/0004-6361/202557247\">10.1051/0004-6361/202557247</a>","short":"J.S.G. Mombarg, V. Vanlaer, S.B. Das, M. Rieutord, C. Aerts, L.A. Bugnet, S. Mathis, D.R. Reese, J. Ballot, Astronomy &#38; Astrophysics 704 (2025)."},"ec_funded":1,"date_created":"2026-01-04T23:01:35Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","month":"12","volume":704,"abstract":[{"lang":"eng","text":"Context. Asymmetries in the observed rotational splittings of a multiplet contain information about the star’s rotation profile and internal magnetic field. Moreover, the frequency regularities of multiplets can be used for mode identification. However, to exploit this information, highly accurate theoretical predictions are needed.\r\n\r\nAims. We aim to quantify the difference in the predicted mode asymmetries between a 1D perturbative method and a 2D method that includes a 2D stellar structure model, which takes rotation into account. We then place these differences between 1D and 2D methods in the context of asteroseismic measurements of internal magnetic fields. We only focus on the asymmetries and not on possible additional frequency peaks that can arise when the magnetic and rotation axis are misaligned.\r\n\r\nMethods. We coupled the 1D pulsation codes GYRE and StORM to the 2D stellar structure code ESTER and compared the oscillation predictions with the results from the 2D TOP pulsation code. We focused on zero-age main-sequence models representative of rotating β Cephei pulsators spinning at up to 20 per cent of the critical Keplerian rotation rate. Specifically, we investigated low-radial-order gravity and pressure modes.\r\n\r\nResults. We find a generally good agreement between the oscillation frequencies resulting from the 1D and 2D pulsation codes. We report differences in predicted mode multiplet asymmetries of mostly below 0.06 d−1. Since the magnetic asymmetries are small compared to the differences in the rotational asymmetries resulting from the 1D and 2D predictions, accurate measurements of the magnetic field are in most cases challenging.\r\n\r\nConclusions. Differences in the predicted mode asymmetries of a rotating star between 1D perturbative methods and 2D non-perturbative methods can greatly hinder accurate measurements of internal magnetic fields in main-sequence pulsators with low-order modes. Nevertheless, reasonably accurate measurements could be possible with npg ≥ 2 modes if the internal rotation is roughly below 10 per cent of the Keplerian critical rotation frequency for (aligned) magnetic fields of the order of a few hundred kilogauss. While the differences between the 1D and 2D frequency predictions are mostly too large for internal magnetic field detections, the rotational asymmetries predicted by StORM are in general accurate enough for asteroseismic modelling of the stellar rotation in main-sequence stars with identified low-order modes."}],"department":[{"_id":"LiBu"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"20936"}]},"status":"public","title":"Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields","article_number":"A336","arxiv":1,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"acknowledgement":"We thank the anonymous referee for their comments on the manuscript, Dario Fritzewski for providing the distribution of fractions of critical rotation for the β Cephei sample, and Zhao Guo for the discussions. The research leading to these results has received funding from the European Research Council (ERC) under the Horizon Europe programme (Synergy Grant agreement N°101071505: 4D-STAR). While partially funded by the European Union, views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. V.V. acknowledges support from the Research Foundation Flanders (FWO) under grant agreement N°1156923N (PhD Fellowship). S.B.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement N°101034413. L.B. gratefully acknowledges support from the European Research Council (ERC) under the Horizon Europe programme (Calcifer; Starting Grant agreement N°101165631). J.B., M.R., S.M. and J.S.G.M have been supported by CNES, focused on the preparation of the PLATO mission. Computations with ESTER and TOP have made use of the HPC resources from the CALMIP supercomputing centre (Grant 2023-P0107). This research made use of the numpy (Harris et al. 2020) and matplotlib (Hunter 2007) Python software packages.","year":"2025","intvolume":"       704","scopus_import":"1","publication":"Astronomy & Astrophysics","date_published":"2025-12-19T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1051/0004-6361/202557247"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","OA_type":"diamond","external_id":{"arxiv":["2507.11045"]},"date_updated":"2026-02-16T12:14:52Z","oa":1,"file_date_updated":"2026-01-05T09:26:17Z","has_accepted_license":"1","ddc":["520"],"author":[{"first_name":"Y.","last_name":"Liu","full_name":"Liu, Y."},{"id":"edaf889c-c7cd-11ef-ab1b-bb28c431bd29","first_name":"Sara","full_name":"Mascia, Sara","last_name":"Mascia"},{"first_name":"L.","last_name":"Pentericci","full_name":"Pentericci, L."},{"last_name":"Watson","full_name":"Watson, P.","first_name":"P."},{"full_name":"Alavi, A.","last_name":"Alavi","first_name":"A."},{"last_name":"Bergamini","full_name":"Bergamini, P.","first_name":"P."},{"first_name":"M.","full_name":"Bradač, M.","last_name":"Bradač"},{"first_name":"A.","full_name":"Calabrò, A.","last_name":"Calabrò"},{"first_name":"K.","full_name":"Glazebrook, K.","last_name":"Glazebrook"},{"full_name":"Henry, A.","last_name":"Henry","first_name":"A."},{"first_name":"M.","full_name":"Llerena, M.","last_name":"Llerena"},{"full_name":"Merlin, E.","last_name":"Merlin","first_name":"E."},{"first_name":"B.","last_name":"Metha","full_name":"Metha, B."},{"first_name":"T.","full_name":"Nanayakkara, T.","last_name":"Nanayakkara"},{"last_name":"Napolitano","full_name":"Napolitano, L.","first_name":"L."},{"last_name":"Roy","full_name":"Roy, N.","first_name":"N."},{"last_name":"Siana","full_name":"Siana, B.","first_name":"B."},{"first_name":"E.","full_name":"Vanzella, E.","last_name":"Vanzella"},{"first_name":"B.","last_name":"Vulcani","full_name":"Vulcani, B."},{"first_name":"X.","full_name":"Wang, X.","last_name":"Wang"}],"_id":"20932","publisher":"EDP Sciences","DOAJ_listed":"1","publication_status":"published","quality_controlled":"1","PlanS_conform":"1","acknowledgement":"We acknowledge support from the National Science Foundation of China – 12225301, INAF Large grant “Spectroscopic survey with JWST” jand from PRIN 2022 MUR project 2022CB3PJ3 – First Light And Galaxy aSsembly (FLAGS) funded by the European Union – Next Generation EU, and Postgraduate Scholarship Program under the grant of China Scholarship Council. P.W. and B.V. acknowledge support from the INAF Mini Grant ‘1.05.24.07.01 RSN1: Spatially Resolved Near-IR Emission of Intermediate-Redshift Jellyfish Galaxies’ (PI Watson). We acknowledge A. Acebron, C. Grillo, and P. Rosati for their fundamental contribution to the strong lensing analysis and results. We also extend our gratitude to the JWST and HST teams for their efforts in designing, building, and operating these transformative missions.","intvolume":"       704","year":"2025","title":"A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field","article_number":"A328","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"arxiv":1,"doi":"10.1051/0004-6361/202556410","language":[{"iso":"eng"}],"date_published":"2025-12-01T00:00:00Z","publication":"Astronomy & Astrophysics","scopus_import":"1","type":"journal_article","article_type":"original","date_created":"2026-01-04T23:01:35Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"checksum":"3e6061f3c4bfb521b3333ea4913c241a","success":1,"date_updated":"2026-01-05T09:26:17Z","file_name":"2025_AstronomyAstrophysics_Liu.pdf","file_size":4642530,"content_type":"application/pdf","access_level":"open_access","file_id":"20938","relation":"main_file","creator":"dernst","date_created":"2026-01-05T09:26:17Z"}],"oa_version":"Published Version","citation":{"short":"Y. Liu, S. Mascia, L. Pentericci, P. Watson, A. Alavi, P. Bergamini, M. Bradač, A. Calabrò, K. Glazebrook, A. Henry, M. Llerena, E. Merlin, B. Metha, T. Nanayakkara, L. Napolitano, N. Roy, B. Siana, E. Vanzella, B. Vulcani, X. Wang, Astronomy &#38; Astrophysics 704 (2025).","ama":"Liu Y, Mascia S, Pentericci L, et al. A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field. <i>Astronomy &#38; Astrophysics</i>. 2025;704. doi:<a href=\"https://doi.org/10.1051/0004-6361/202556410\">10.1051/0004-6361/202556410</a>","chicago":"Liu, Y., Sara Mascia, L. Pentericci, P. Watson, A. Alavi, P. Bergamini, M. Bradač, et al. “A Lyman Continuum Analysis of ∼100 Galaxies at z Spec∼ 3 in the Abell 2744 Cluster Field.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202556410\">https://doi.org/10.1051/0004-6361/202556410</a>.","apa":"Liu, Y., Mascia, S., Pentericci, L., Watson, P., Alavi, A., Bergamini, P., … Wang, X. (2025). A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202556410\">https://doi.org/10.1051/0004-6361/202556410</a>","mla":"Liu, Y., et al. “A Lyman Continuum Analysis of ∼100 Galaxies at z Spec∼ 3 in the Abell 2744 Cluster Field.” <i>Astronomy &#38; Astrophysics</i>, vol. 704, A328, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202556410\">10.1051/0004-6361/202556410</a>.","ieee":"Y. Liu <i>et al.</i>, “A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field,” <i>Astronomy &#38; Astrophysics</i>, vol. 704. EDP Sciences, 2025.","ista":"Liu Y, Mascia S, Pentericci L, Watson P, Alavi A, Bergamini P, Bradač M, Calabrò A, Glazebrook K, Henry A, Llerena M, Merlin E, Metha B, Nanayakkara T, Napolitano L, Roy N, Siana B, Vanzella E, Vulcani B, Wang X. 2025. A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field. Astronomy &#38; Astrophysics. 704, A328."