[{"month":"12","publication_status":"published","volume":62,"OA_type":"hybrid","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-01-05T12:27:41Z","status":"public","related_material":{"record":[{"status":"public","id":"14405","relation":"earlier_version"}]},"article_number":"43","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20866","oa_version":"Published Version","language":[{"iso":"eng"}],"project":[{"grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"grant_number":"F8502","_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","name":"Interface Theory for Security and Privacy"}],"publication":"Acta Informatica","corr_author":"1","scopus_import":"1","ec_funded":1,"department":[{"_id":"ToHe"}],"OA_place":"publisher","type":"journal_article","external_id":{"arxiv":["2305.02836"]},"publication_identifier":{"issn":["0001-5903"],"eissn":["1432-0525"]},"date_created":"2025-12-29T12:07:12Z","year":"2025","intvolume":" 62","has_accepted_license":"1","title":"Hypernode automata","file":[{"date_created":"2026-01-05T12:26:43Z","date_updated":"2026-01-05T12:26:43Z","file_size":7117003,"content_type":"application/pdf","creator":"dernst","success":1,"file_name":"2025_ActaInformatica_Bartocci.pdf","access_level":"open_access","checksum":"06ed45a1218ad8464818803ae2968aaf","relation":"main_file","file_id":"20944"}],"publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","citation":{"ama":"Bartocci E, Chalupa M, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata. Acta Informatica. 2025;62(4). doi:10.1007/s00236-025-00509-8","mla":"Bartocci, Ezio, et al. “Hypernode Automata.” Acta Informatica, vol. 62, no. 4, 43, Springer Nature, 2025, doi:10.1007/s00236-025-00509-8.","short":"E. Bartocci, M. Chalupa, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, Acta Informatica 62 (2025).","apa":"Bartocci, E., Chalupa, M., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A. (2025). Hypernode automata. Acta Informatica. Springer Nature. https://doi.org/10.1007/s00236-025-00509-8","chicago":"Bartocci, Ezio, Marek Chalupa, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da Costa. “Hypernode Automata.” Acta Informatica. Springer Nature, 2025. https://doi.org/10.1007/s00236-025-00509-8.","ieee":"E. Bartocci, M. Chalupa, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode automata,” Acta Informatica, vol. 62, no. 4. Springer Nature, 2025.","ista":"Bartocci E, Chalupa M, Henzinger TA, Nickovic D, Oliveira da Costa A. 2025. Hypernode automata. Acta Informatica. 62(4), 43."},"file_date_updated":"2026-01-05T12:26:43Z","ddc":["000"],"author":[{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"},{"first_name":"Ana","full_name":"Oliveira da Costa, Ana","orcid":"0000-0002-8741-5799","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4","last_name":"Oliveira da Costa"}],"arxiv":1,"oa":1,"date_published":"2025-12-09T00:00:00Z","day":"09","abstract":[{"lang":"eng","text":"In this work, we present hypernode automata as a specification formalism for hyperproperties of systems whose executions may be misaligned among themselves, such as concurrent systems. These automata consist of nodes labeled with hypernode logic formulas and transitions marked with synchronizing actions. Hypernode logic formulas establish relations between sequences of variable values among different system executions. This logic enables both synchronous and asynchronous analysis of traces. In its asynchronous view on execution traces, hypernode formulas establish relations on the order of value changes for each variable without correlating their timing. In both views, the analysis of different execution traces is synchronized through the transitions of hypernode automata. By combining logic’s declarative nature with automata’s procedural power, hypernode automata seamlessly integrate asynchronicity requirements at the node level with synchronicity between node transitions. We show that the model-checking problem for hypernode automata is decidable for specifications where each node specifies either a synchronous or an asynchronous requirement for the system’s executions, but not both."}],"doi":"10.1007/s00236-025-00509-8","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF) SFB project SpyCoDe 10.55776/F85, by the FWF projects ZK-35 and W1255-N23, and by the ERC Advanced Grant VAMOS 101020093. Open access funding provided by Institute of Science and Technology (IST Austria).","issue":"4","article_type":"original"},{"abstract":[{"lang":"eng","text":"We discuss the embeddability of subspaces of the Gromov–Hausdorff space, which consists of isometry classes of compact metric spaces endowed with the Gromov–Hausdorff distance, into Hilbert spaces. These embeddings are particularly valuable for applications to topological data analysis. We prove that its subspace consisting of metric spaces with at most n points has asymptotic dimension n(n−1)∕2. Thus, there exists a coarse embedding of that space into a Hilbert space. On the contrary, if the number of points is not bounded, then the subspace cannot be coarsely embedded into any uniformly convex Banach space and so, in particular, into any Hilbert space. Furthermore, we prove that, even if we restrict to finite metric spaces whose diameter is bounded by some constant, the subspace still cannot be bi-Lipschitz embedded into any finite-dimensional Hilbert space. We obtain both nonembeddability results by finding obstructions to coarse and bi-Lipschitz embeddings in families of isometry classes of finite subsets of the real line endowed with the Euclidean–Hausdorff distance."}],"day":"20","date_published":"2025-11-20T00:00:00Z","author":[{"first_name":"Nicolò","full