},"OA_place":"publisher","status":"public","abstract":[{"lang":"eng","text":"Identifying Lyman continuum (LyC) leakers at intermediate redshifts is crucial for understanding the properties of cosmic reionizers because the opacity of the intergalactic medium (IGM) prevents the direct detection of LyC emission from sources during the Epoch of Reionization (EoR). In this study, we confirm two new LyC candidate leakers at z ∼ 3 in the Abell 2744 cluster field, with absolute escape fractions (fesc) of 0.83−0.80+0.15 and 0.74−0.70+0.23, respectively. The LyC emission was detected using HST/WFC3/F275W and F336W imaging. These two candidate leakers appear to be faint (MUV = −17.61 ± 0.06 and −18.22 ± 0.10), exhibit blue UV continuum slopes (β = −2.43 ± 0.05 and −1.92 ± 0.09), have low masses (M★ ∼ 107.51 ± 0.03 and 107.17 ± 0.15 M⊙) and Lyα equivalent widths of 90 ± 3 Å and 28 ± 12 Å, respectively. These two LyC candidate leakers were detected in a catalog of 91 spectroscopically confirmed sources using public spectra from the JWST and/or MUSE. We also analyzed properties that were proposed as indirect indicators of LyC emission, such as Lyα, the O32 ratio, and M★. We created a galaxy subsample that was selected according to these properties, stacked the LyC observations of this subsample, and assessed the limits of the escape fractions in the stacks. We aim to enhance our understanding of LyC escape mechanisms and improve our predictions of the LyC fesc during the EoR by analyzing the individual candidates and the stacks in the context of the currently limited sample of known LyC leakers at z ∼ 3."}],"volume":704,"month":"12","article_processing_charge":"No","department":[{"_id":"JoMa"}]},{"status":"public","department":[{"_id":"RaKl"}],"abstract":[{"text":"Photo-responsive systems based on azobenzenes usually require UV light for E→Z isomerization, limiting their applicability, especially in biomedical contexts. Disequilibration by sensitization of azobenzene under confinement (DESC) has recently emerged as a supramolecular strategy to bypass this limitation without the need to derivatize the azobenzene scaffold. Here, we expand DESC to water-soluble azopolymers obtained by RAFT polymerization and systematically investigate the interplay between the polymer structure and DESC efficiency. Using this approach, we achieved as much as 85% of the direct photoexcitation (UV) switching efficiency, while utilizing low-energy (yellow) light. These results establish general design principles for combining DESC with polymeric systems, opening new opportunities for the development of functional materials driven with low-energy light.","lang":"eng"}],"month":"12","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_created":"2026-01-04T23:01:35Z","citation":{"ieee":"H. J. Meteling, J. Gemen, S. Häkkinen, R. Klajn, and A. Priimagi, “Sensitized disequilibration of water-soluble azopolymers,” <i>Angewandte Chemie International Edition</i>. Wiley, 2025.","ista":"Meteling HJ, Gemen J, Häkkinen S, Klajn R, Priimagi A. 2025. Sensitized disequilibration of water-soluble azopolymers. Angewandte Chemie International Edition., e23447.","apa":"Meteling, H. J., Gemen, J., Häkkinen, S., Klajn, R., &#38; Priimagi, A. (2025). Sensitized disequilibration of water-soluble azopolymers. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202523447\">https://doi.org/10.1002/anie.202523447</a>","mla":"Meteling, Henning Jörn, et al. “Sensitized Disequilibration of Water-Soluble Azopolymers.” <i>Angewandte Chemie International Edition</i>, e23447, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/anie.202523447\">10.1002/anie.202523447</a>.","chicago":"Meteling, Henning Jörn, Julius Gemen, Satu Häkkinen, Rafal Klajn, and Arri Priimagi. “Sensitized Disequilibration of Water-Soluble Azopolymers.” <i>Angewandte Chemie International Edition</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/anie.202523447\">https://doi.org/10.1002/anie.202523447</a>.","ama":"Meteling HJ, Gemen J, Häkkinen S, Klajn R, Priimagi A. Sensitized disequilibration of water-soluble azopolymers. <i>Angewandte Chemie International Edition</i>. 2025. doi:<a href=\"https://doi.org/10.1002/anie.202523447\">10.1002/anie.202523447</a>","short":"H.J. Meteling, J. Gemen, S. Häkkinen, R. Klajn, A. Priimagi, Angewandte Chemie International Edition (2025)."},"OA_place":"publisher","oa_version":"Published Version","doi":"10.1002/anie.202523447","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2025-12-23T00:00:00Z","publication":"Angewandte Chemie International Edition","scopus_import":"1","year":"2025","acknowledgement":"This work is supported by the European Research Council (Consolidator Grand project MULTIMODAL, no. 101045223), the Research Council of Finland Center of Excellence “Life-Inspired Hybrid Materials Research” (LIBER, no. 346107) and the Research Council of Finland Flagship Programme on Photonics Research and Innovation (PREIN, no. 320165). H.M. gratefully acknowledges Oommen Podivan for providing access to their Zetasizer for DLS measurements and the Faculty of Medicine and Health Technologies at Tampere University for access to their laboratory facilities. R.K. acknowledges funding through the Award for Research Cooperation and High Excellence in Science (ARCHES) from the Federal German Ministry for Education and Research. S.H. acknowledges financial support through the profi7 profiling action SUSBIO from the Research Council of Finland (no. 352754).\r\nOpen access publishing facilitated by Tampereen yliopisto ja Tampereen ammattikorkeakoulu, as part of the Wiley - FinELib agreement.","article_number":"e23447","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"pmid":1,"title":"Sensitized disequilibration of water-soluble azopolymers","publication_status":"epub_ahead","PlanS_conform":"1","quality_controlled":"1","oa":1,"publisher":"Wiley","ddc":["540"],"has_accepted_license":"1","author":[{"last_name":"Meteling","full_name":"Meteling, Henning Jörn","first_name":"Henning Jörn"},{"first_name":"Julius","full_name":"Gemen, Julius","last_name":"Gemen"},{"full_name":"Häkkinen, Satu","last_name":"Häkkinen","first_name":"Satu"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"full_name":"Priimagi, Arri","last_name":"Priimagi","first_name":"Arri"}],"_id":"20933","date_updated":"2026-01-05T09:42:56Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202523447"}],"external_id":{"pmid":["41437660"]},"OA_type":"hybrid","day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"713490","name":"Integrating Molecular Photoswitches with PH-Feedback Mechanisms: Towards Life-like Materials","_id":"7bf494dc-9f16-11ee-852c-9fe37e3f50f0"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_created":"2026-01-04T23:01:35Z","citation":{"ama":"Montagna F, Cairney-Leeming MT, Sridhar D, Locatello F. Demystifying amortized causal discovery with transformers. <i>Transactions on Machine Learning Research</i>. 2025.","short":"F. Montagna, M.T. Cairney-Leeming, D. Sridhar, F. Locatello, Transactions on Machine Learning Research (2025).","mla":"Montagna, Francesco, et al. “Demystifying Amortized Causal Discovery with Transformers.” <i>Transactions on Machine Learning Research</i>, ML Research Press, 2025.","apa":"Montagna, F., Cairney-Leeming, M. T., Sridhar, D., &#38; Locatello, F. (2025). Demystifying amortized causal discovery with transformers. <i>Transactions on Machine Learning Research</i>. ML Research Press.","chicago":"Montagna, Francesco, Maximilian T Cairney-Leeming, Dhanya Sridhar, and Francesco Locatello. “Demystifying Amortized Causal Discovery with Transformers.” <i>Transactions on Machine Learning Research</i>. ML Research Press, 2025.","ista":"Montagna F, Cairney-Leeming MT, Sridhar D, Locatello F. 2025. Demystifying amortized causal discovery with transformers. Transactions on Machine Learning Research.","ieee":"F. Montagna, M. T. Cairney-Leeming, D. Sridhar, and F. Locatello, “Demystifying amortized causal discovery with transformers,” <i>Transactions on Machine Learning Research</i>. ML Research Press, 2025."},"OA_place":"publisher","alternative_title":["TMLR"],"file":[{"file_id":"20939","creator":"dernst","date_created":"2026-01-05T09:51:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-01-05T09:51:28Z","file_size":1030280,"file_name":"2025_PMLR_Montagna.pdf","checksum":"968c471bb1f682cf823b2d4cadea8a3f","success":1}],"oa_version":"Published Version","status":"public","related_material":{"link":[{"relation":"software","url":"https://github.com/francescomontagna/learning-to-induce.git"}]},"department":[{"_id":"FrLo"}],"abstract":[{"lang":"eng","text":" Supervised learning for causal discovery from observational data often achieves competitive performance despite seemingly avoiding the explicit assumptions that traditional methods require for identifiability. In this work, we analyze CSIvA (Ke et al., 2023) on bivariate causal models, a transformer architecture for amortized inference promising to train on synthetic data and transfer to real ones. First, we bridge the gap with identifiability theory, showing that the training distribution implicitly defines a prior on the causal model of the test observations: consistent with classical approaches, good performance is achieved when we have a good prior on the test data, and the underlying model is identifiable. Second, we find that CSIvA can not generalize to classes of causal models unseen during training: to overcome this limitation, we theoretically and empirically analyze \\textit{when} training CSIvA on datasets generated by multiple identifiable causal models with different structural assumptions improves its generalization at test time. Overall, we find that amortized causal discovery still adheres to identifiability theory, violating the previous hypothesis from Lopez-Paz et al. (2015) that supervised learning methods could overcome its restrictions."}],"month":"12","article_processing_charge":"No","year":"2025","arxiv":1,"publication_identifier":{"eissn":["2835-8856"]},"title":"Demystifying amortized causal discovery with transformers","type":"journal_article","publication":"Transactions on Machine Learning Research","language":[{"iso":"eng"}],"date_published":"2025-12-18T00:00:00Z","scopus_import":"1","oa":1,"file_date_updated":"2026-01-05T09:51:28Z","publisher":"ML Research Press","ddc":["000"],"has_accepted_license":"1","author":[{"id":"353afc8e-19f4-11f0-9db9-811f1723c83f","first_name":"Francesco","last_name":"Montagna","full_name":"Montagna, Francesco"},{"last_name":"Cairney-Leeming","full_name":"Cairney-Leeming, Maximilian T","id":"2214a80c-31f8-11ee-a48d-cf52cc58759b","first_name":"Maximilian T"},{"full_name":"Sridhar, Dhanya","last_name":"Sridhar","first_name":"Dhanya"},{"full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"}],"_id":"20934","publication_status":"published","PlanS_conform":"1","corr_author":"1","quality_controlled":"1","day":"18","OA_type":"gold","external_id":{"arxiv":["2405.16924"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-01-05T09:54:59Z"},{"ddc":["570"],"author":[{"last_name":"Kelley","full_name":"Kelley, Ron","first_name":"Ron"},{"full_name":"Khavnekar, Sagar","last_name":"Khavnekar","first_name":"Sagar"},{"first_name":"Ricardo D.","full_name":"Righetto, Ricardo D.","last_name":"Righetto"},{"first_name":"Jessica","full_name":"Heebner, Jessica","last_name":"Heebner"},{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","last_name":"Obr"},{"first_name":"Xianjun","full_name":"Zhang, Xianjun","last_name":"Zhang"},{"last_name":"Chakraborty","full_name":"Chakraborty, Saikat","first_name":"Saikat"},{"full_name":"Tagiltsev, Grigory","last_name":"Tagiltsev","first_name":"Grigory"},{"first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia"},{"first_name":"Sofie","full_name":"Van Dorst, Sofie","last_name":"Van Dorst"},{"first_name":"Florent","full_name":"Waltz, Florent","last_name":"Waltz"},{"first_name":"Caitlyn L.","full_name":"Mccafferty, Caitlyn L.","last_name":"Mccafferty"},{"last_name":"Lamm","full_name":"Lamm, Lorenz","first_name":"Lorenz"},{"full_name":"Zufferey, Simon","last_name":"Zufferey","first_name":"Simon"},{"last_name":"Van Der Stappen","full_name":"Van Der Stappen, Philippe","first_name":"Philippe"},{"first_name":"Hugo","full_name":"Van Den Hoek, Hugo","last_name":"Van Den Hoek"},{"first_name":"Wojciech","full_name":"Wietrzynski, Wojciech","last_name":"Wietrzynski"},{"id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","first_name":"Pavol","full_name":"Harar, Pavol","last_name":"Harar","orcid":"0000-0001-5206-1794"},{"full_name":"Wan, William","last_name":"Wan","first_name":"William"},{"full_name":"Briggs, John A.G.","last_name":"Briggs","first_name":"John A.G."},{"last_name":"Plitzko","full_name":"Plitzko, Jürgen M.","first_name":"Jürgen M."},{"full_name":"Engel, Benjamin D.","last_name":"Engel","first_name":"Benjamin D."},{"first_name":"Abhay","last_name":"Kotecha","full_name":"Kotecha, Abhay"}],"_id":"20935","publisher":"Elsevier","oa":1,"PlanS_conform":"1","quality_controlled":"1","publication_status":"inpress","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","OA_type":"hybrid","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2025.11.029"}],"date_updated":"2026-01-05T08:32:47Z","oa_version":"Published Version","citation":{"short":"R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S. Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty, L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P. Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular Cell (n.d.).","ama":"Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>","ista":"Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG, Plitzko JM, Engel BD, Kotecha A. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.","ieee":"R. Kelley <i>et al.</i>, “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” <i>Molecular Cell</i>. Elsevier.","chicago":"Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>.","mla":"Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>.","apa":"Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., … Kotecha, A. (n.d.). Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>"},"OA_place":"publisher","article_type":"original","date_created":"2026-01-04T23:01:36Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"12","abstract":[{"text":"In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"AlMi"}],"status":"public","title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"acknowledgement":"Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.","year":"2025","publication":"Molecular Cell","date_published":"2025-12-19T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","type":"journal_article","doi":"10.1016/j.molcel.2025.11.029"},{"type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.17580178","open_access":"1"}],"date_published":"2025-11-11T00:00:00Z","doi":"10.5281/ZENODO.17580178","date_updated":"2026-02-16T12:14:36Z","title":"Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators?","day":"11","OA_type":"gold","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LiBu"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Supplementary material for Mombarg et al. (2025, A&A). Title: \"Is a 1D perturbative method sufficient for asteroseismic modelling of \r\n~Cephei pulsators? Implications for measurements of rotation and internal magnetic fields\"\r\n\r\nContent:\r\n- Non-rotating ESTER models and associated .GSM models. (Xini = 0.71, Zini = 0.014, vertical/horizonal viscosity 10^7 cm^2/s, vertical chemical diffusion 10^4 cm^2/s for evolution model. More details on the ESTER models can be found in the ESTER manual.\r\n\r\n- Rotational asymmetries computed with StORM and TOP in 1/d, and the central m=0 frequency from TOP in 1/d. (all_A*_new.pkl)\r\n\r\n- Magnetic asymmetries in 1/d for different obliquity angles between 0 and 90 deg for ZAMS and MAMS model, for B_0 = 75 kG. *_nu key gives unperturbed mode frequencies, *_npg the radial order (asym_dict.pkl, asym_dict_evol.pkl)"}],"month":"11","status":"public","related_material":{"record":[{"status":"public","id":"20931","relation":"used_in_publication"}]},"publisher":"Zenodo","OA_place":"repository","citation":{"mla":"Mombarg, Joey, et al. <i>Is a 1D Perturbative Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators?</i> Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/ZENODO.17580178\">10.5281/ZENODO.17580178</a>.","apa":"Mombarg, J., Vanlaer, V., Das, S. B., Rieutord, M., Aerts, C., Bugnet, L. A., … Ballot, J. (2025). Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.17580178\">https://doi.org/10.5281/ZENODO.17580178</a>","chicago":"Mombarg, Joey, Vincent Vanlaer, Srijan B Das, Michel Rieutord, Conny Aerts, Lisa Annabelle Bugnet, Stephane Mathis, Daniel Reese, and Jerome Ballot. “Is a 1D Perturbative Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators?” Zenodo, 2025. <a href=\"https://doi.org/10.5281/ZENODO.17580178\">https://doi.org/10.5281/ZENODO.17580178</a>.","ista":"Mombarg J, Vanlaer V, Das SB, Rieutord M, Aerts C, Bugnet LA, Mathis S, Reese D, Ballot J. 2025. Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators?, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.17580178\">10.5281/ZENODO.17580178</a>.","ieee":"J. Mombarg <i>et al.</i>, “Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators?” Zenodo, 2025.","ama":"Mombarg J, Vanlaer V, Das SB, et al. Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? 2025. doi:<a href=\"https://doi.org/10.5281/ZENODO.17580178\">10.5281/ZENODO.17580178</a>","short":"J. Mombarg, V. Vanlaer, S.B. Das, M. Rieutord, C. Aerts, L.A. Bugnet, S. Mathis, D. Reese, J. Ballot, (2025)."},"_id":"20936","author":[{"last_name":"Mombarg","full_name":"Mombarg, Joey","first_name":"Joey"},{"last_name":"Vanlaer","full_name":"Vanlaer, Vincent","first_name":"Vincent"},{"id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","first_name":"Srijan B","full_name":"Das, Srijan B","last_name":"Das","orcid":"0000-0003-0896-7972"},{"last_name":"Rieutord","full_name":"Rieutord, Michel","first_name":"Michel"},{"first_name":"Conny","last_name":"Aerts","full_name":"Aerts, Conny"},{"orcid":"0000-0003-0142-4000","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle"},{"full_name":"Mathis, Stephane","last_name":"Mathis","first_name":"Stephane"},{"last_name":"Reese","full_name":"Reese, Daniel","first_name":"Daniel"},{"first_name":"Jerome","last_name":"Ballot","full_name":"Ballot, Jerome"}],"oa_version":"Submitted Version","ddc":["520"],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2026-01-05T08:39:33Z"},{"title":"Mode dispersion with magnetic field in a cavity-magnonics system","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","day":"02","year":"2025","date_published":"2025-05-02T00:00:00Z","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.15321721"}],"doi":"10.5281/ZENODO.15321721","date_updated":"2026-01-05T10:07:04Z","author":[{"first_name":"Supriya","full_name":"Mandal, Supriya","last_name":"Mandal"},{"id":"76bc9e9f-ba0b-11ee-8184-90edabd17a58","first_name":"Krishnendu","last_name":"Maji","full_name":"Maji, Krishnendu"},{"full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky"},{"first_name":"Souvik","last_name":"Sasmal","full_name":"Sasmal, Souvik"},{"last_name":"Manni","full_name":"Manni, Soham","first_name":"Soham"},{"first_name":"John","last_name":"Jesudasan","full_name":"Jesudasan, John"},{"first_name":"Pratap","last_name":"Raychaudhuri","full_name":"Raychaudhuri, Pratap"},{"full_name":"Thamizhavel, Arumugam","last_name":"Thamizhavel","first_name":"Arumugam"},{"first_name":"Mandar M.","full_name":"Deshmukh, Mandar M.","last_name":"Deshmukh"}],"_id":"20940","oa_version":"Submitted Version","has_accepted_license":"1","OA_place":"repository","publisher":"Zenodo","citation":{"ieee":"S. Mandal <i>et al.</i>, “Mode dispersion with magnetic field in a cavity-magnonics system.” Zenodo, 2025.","ista":"Mandal S, Maji K, Kapoor L, Sasmal S, Manni S, Jesudasan J, Raychaudhuri P, Thamizhavel A, Deshmukh MM. 2025. Mode dispersion with magnetic field in a cavity-magnonics system, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.15321721\">10.5281/ZENODO.15321721</a>.","mla":"Mandal, Supriya, et al. <i>Mode Dispersion with Magnetic Field in a Cavity-Magnonics System</i>. Zenodo, 2025, doi:<a href=\"https://doi.org/10.5281/ZENODO.15321721\">10.5281/ZENODO.15321721</a>.","apa":"Mandal, S., Maji, K., Kapoor, L., Sasmal, S., Manni, S., Jesudasan, J., … Deshmukh, M. M. (2025). Mode dispersion with magnetic field in a cavity-magnonics system. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.15321721\">https://doi.org/10.5281/ZENODO.15321721</a>","chicago":"Mandal, Supriya, Krishnendu Maji, Lucky Kapoor, Souvik Sasmal, Soham Manni, John Jesudasan, Pratap Raychaudhuri, Arumugam Thamizhavel, and Mandar M. Deshmukh. “Mode Dispersion with Magnetic Field in a Cavity-Magnonics System.” Zenodo, 2025. <a href=\"https://doi.org/10.5281/ZENODO.15321721\">https://doi.org/10.5281/ZENODO.15321721</a>.","ama":"Mandal S, Maji K, Kapoor L, et al. Mode dispersion with magnetic field in a cavity-magnonics system. 2025. doi:<a href=\"https://doi.org/10.5281/ZENODO.15321721\">10.5281/ZENODO.15321721</a>","short":"S. Mandal, K. Maji, L. Kapoor, S. Sasmal, S. Manni, J. Jesudasan, P. Raychaudhuri, A. Thamizhavel, M.M. Deshmukh, (2025)."},"date_created":"2026-01-05T10:00:06Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","month":"05","abstract":[{"lang":"eng","text":"These are the raw data files that supplement our study of mode dispersion with magnetic field of a cavity-magnonics system containing chromium trichloride on coplanar waveguide resonator."}],"department":[{"_id":"MaIb"},{"_id":"JoFi"}],"related_material":{"record":[{"relation":"used_in_publication","id":"20927","status":"public"}]},"status":"public"},{"date_updated":"2026-01-12T09:37:19Z","OA_type":"closed access","day":"30","external_id":{"pmid":["41470065"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"epub_ahead","quality_controlled":"1","publisher":"Wiley","author":[{"full_name":"Meng, Weite","last_name":"Meng","first_name":"Weite"},{"last_name":"Li","full_name":"Li, Mingquan","first_name":"Mingquan"},{"first_name":"Qingyue","last_name":"Wang","full_name":"Wang, Qingyue"},{"last_name":"Song","full_name":"Song, Pingan","first_name":"Pingan"},{"first_name":"Xuan","last_name":"Yang","full_name":"Yang, Xuan"},{"first_name":"Wen Jun","last_name":"Wang","full_name":"Wang, Wen Jun"},{"first_name":"Min","full_name":"Hong, Min","last_name":"Hong"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Yu","last_name":"Liu","full_name":"Liu, Yu"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"}],"_id":"20973","doi":"10.1002/smll.202513035","type":"journal_article","date_published":"2025-12-30T00:00:00Z","publication":"Small","language":[{"iso":"eng"}],"scopus_import":"1","year":"2025","acknowledgement":"K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant Number 22208293) and the National Foreign Expert Project (Y20240175). Y.L. acknowledges funding from the NSFC (Grant Number 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant Number 2022LCX002), and the Fundamental Research Funds for the Central Universities (JZ2024HGTB0239). Y.Z. acknowledges funding from the NSFC (Grant Number 52502313) and Wenzhou Basic Scientific Research Project (Grant Number G20240034). Q. W. acknowledges financial support from the NSFC (Grant Number 22208292), the High-Level Overseas-Educated Talents Return Program, and the “Pioneer” and “Leading Goose” R&D Program of Zhejiang [2025C04021]. K.H.L., Q. W., and X. Y. also acknowledge the Research Funds of the Institute of Zhejiang University-Quzhou (Grants No. IZQ2022RCZX101, IZQ2021RCZX003, IZQ2021RCZX002, and IZQ2024KJ0004). M.H. acknowledges the funding from the Australian Research Council and the iLAuNCH Trailblazer, Department of Education, Australia. M.H. acknowledges the computational support from the National Computational Infrastructure (NCI), Australia, and Pawsey Supercomputing Centre, Australia.","article_number":"e13035","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"pmid":1,"title":"Efficient near room temperature thermoelectric cooling and power generation with CuAgSe","status":"public","department":[{"_id":"MaIb"}],"abstract":[{"text":"CuAgSe-based materials are attractive for low-temperature thermoelectric (TE) applications but are limited by bipolar conduction and relatively high thermal conductivity. Herein, we report a ligand-free aqueous synthesis of Te-doped CuAgSe (CuAgSe1-xTex), where structural and electronic modulation improve carrier transport and suppress phonon propagation. Ex-situ time-resolved X-ray diffraction reveals a spontaneous growth mechanism, while density functional theory calculations show that Te-5s and 5p orbitals hybridization generates localized states and an asymmetric density of states, thereby enhancing the Seebeck coefficient. Electron microscopy and strain analyses confirm that Te-doping introduces a high density of lattice dislocations and grain boundaries, leading to a reduced lattice thermal conductivity of 0.11 W m−1K−1 at 443 K. These synergistic effects translate into device-level performance—the first integrated CuAgSe thermoelectric modules, exhibit a maximum cooling temperature difference of 27.3 K, and power density of 0.34 W cm−2 with a conversion efficiency of 3.6% at a modest temperature gradient of 136 K. These results demonstrate that CuAgSe1-xTex enables efficient energy harvesting and localized cooling under small temperature gradient, underscoring the importance of structural and electronic design beyond conventional zT benchmarks.","lang":"eng"}],"month":"12","article_processing_charge":"No","article_type":"original","date_created":"2026-01-11T23:01:34Z","citation":{"ista":"Meng W, Li M, Wang Q, Song P, Yang X, Wang WJ, Hong M, Ibáñez M, Cabot A, Zhang Y, Liu Y, Lim KH. 2025. Efficient near room temperature thermoelectric cooling and power generation with CuAgSe. Small., e13035.","ieee":"W. Meng <i>et al.</i>, “Efficient near room temperature thermoelectric cooling and power generation with CuAgSe,” <i>Small</i>. Wiley, 2025.","chicago":"Meng, Weite, Mingquan Li, Qingyue Wang, Pingan Song, Xuan Yang, Wen Jun Wang, Min Hong, et al. “Efficient near Room Temperature Thermoelectric Cooling and Power Generation with CuAgSe.” <i>Small</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/smll.202513035\">https://doi.org/10.1002/smll.202513035</a>.","mla":"Meng, Weite, et al. “Efficient near Room Temperature Thermoelectric Cooling and Power Generation with CuAgSe.” <i>Small</i>, e13035, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/smll.202513035\">10.1002/smll.202513035</a>.","apa":"Meng, W., Li, M., Wang, Q., Song, P., Yang, X., Wang, W. J., … Lim, K. H. (2025). Efficient near room temperature thermoelectric cooling and power generation with CuAgSe. <i>Small</i>. Wiley. <a href=\"https://doi.org/10.1002/smll.202513035\">https://doi.org/10.1002/smll.202513035</a>","short":"W. Meng, M. Li, Q. Wang, P. Song, X. Yang, W.J. Wang, M. Hong, M. Ibáñez, A. Cabot, Y. Zhang, Y. Liu, K.H. Lim, Small (2025).","ama":"Meng W, Li M, Wang Q, et al. Efficient near room temperature thermoelectric cooling and power generation with CuAgSe. <i>Small</i>. 2025. doi:<a href=\"https://doi.org/10.1002/smll.202513035\">10.1002/smll.202513035</a>"},"oa_version":"None"},{"date_created":"2026-01-11T23:01:34Z","article_type":"original","oa_version":"Preprint","OA_place":"repository","citation":{"ieee":"L. Patel, S. Hawaldar, A. Panikkar, A. Shankar, and B. Suri, “Impedance-engineered Josephson parametric amplifier with single-step lithography,” <i>Applied Physics Letters</i>, vol. 127, no. 25. AIP Publishing, 2025.","ista":"Patel L, Hawaldar S, Panikkar A, Shankar A, Suri B. 2025. Impedance-engineered Josephson parametric amplifier with single-step lithography. Applied Physics Letters. 127(25), 254001.","chicago":"Patel, Lipi, Samarth Hawaldar, Aditya Panikkar, Athreya Shankar, and Baladitya Suri. “Impedance-Engineered Josephson Parametric Amplifier with Single-Step Lithography.” <i>Applied Physics Letters</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0290636\">https://doi.org/10.1063/5.0290636</a>.","mla":"Patel, Lipi, et al. “Impedance-Engineered Josephson Parametric Amplifier with Single-Step Lithography.” <i>Applied Physics Letters</i>, vol. 127, no. 25, 254001, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0290636\">10.1063/5.0290636</a>.","apa":"Patel, L., Hawaldar, S., Panikkar, A., Shankar, A., &#38; Suri, B. (2025). Impedance-engineered Josephson parametric amplifier with single-step lithography. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0290636\">https://doi.org/10.1063/5.0290636</a>","short":"L. Patel, S. Hawaldar, A. Panikkar, A. Shankar, B. Suri, Applied Physics Letters 127 (2025).","ama":"Patel L, Hawaldar S, Panikkar A, Shankar A, Suri B. Impedance-engineered Josephson parametric amplifier with single-step lithography. <i>Applied Physics Letters</i>. 2025;127(25). doi:<a href=\"https://doi.org/10.1063/5.0290636\">10.1063/5.0290636</a>"},"status":"public","article_processing_charge":"No","volume":127,"month":"12","abstract":[{"text":"We present an experimental demonstration of an impedance-engineered Josephson parametric amplifier (IEJPA) fabricated in a single-step lithography process. Impedance-engineering is implemented using a lumped-element series LC circuit. We use a simpler lithography process where the entire device—impedance transformer and Josephson parametric amplifier (JPA)—is patterned in a single electron beam lithography step, followed by a double-angle Dolan-bridge technique for Al–AlOx–Al deposition. We observe amplification with 18 dB gain over a wide 400 MHz bandwidth centered around 5.3 GHz with added noise approaching the quantum limit, and a saturation power of −114 dBm. To accurately explain our experimental results, we extend existing theories for IEJPAs to incorporate the full sine nonlinearity of both the JPA and the transformer. Our work provides a route to simpler realization of broadband JPAs and a theoretical foundation for a regime of JPA operation that has been less explored in literature.","lang":"eng"}],"department":[{"_id":"JoFi"}],"acknowledgement":"The authors acknowledge receiving support from the Space Technology Cell at IISc and ISRO through the project STC-0444(2022) and the Ministry of Electronics and Information Technology of the Government of India, under the centre of Excellence of Quantum Technology at the Indian Institute of Science, as well as the office of Principle Scientific Advisor, Government of India. S.H. and A.P. acknowledge the support of the Kishore Vaigyanik Protsahan Yojana (KVPY). A.S. acknowledges the support of a New Faculty Initiation Grant (NFIG) from IIT Madras.","issue":"25","year":"2025","intvolume":"       127","title":"Impedance-engineered Josephson parametric amplifier with single-step lithography","article_number":"254001","arxiv":1,"publication_identifier":{"eissn":["1077-3118"],"issn":["0003-6951"]},"doi":"10.1063/5.0290636","scopus_import":"1","publication":"Applied Physics Letters","date_published":"2025-12-22T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"_id":"20976","author":[{"full_name":"Patel, Lipi","last_name":"Patel","first_name":"Lipi"},{"first_name":"Samarth","id":"221708e1-1ff6-11ee-9fa6-85146607433e","full_name":"Hawaldar, Samarth","last_name":"Hawaldar","orcid":"0000-0002-1965-4309"},{"full_name":"Panikkar, Aditya","last_name":"Panikkar","first_name":"Aditya"},{"first_name":"Athreya","last_name":"Shankar","full_name":"Shankar, Athreya"},{"first_name":"Baladitya","full_name":"Suri, Baladitya","last_name":"Suri"}],"publisher":"AIP Publishing","publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","day":"22","external_id":{"arxiv":["2507.09298"]},"date_updated":"2026-01-12T09:57:53Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2507.09298"}]},{"file_date_updated":"2026-01-12T09:30:15Z","oa":1,"publisher":"Springer Nature","has_accepted_license":"1","ddc":["570"],"author":[{"last_name":"Maslarova","full_name":"Maslarova, Anna","first_name":"Anna"},{"full_name":"Shin, Jiyun N.","last_name":"Shin","first_name":"Jiyun N."},{"orcid":"0000-0002-9280-8597","last_name":"Navas Olivé","full_name":"Navas Olivé, Andrea C","first_name":"Andrea C","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce"},{"full_name":"Vöröslakos, Mihály","last_name":"Vöröslakos","first_name":"Mihály"},{"first_name":"Hajo","last_name":"Hamer","full_name":"Hamer, Hajo"},{"first_name":"Arnd","last_name":"Doerfler","full_name":"Doerfler, Arnd"},{"last_name":"Henin","full_name":"Henin, Simon","first_name":"Simon"},{"first_name":"György","full_name":"Buzsáki, György","last_name":"Buzsáki"},{"first_name":"Anli","last_name":"Liu","full_name":"Liu, Anli"}],"_id":"20977","DOAJ_listed":"1","publication_status":"published","quality_controlled":"1","day":"30","external_id":{"pmid":["39975118"]},"OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"date_updated":"2026-01-12T09:31:56Z","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_type":"original","date_created":"2026-01-11T23:01:35Z","citation":{"ama":"Maslarova A, Shin JN, Navas Olivé AC, et al. Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-66562-6\">10.1038/s41467-025-66562-6</a>","short":"A. Maslarova, J.N. Shin, A.C. Navas Olivé, M. Vöröslakos, H. Hamer, A. Doerfler, S. Henin, G. Buzsáki, A. Liu, Nature Communications 16 (2025).","mla":"Maslarova, Anna, et al. “Spatiotemporal Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans.” <i>Nature Communications</i>, vol. 16, 11636, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-66562-6\">10.1038/s41467-025-66562-6</a>.","apa":"Maslarova, A., Shin, J. N., Navas Olivé, A. C., Vöröslakos, M., Hamer, H., Doerfler, A., … Liu, A. (2025). Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-66562-6\">https://doi.org/10.1038/s41467-025-66562-6</a>","chicago":"Maslarova, Anna, Jiyun N. Shin, Andrea C Navas Olivé, Mihály Vöröslakos, Hajo Hamer, Arnd Doerfler, Simon Henin, György Buzsáki, and Anli Liu. “Spatiotemporal Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-66562-6\">https://doi.org/10.1038/s41467-025-66562-6</a>.","ista":"Maslarova A, Shin JN, Navas Olivé AC, Vöröslakos M, Hamer H, Doerfler A, Henin S, Buzsáki G, Liu A. 2025. Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans. Nature Communications. 16, 11636.","ieee":"A. Maslarova <i>et al.</i>, “Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"OA_place":"publisher","file":[{"relation":"main_file","date_created":"2026-01-12T09:30:15Z","creator":"dernst","file_id":"20978","access_level":"open_access","date_updated":"2026-01-12T09:30:15Z","file_name":"2025_NatureComm_Maslarova.pdf","file_size":7629997,"content_type":"application/pdf","success":1,"checksum":"a8a1670e197484382e087be60f643945"}],"oa_version":"Published Version","status":"public","department":[{"_id":"PeJo"}],"volume":16,"abstract":[{"lang":"eng","text":"Hippocampal sharp-wave ripples (SPW-Rs) are high-frequency oscillations critical for memory consolidation. Despite extensive characterization in rodents, their detection in humans is limited by coarse spatial sampling, interictal epileptiform discharges (IEDs), and a lack of consensus on human ripple localization and morphology. Here, we demonstrate that mouse and human hippocampal ripples share spatial, spectral and temporal features, which are clearly distinct from IEDs. In recordings from male APP/PS1 mice, SPW-Rs were distinguishable from IEDs by multiple criteria. Hippocampal ripples recorded during NREM sleep in female and male surgical epilepsy patients exhibited similar narrowband frequency peaks and multiple ripple cycles in the CA1 and subiculum regions. Conversely, IEDs showed a broad spatial extent and wide-band frequency power. We developed a semi-automated, ripple curation toolbox (ripmap) to separate event waveforms by low-dimensional embedding to reduce false-positive rate in selected ripple channels. Our approach improves ripple detection and provides a firm foundation for future human memory research."}],"month":"12","article_processing_charge":"Yes","intvolume":"        16","year":"2025","acknowledgement":"We thank Karl Rössler and Sebastian Brandner for the human SEEG implantations; Katja Kobow for providing the histopathological findings of the patients; Jay Jeschke for help with human electrode localization; Esha Brahmbhatt and Deren Aykan for help with animal habituation; Mursel Karadas for the rodent treadmill design; Nicholas Paleologos, Noam Nitzan, Michael D Hadler and Samuel McKenzie for rating events in a human ripple survey included in a previous version of the manuscript; Nicholas Paleologos for sharing NYU iEEG data for validating UMAP parameters; Julio Esparza for help on the topological analysis through discussions; Thomas Hainmüller, Yiyao Zhang and Mursel Karadas for feedback on the manuscript. We would like to acknowledge Corticale SRL (Genoa, Italy) for providing the SiNAPS probes, and NeuroNexus (Ann Arbor, MI) for their contribution of the data acquisition system and Radiens software. We further acknowledge both Corticale and NeuroNexus for training and support making this research possible. This work was supported by the German Research Foundation (DFG; Walter Benjamin Fellowship MA 10301/1-1, A.M.), NYU Langone Health Finding a Cure for Epilepsy and Seizures (FACES, A.M.), the NOMIS Fellowship (A.N.-O.), the National Institutes of Health (R01NS127954, K23NS104252, A.L.; MH122391, U19NS107616, R01MH139216 G.B.,), and the NYU Department of Neurology (A.L.).","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"article_number":"11636","title":"Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans","doi":"10.1038/s41467-025-66562-6","type":"journal_article","language":[{"iso":"eng"}],"publication":"Nature Communications","date_published":"2025-12-30T00:00:00Z","scopus_import":"1"},{"corr_author":"1","department":[{"_id":"JiFr"}],"month":"05","abstract":[{"lang":"eng","text":"Plant cells respond to a wide range of stimuli through intracellular calcium (Ca2+) signaling. Cyclic nucleotide-gated channels (CNGCs) are a major class of plant Ca2+ channels, with 20 homologs in Arabidopsis. These tetrameric plasma membrane proteins act downstream of diverse signals, such as phytohormones, extracellular damage, cell wall integrity or temperature. Here, we identify a class of plant-specific proteins, Armadillo Repeat Only (ARO), as essential regulators of possibly all plant CNGCs. Abrogation of functional sporophytic AROs results in a phenotypic pattern strongly reminiscent of CNGC dysfunction, including defects in root gravitropism, root hair growth and morphology, stomatal movement, and responses to extracellular ATP and the phytohormone auxin. aro2/3/4 mutants are fully resistant to the toxic effects caused by overexpression of CNGCs. AROs colocalize and physically interact with multiple CNGCs and modulate CNGC-dependent currents in Xenopus oocytes. Structural modeling and site-directed mutagenesis reveal AROs tetramer formation surrounding the CNGC channel, interacting via its IQ domain. Taken together, plant CNGC channels don’t act alone, but in a larger complex - channelosome, first of a kind in plants."}],"article_processing_charge":"No","publication_status":"draft","status":"public","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20964"}]},"citation":{"apa":"Kulich, I., Oulehlová, D., Vladimirtsev, D., Zou, M., Lileikyte, E., Bondar, A., … Friml, J. (n.d.). Armadillo repeat only proteins are required for the function of plant CNGC channels. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.01.06.631460\">https://doi.org/10.1101/2025.01.06.631460</a>","mla":"Kulich, Ivan, et al. “Armadillo Repeat Only Proteins Are Required for the Function of Plant CNGC Channels.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.01.06.631460\">10.1101/2025.01.06.631460</a>.","chicago":"Kulich, Ivan, Denisa Oulehlová, Dmitrii Vladimirtsev, Minxia Zou, Edita Lileikyte, Alexey Bondar, Katarína Kulichová, et al. “Armadillo Repeat Only Proteins Are Required for the Function of Plant CNGC Channels.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.01.06.631460\">https://doi.org/10.1101/2025.01.06.631460</a>.","ieee":"I. Kulich <i>et al.</i>, “Armadillo repeat only proteins are required for the function of plant CNGC channels,” <i>bioRxiv</i>. .","ista":"Kulich I, Oulehlová D, Vladimirtsev D, Zou M, Lileikyte E, Bondar A, Kulichová K, Janda M, Iakovenko O, Neubergerová M, Studtrucker T, Pleskot R, Dietrich P, Fendrych M, Friml J. Armadillo repeat only proteins are required for the function of plant CNGC channels. bioRxiv, <a href=\"https://doi.org/10.1101/2025.01.06.631460\">10.1101/2025.01.06.631460</a>.","ama":"Kulich I, Oulehlová D, Vladimirtsev D, et al. Armadillo repeat only proteins are required for the function of plant CNGC channels. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.01.06.631460\">10.1101/2025.01.06.631460</a>","short":"I. Kulich, D. Oulehlová, D. Vladimirtsev, M. Zou, E. Lileikyte, A. Bondar, K. Kulichová, M. Janda, O. Iakovenko, M. Neubergerová, T. Studtrucker, R. Pleskot, P. Dietrich, M. Fendrych, J. Friml, BioRxiv (n.d.)."},"OA_place":"repository","_id":"20982","author":[{"last_name":"Kulich","full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan"},{"last_name":"Oulehlová","full_name":"Oulehlová, Denisa","first_name":"Denisa"},{"full_name":"Vladimirtsev, Dmitrii","last_name":"Vladimirtsev","first_name":"Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia","last_name":"Zou"},{"first_name":"Edita","last_name":"Lileikyte","full_name":"Lileikyte, Edita"},{"first_name":"Alexey","last_name":"Bondar","full_name":"Bondar, Alexey"},{"first_name":"Katarína","last_name":"Kulichová","full_name":"Kulichová, Katarína"},{"first_name":"Martin","full_name":"Janda, Martin","last_name":"Janda"},{"first_name":"Oksana","full_name":"Iakovenko, Oksana","last_name":"Iakovenko"},{"first_name":"Michaela","last_name":"Neubergerová","full_name":"Neubergerová, Michaela"},{"first_name":"Tanja","last_name":"Studtrucker","full_name":"Studtrucker, Tanja"},{"last_name":"Pleskot","full_name":"Pleskot, Roman","first_name":"Roman"},{"first_name":"Petra","last_name":"Dietrich","full_name":"Dietrich, Petra"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"oa_version":"Preprint","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa":1,"date_created":"2026-01-13T14:07:58Z","main_file_link":[{"url":"https://doi.org/10.1101/2025.01.06.631460","open_access":"1"}],"type":"preprint","language":[{"iso":"eng"}],"date_published":"2025-05-16T00:00:00Z","publication":"bioRxiv","date_updated":"2026-04-07T11:41:43Z","doi":"10.1101/2025.01.06.631460","title":"Armadillo repeat only proteins are required for the function of plant CNGC channels","day":"16","year":"2025","acknowledgement":"This project was supported by the Czech Science Foundation grant Nr. 25-16449S and by European\r\nUnion, Horizon Europe, project MOLIPEC, ID 101087030. Computational resources used for structural\r\nmodeling were provided by the e-INFRA CZ project (ID:90254), supported by the Ministry of Education,\r\nYouth and Sports of the Czech Republic. Part of the work was carried out with the support of a Growth\r\nFacility (BC Core Facilities; IPMB BC CAS). X. laevis oocytes were kindly provided by C. Korbmacher on\r\na regular basis (FAU Erlangen-Nürnberg). MF received support from the European Research Council\r\n(Grant 480 No. 101125499). We acknowledge the core facility LMH, the BC CAS supported by the MEYS\r\nCR (LM 2023050 Czech-BioImaging). DO received support from the Czech Science Foundation grant Nr.\r\n24-12107S\r\n","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"quality_controlled":"1","PlanS_conform":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1","ddc":["540"],"_id":"20990","author":[{"first_name":"Peichen","last_name":"Zhong","full_name":"Zhong, Peichen"},{"full_name":"Kim, Dongjin","last_name":"Kim","first_name":"Dongjin"},{"full_name":"King, Daniel S.","last_name":"King","first_name":"Daniel S."},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}],"publisher":"Springer Nature","file_date_updated":"2026-01-20T07:22:04Z","oa":1,"date_updated":"2026-01-20T07:23:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","OA_type":"gold","volume":11,"abstract":[{"text":"Modeling the response of material and chemical systems to electric fields remains a longstanding challenge. Machine learning interatomic potentials (MLIPs) offer an efficient and scalable alternative to quantum mechanical methods, but do not by themselves incorporate electrical response. Here, we show that polarization and Born effective charge (BEC) tensors can be directly extracted from long-range MLIPs within the Latent Ewald Summation (LES) framework, solely by learning from energy and force data. Using this approach, we predict the infrared spectra of bulk water under zero or finite external electric fields, ionic conductivities of high-pressure superionic ice, and the phase transition and hysteresis in ferroelectric PbTiO3 perovskite. This work thus extends the capability of MLIPs to predict electrical response –without training on charges or polarization or BECs– and enables accurate modeling of electric-field-driven processes in diverse systems at scale.","lang":"eng"}],"month":"12","article_processing_charge":"Yes","department":[{"_id":"BiCh"}],"status":"public","file":[{"date_created":"2026-01-20T07:22:04Z","creator":"dernst","relation":"main_file","file_id":"21005","access_level":"open_access","content_type":"application/pdf","file_name":"2025_npj_Zhong.pdf","file_size":2686255,"date_updated":"2026-01-20T07:22:04Z","success":1,"checksum":"cc999804ba3bfed809ae46c73869e4e3"}],"oa_version":"Published Version","citation":{"short":"P. Zhong, D. Kim, D.S. King, B. Cheng, Npj Computational Materials 11 (2025).","ama":"Zhong P, Kim D, King DS, Cheng B. Machine learning interatomic potential can infer electrical response. <i>npj Computational Materials</i>. 2025;11. doi:<a href=\"https://doi.org/10.1038/s41524-025-01911-z\">10.1038/s41524-025-01911-z</a>","ieee":"P. Zhong, D. Kim, D. S. King, and B. Cheng, “Machine learning interatomic potential can infer electrical response,” <i>npj Computational Materials</i>, vol. 11. Springer Nature, 2025.","ista":"Zhong P, Kim D, King DS, Cheng B. 2025. Machine learning interatomic potential can infer electrical response. npj Computational Materials. 11, 384.","chicago":"Zhong, Peichen, Dongjin Kim, Daniel S. King, and Bingqing Cheng. “Machine Learning Interatomic Potential Can Infer Electrical Response.” <i>Npj Computational Materials</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41524-025-01911-z\">https://doi.org/10.1038/s41524-025-01911-z</a>.","apa":"Zhong, P., Kim, D., King, D. S., &#38; Cheng, B. (2025). Machine learning interatomic potential can infer electrical response. <i>Npj Computational Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41524-025-01911-z\">https://doi.org/10.1038/s41524-025-01911-z</a>","mla":"Zhong, Peichen, et al. “Machine Learning Interatomic Potential Can Infer Electrical Response.” <i>Npj Computational Materials</i>, vol. 11, 384, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41524-025-01911-z\">10.1038/s41524-025-01911-z</a>."},"OA_place":"publisher","date_created":"2026-01-15T12:17:07Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_published":"2025-12-29T00:00:00Z","language":[{"iso":"eng"}],"publication":"npj Computational Materials","scopus_import":"1","type":"journal_article","doi":"10.1038/s41524-025-01911-z","title":"Machine learning interatomic potential can infer electrical response","publication_identifier":{"eissn":["2057-3960"]},"article_number":"384","acknowledgement":"The authors thank for valuable discussions with Pinchen Xie, David Limmer, Jeff Neaton, and Greg Voth. The authors thank Sebastien Hamel for providing the DFT MD trajectories for superionic water, and help clarifying questions related to the pseudopotentials. The authors thank Federico Grasselli and Stefano Baroni for providing data and notebooks for computing the conductivity of a molten salt. This research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California, Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). D.S.K. and P.Z. acknowledge funding from the BIDMaP Postdoctoral Fellowship.","intvolume":"        11","year":"2025"},{"publication_status":"published","corr_author":"1","oa":1,"file_date_updated":"2026-02-12T07:50:47Z","publisher":"Cambridge: Alliance of Diamond Open Access Journals","_id":"21003","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177"},{"first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo","last_name":"Verzobio","orcid":"0000-0002-0854-0306"}],"ddc":["510"],"has_accepted_license":"1","date_updated":"2026-02-12T08:03:12Z","OA_type":"diamond","day":"01","external_id":{"arxiv":["2408.11453"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"},{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"}],"status":"public","department":[{"_id":"TiBr"}],"article_processing_charge":"No","abstract":[{"text":"We extend work of Heath-Brown and Salberger, based on the determinant method, to provide a uniform upper bound for the number of integral points of bounded height on an affine surface, which are subject to a polynomial congruence condition. This is applied to get a new uniform bound for points on diagonal quadric surfaces, and to a problem about the representation of integers as a sum of four unlike powers.","lang":"eng"}],"volume":2025,"month":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2026-01-18T23:02:44Z","article_type":"original","ec_funded":1,"OA_place":"publisher","citation":{"short":"T.D. Browning, M. Verzobio, Discrete Analysis 2025 (2025).","ama":"Browning TD, Verzobio M. Counting integer points on affine surfaces with a side condition. <i>Discrete Analysis</i>. 2025;2025. doi:<a href=\"https://doi.org/10.19086/da.143787\">10.19086/da.143787</a>","ieee":"T. D. Browning and M. Verzobio, “Counting integer points on affine surfaces with a side condition,” <i>Discrete Analysis</i>, vol. 2025. Cambridge: Alliance of Diamond Open Access Journals, 2025.","ista":"Browning TD, Verzobio M. 2025. Counting integer points on affine surfaces with a side condition. Discrete Analysis. 2025, 12.","chicago":"Browning, Timothy D, and Matteo Verzobio. “Counting Integer Points on Affine Surfaces with a Side Condition.” <i>Discrete Analysis</i>. Cambridge: Alliance of Diamond Open Access Journals, 2025. <a href=\"https://doi.org/10.19086/da.143787\">https://doi.org/10.19086/da.143787</a>.","mla":"Browning, Timothy D., and Matteo Verzobio. “Counting Integer Points on Affine Surfaces with a Side Condition.” <i>Discrete Analysis</i>, vol. 2025, 12, Cambridge: Alliance of Diamond Open Access Journals, 2025, doi:<a href=\"https://doi.org/10.19086/da.143787\">10.19086/da.143787</a>.","apa":"Browning, T. D., &#38; Verzobio, M. (2025). Counting integer points on affine surfaces with a side condition. <i>Discrete Analysis</i>. Cambridge: Alliance of Diamond Open Access Journals. <a href=\"https://doi.org/10.19086/da.143787\">https://doi.org/10.19086/da.143787</a>"},"oa_version":"Published Version","file":[{"date_updated":"2026-02-12T07:50:47Z","file_size":393625,"file_name":"2025_DiscreteAnalysis_Browning.pdf","content_type":"application/pdf","success":1,"checksum":"3d38e850b40f3e1abbfd30073bd4388a","relation":"main_file","date_created":"2026-02-12T07:50:47Z","creator":"dernst","file_id":"21214","access_level":"open_access"}],"doi":"10.19086/da.143787","type":"journal_article","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Discrete Analysis","date_published":"2025-09-01T00:00:00Z","year":"2025","intvolume":"      2025","acknowledgement":"Supported by FWF grant (DOI 10.55776/P36278), Supported by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413.","arxiv":1,"article_number":"12","publication_identifier":{"eissn":["2397-3129"]},"title":"Counting integer points on affine surfaces with a side condition"},{"intvolume":"        21","year":"2025","issue":"4","arxiv":1,"publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"title":"A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT","doi":"10.1145/3748723","type":"journal_article","publication":"ACM Transactions on Algorithms","language":[{"iso":"eng"}],"date_published":"2025-10-01T00:00:00Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2026-01-20T10:04:02Z","article_type":"original","citation":{"chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for SPARSEST CUT.” <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3748723\">https://doi.org/10.1145/3748723</a>.","apa":"Kolmogorov, V. (2025). A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3748723\">https://doi.org/10.1145/3748723</a>","mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for SPARSEST CUT.” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 4, Association for Computing Machinery, 2025, pp. 1–22, doi:<a href=\"https://doi.org/10.1145/3748723\">10.1145/3748723</a>.","ista":"Kolmogorov V. 2025. A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. ACM Transactions on Algorithms. 21(4), 1–22.","ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT,” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 4. Association for Computing Machinery, pp. 1–22, 2025.","short":"V. Kolmogorov, ACM Transactions on Algorithms 21 (2025) 1–22.","ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. <i>ACM Transactions on Algorithms</i>. 2025;21(4):1-22. doi:<a href=\"https://doi.org/10.1145/3748723\">10.1145/3748723</a>"},"OA_place":"publisher","file":[{"access_level":"open_access","date_created":"2026-01-21T09:38:09Z","creator":"dernst","relation":"main_file","file_id":"21031","success":1,"checksum":"4a80fdb1e3711b9a2768d2bb8f6d3b4e","content_type":"application/pdf","file_name":"2025_ACMToA_Kolmogorov.pdf","date_updated":"2026-01-21T09:38:09Z","file_size":2208302}],"oa_version":"Published Version","status":"public","related_material":{"record":[{"status":"public","id":"17236","relation":"shorter_version"}]},"department":[{"_id":"VlKo"}],"abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm. We present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors. We also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}],"month":"10","volume":21,"article_processing_charge":"Yes (via OA deal)","day":"01","OA_type":"hybrid","external_id":{"arxiv":["2307.00115"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1-22","date_updated":"2026-01-21T09:46:26Z","file_date_updated":"2026-01-21T09:38:09Z","oa":1,"publisher":"Association for Computing Machinery","has_accepted_license":"1","ddc":["510"],"author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"_id":"21007","publication_status":"published","PlanS_conform":"1","quality_controlled":"1","corr_author":"1"},{"publication_status":"submitted","status":"public","department":[{"_id":"HeEd"}],"article_processing_charge":"No","abstract":[{"text":"Motivated by applications in chemistry, we give a homlogical definition of tunnels, or more generally cobordisms, connecting disjoint parts of a cell complex. For a filtered complex, this defines a persistence module. We give a method for identifying birth and death times using kernel persistence and a matrix reduction algorithm for pairing birth and death times.","lang":"eng"}],"month":"05","oa":1,"ec_funded":1,"date_created":"2026-01-20T10:12:21Z","OA_place":"repository","citation":{"ista":"Bokor Bleile Y, Fajstrup L, Heiss T, Svane AM, Sørensen SS. Identifying cobordisms using kernel persistence. arXiv, 2505.17858.","ieee":"Y. Bokor Bleile, L. Fajstrup, T. Heiss, A. M. Svane, and S. S. Sørensen, “Identifying cobordisms using kernel persistence,” <i>arXiv</i>. .","apa":"Bokor Bleile, Y., Fajstrup, L., Heiss, T., Svane, A. M., &#38; Sørensen, S. S. (n.d.). Identifying cobordisms using kernel persistence. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2505.17858\">https://doi.org/10.48550/arXiv.2505.17858</a>","mla":"Bokor Bleile, Yossi, et al. “Identifying Cobordisms Using Kernel Persistence.” <i>ArXiv</i>, 2505.17858, doi:<a href=\"https://doi.org/10.48550/arXiv.2505.17858\">10.48550/arXiv.2505.17858</a>.","chicago":"Bokor Bleile, Yossi, Lisbeth Fajstrup, Teresa Heiss, Anne Marie Svane, and Søren Strandskov Sørensen. “Identifying Cobordisms Using Kernel Persistence.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2505.17858\">https://doi.org/10.48550/arXiv.2505.17858</a>.","ama":"Bokor Bleile Y, Fajstrup L, Heiss T, Svane AM, Sørensen SS. Identifying cobordisms using kernel persistence. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2505.17858\">10.48550/arXiv.2505.17858</a>","short":"Y. Bokor Bleile, L. Fajstrup, T. Heiss, A.M. Svane, S.S. Sørensen, ArXiv (n.d.)."},"_id":"21016","author":[{"full_name":"Bleile, Yossi","orcid":"0000-0002-4861-9174","last_name":"Bleile","first_name":"Yossi","id":"920a7385-7995-11ef-9bfd-8c434cd8f3c2"},{"last_name":"Fajstrup","full_name":"Fajstrup, Lisbeth","first_name":"Lisbeth"},{"orcid":"0000-0002-1780-2689","last_name":"Heiss","full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa"},{"full_name":"Svane, Anne Marie","last_name":"Svane","first_name":"Anne Marie"},{"last_name":"Sørensen","full_name":"Sørensen, Søren Strandskov","first_name":"Søren Strandskov"}],"oa_version":"Preprint","doi":"10.48550/arXiv.2505.17858","date_updated":"2026-06-11T11:51:13Z","type":"preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2505.17858","open_access":"1"}],"publication":"arXiv","date_published":"2025-05-23T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2505.17858"]},"year":"2025","day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Y. B. B. and L. F. were funded by the Independent Research Fund Denmark, grant\r\nnumber 1026-00037. T. H. was partially supported by the European Research Council\r\n(ERC) Horizon 2020, grant number 788183.","project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020"}],"arxiv":1,"article_number":"2505.17858","title":"Identifying cobordisms using kernel persistence"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","day":"05","project":[{"name":"Interface Theory for Security and Privacy","_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","grant_number":"F8502"},{"_id":"7bdd2f70-9f16-11ee-852c-b7950bc6d277","name":"SeCure, privAte, and interoperabLe layEr 2","grant_number":"ICT22-045"}],"date_updated":"2026-06-18T18:28:26Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3769423"}],"oa":1,"_id":"21017","author":[{"full_name":"Neiheiser, Ray","orcid":"0000-0001-7227-8309","last_name":"Neiheiser","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4","first_name":"Ray"},{"first_name":"Miguel","last_name":"Matos","full_name":"Matos, Miguel"},{"last_name":"Rodrigues","full_name":"Rodrigues, Luis","first_name":"Luis"}],"ddc":["000"],"has_accepted_license":"1","publisher":"Association for Computing Machinery","publication_status":"epub_ahead","quality_controlled":"1","PlanS_conform":"1","corr_author":"1","acknowledgement":"We thank the ACM TOCS Editors and the reviewers for their help in improving the manuscript. This work was partially supported by CAPES - Brazil (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) and byFundação para a Ciência e Tecnologia (FCT) under project UIDB/50021/2020 and grant 2020.05270.BD, and via project COSMOS (via the OE with ref. PTDC/EEI-COM/29271/2017, via the łPrograma Operacional Regional de Lisboa na sua componente FEDER” with ref. Lisboa-01-0145-FEDER-029271) and project Angainor with reference LISBOA-01-0145-FEDER-031456, grant agreement number 952226, and project GLOG, with reference LISBOA2030-FEDER-00771200, and project BIG (Enhancing the research and innovation potential of Tecnico through blockchain technologies and design Innovation for social Good), and project ScalableCosmosConsensus, and the Austrian Science Fund (FWF) SFB project SpyCoDe F8502 and the Vienna Science and Technology Fund (WWTF) project SCALE2 CT22-045","year":"2025","title":"Kauri: BFT consensus with pipelined tree-based dissemination and aggregation","article_number":"3769423","publication_identifier":{"issn":["0734-2071"],"eissn":["1557-7333"]},"doi":"10.1145/3769423","scopus_import":"1","date_published":"2025-09-05T00:00:00Z","publication":"ACM Transactions on Computer Systems","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2026-01-20T10:14:23Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","OA_place":"publisher","citation":{"ama":"Neiheiser R, Matos M, Rodrigues L. Kauri: BFT consensus with pipelined tree-based dissemination and aggregation. <i>ACM Transactions on Computer Systems</i>. 2025. doi:<a href=\"https://doi.org/10.1145/3769423\">10.1145/3769423</a>","short":"R. Neiheiser, M. Matos, L. Rodrigues, ACM Transactions on Computer Systems (2025).","ieee":"R. Neiheiser, M. Matos, and L. Rodrigues, “Kauri: BFT consensus with pipelined tree-based dissemination and aggregation,” <i>ACM Transactions on Computer Systems</i>. Association for Computing Machinery, 2025.","ista":"Neiheiser R, Matos M, Rodrigues L. 2025. Kauri: BFT consensus with pipelined tree-based dissemination and aggregation. ACM Transactions on Computer Systems., 3769423.","mla":"Neiheiser, Ray, et al. “Kauri: BFT Consensus with Pipelined Tree-Based Dissemination and Aggregation.” <i>ACM Transactions on Computer Systems</i>, 3769423, Association for Computing Machinery, 2025, doi:<a href=\"https://doi.org/10.1145/3769423\">10.1145/3769423</a>.","apa":"Neiheiser, R., Matos, M., &#38; Rodrigues, L. (2025). Kauri: BFT consensus with pipelined tree-based dissemination and aggregation. <i>ACM Transactions on Computer Systems</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3769423\">https://doi.org/10.1145/3769423</a>","chicago":"Neiheiser, Ray, Miguel Matos, and Luis Rodrigues. “Kauri: BFT Consensus with Pipelined Tree-Based Dissemination and Aggregation.” <i>ACM Transactions on Computer Systems</i>. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3769423\">https://doi.org/10.1145/3769423</a>."},"status":"public","article_processing_charge":"Yes (via OA deal)","month":"09","abstract":[{"text":"With the growing interest in blockchains, permissioned approaches to consensus have received increasing attention. Unfortunately, the BFT consensus algorithms that are the backbone of most of these blockchains scale poorly and offer limited throughput. In fact, many state-of-the-art BFT consensus algorithms require a single leader process to receive and validate votes from a quorum of processes and then broadcast the result, which is inherently non-scalable. Recent approaches avoid this bottleneck by using dissemination/aggregation trees to propagate values and collect and validate votes. However, the use of trees increases the round latency, which limits the throughput for deeper trees. In this paper we propose Kauri, a BFT communication abstraction that sustains high throughput as the system size grows by leveraging a novel pipelining technique to perform scalable dissemination and aggregation on trees. Furthermore, when the number of faults is moderate (arguably the most common case in practice), our construction is able to recover from faults in an optimal number of reconfiguration steps. We implemented and experimentally evaluated Kauri with up to 800 processes. Our results show that Kauri outperforms the throughput of state-of-the-art permissioned blockchain protocols, by up to 58x without compromising latency. Interestingly, in some cases, the parallelization provided by Kauri can also decrease the latency.","lang":"eng"}],"department":[{"_id":"KrPi"}]},{"article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Runtime verification offers scalable solutions to improve the safety and reliability of systems. However, systems that require verification or monitoring by a third party to ensure compliance with a specification might contain sensitive information, causing privacy concerns when usual runtime verification approaches are used. Privacy is compromised if protected information about the system, or sensitive data that is processed by the system, is revealed. In addition, revealing the specification being monitored may undermine the essence of third-party verification.\r\nIn this work, we propose two novel protocols for the privacy-preserving runtime verification of systems against formal sequential specifications. In our first protocol, the monitor verifies whether the system satisfies the specification without learning anything else, though both parties are aware of the specification. Our second protocol ensures that the system remains oblivious to the monitored specification, while the monitor learns only whether the system satisfies the specification and nothing more. Our protocols adapt and improve existing techniques used in cryptography, and more specifically, multi-party computation.\r\nThe sequential specification defines the observation step of the monitor, whose granularity depends on the situation (e.g., banks may be monitored on a daily basis). Our protocols exchange a single message per observation step, after an initialisation phase. This design minimises communication overhead, enabling relatively lightweight privacy-preserving monitoring. We implement our approach for monitoring specifications described by register automata and evaluate it experimentally.","lang":"eng"}],"month":"11","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"related_material":{"record":[{"id":"21401","status":"public","relation":"dissertation_contains"}]},"status":"public","oa_version":"Published Version","file":[{"date_updated":"2026-01-21T07:34:58Z","file_size":1241912,"file_name":"2025_CCS_HenzingerT.pdf","content_type":"application/pdf","success":1,"checksum":"615ffddab6c7285158c2953acec6fa6f","relation":"main_file","date_created":"2026-01-21T07:34:58Z","creator":"dernst","file_id":"21024","access_level":"open_access"}],"OA_place":"publisher","citation":{"ama":"Henzinger TA, Karimi M, Thejaswini KS. Privacy-preserving runtime verification. In: <i>Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security</i>. Association for Computing Machinery; 2025:2774-2787. doi:<a href=\"https://doi.org/10.1145/3719027.3765137\">10.1145/3719027.3765137</a>","short":"T.A. Henzinger, M. Karimi, K.S. Thejaswini, in:, Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2025, pp. 2774–2787.","ieee":"T. A. Henzinger, M. Karimi, and K. S. Thejaswini, “Privacy-preserving runtime verification,” in <i>Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security</i>, Taipei, Taiwan, 2025, pp. 2774–2787.","ista":"Henzinger TA, Karimi M, Thejaswini KS. 2025. Privacy-preserving runtime verification. Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 2774–2787.","mla":"Henzinger, Thomas A., et al. “Privacy-Preserving Runtime Verification.” <i>Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security</i>, Association for Computing Machinery, 2025, pp. 2774–87, doi:<a href=\"https://doi.org/10.1145/3719027.3765137\">10.1145/3719027.3765137</a>.","apa":"Henzinger, T. A., Karimi, M., &#38; Thejaswini, K. S. (2025). Privacy-preserving runtime verification. In <i>Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security</i> (pp. 2774–2787). Taipei, Taiwan: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3719027.3765137\">https://doi.org/10.1145/3719027.3765137</a>","chicago":"Henzinger, Thomas A, Mahyar Karimi, and K. S. Thejaswini. “Privacy-Preserving Runtime Verification.” In <i>Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security</i>, 2774–87. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3719027.3765137\">https://doi.org/10.1145/3719027.3765137</a>."},"ec_funded":1,"date_created":"2026-01-20T10:17:10Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2025-11-22T00:00:00Z","publication":"Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security","type":"conference","doi":"10.1145/3719027.3765137","title":"Privacy-preserving runtime verification","arxiv":1,"publication_identifier":{"isbn":["9798400715259"]},"acknowledgement":"This work is a part of projects VAMOS that has received fund-ing from the European Research Council (ERC), grant agreementNo 101020093 and the Austrian Science Fund (FWF) SFB projectSpyCoDe F8502.We thank anonymous reviewers for pointing us to related work [ 3] and for their valuable suggestions that improved this paper.","year":"2025","corr_author":"1","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mahyar","id":"6e5417ba-5355-11ee-ae5a-94c2e510b26b","full_name":"Karimi, Mahyar","last_name":"Karimi","orcid":"0009-0005-0820-1696"},{"id":"3807fb92-fdc1-11ee-bb4a-b4d8a431c753","first_name":"K. S.","last_name":"Thejaswini","full_name":"Thejaswini, K. S."}],"_id":"21020","ddc":["000"],"has_accepted_license":"1","publisher":"Association for Computing Machinery","oa":1,"file_date_updated":"2026-01-21T07:34:58Z","conference":{"location":"Taipei, Taiwan","end_date":"2025-10-17","start_date":"2025-10-13","name":"CCS: Conference on Computer and Communications Security"},"date_updated":"2026-03-13T13:37:19Z","page":"2774-2787","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"},{"grant_number":"F8502","_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","name":"Interface Theory for Security and Privacy"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","external_id":{"arxiv":["2505.09276"]},"day":"22"},{"author":[{"first_name":"Siddhartha","id":"fb21489d-057c-11f1-b1b6-d68cd6ae64f5","full_name":"Gairola, Siddhartha","last_name":"Gairola"},{"first_name":"Moritz","last_name":"Böhle","full_name":"Böhle, Moritz"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"last_name":"Schiele","full_name":"Schiele, Bernt","first_name":"Bernt"}],"_id":"21049","ddc":["000"],"has_accepted_license":"1","publisher":"ICLR","file_date_updated":"2026-02-09T06:06:14Z","oa":1,"conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2025-04-24","location":"Singapore","end_date":"2025-04-28"},"corr_author":"1","quality_controlled":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","OA_type":"gold","external_id":{"arxiv":["2503.00641"]},"date_updated":"2026-02-09T06:11:17Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_id":"21162","creator":"dernst","date_created":"2026-02-09T06:06:14Z","relation":"main_file","checksum":"6c8dfe4291c41d5a2c2fd838105e10b9","success":1,"content_type":"application/pdf","date_updated":"2026-02-09T06:06:14Z","file_name":"2025_ICLR_Gairola.pdf","file_size":24386863}],"OA_place":"publisher","citation":{"ama":"Gairola S, Böhle M, Locatello F, Schiele B. How to probe: Simple yet effective techniques for improving post-hoc explanations. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025.","short":"S. Gairola, M. Böhle, F. Locatello, B. Schiele, in:, 13th International Conference on Learning Representations, ICLR, 2025.","apa":"Gairola, S., Böhle, M., Locatello, F., &#38; Schiele, B. (2025). How to probe: Simple yet effective techniques for improving post-hoc explanations. In <i>13th International Conference on Learning Representations</i>. Singapore: ICLR.","mla":"Gairola, Siddhartha, et al. “How to Probe: Simple yet Effective Techniques for Improving Post-Hoc Explanations.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025.","chicago":"Gairola, Siddhartha, Moritz Böhle, Francesco Locatello, and Bernt Schiele. “How to Probe: Simple yet Effective Techniques for Improving Post-Hoc Explanations.” In <i>13th International Conference on Learning Representations</i>. ICLR, 2025.","ieee":"S. Gairola, M. Böhle, F. Locatello, and B. Schiele, “How to probe: Simple yet effective techniques for improving post-hoc explanations,” in <i>13th International Conference on Learning Representations</i>, Singapore, 2025.","ista":"Gairola S, Böhle M, Locatello F, Schiele B. 2025. How to probe: Simple yet effective techniques for improving post-hoc explanations. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"date_created":"2026-01-27T12:48:35Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Post-hoc importance attribution methods are a popular tool for “explaining” Deep Neural Networks (DNNs) and are inherently based on the assumption that the explanations can be applied independently of how the models were trained. Contrarily, in this work we bring forward empirical evidence that challenges this very notion. Surprisingly, we discover a strong dependency on and demonstrate that the training details of a pre-trained model’s classification layer (<10% of model parameters) play a crucial role, much more than the pre-training scheme itself. This is of high practical relevance: (1) as techniques for pre-training models are becoming increasingly diverse, understanding the interplay between these techniques and attribution methods is critical; (2) it sheds light on an important yet overlooked assumption of post-hoc attribution methods which can drastically impact model explanations and how they are interpreted eventually. With this finding we also present simple yet effective adjustments to the classification layers, that can significantly enhance the quality of model explanations. We validate our findings across several visual pre-training frameworks (fully-supervised, self-supervised, contrastive vision-language training) and analyse how they impact explanations for a wide range of attribution methods on a diverse set of evaluation metrics."}],"month":"01","department":[{"_id":"FrLo"}],"related_material":{"link":[{"url":"https://github.com/sidgairo18/how-to-probe","relation":"software"}]},"status":"public","title":"How to probe: Simple yet effective techniques for improving post-hoc explanations","arxiv":1,"acknowledgement":"We sincerely thank Sukrut Rao and Yue Fan for their valuable feedback on the paper and insightful discussions throughout the project. Additionally, we appreciate Sukrut’s help\r\nwith some LATEX sorcery. This work was partially supported by ELSA Mobility Program1\r\nas part of the ELLIS2 exchange program to the Institute of Science and Technology Austria (ISTA), where a portion of this research was conducted.","year":"2025","language":[{"iso":"eng"}],"date_published":"2025-01-22T00:00:00Z","publication":"13th International Conference on Learning Representations","type":"conference"}]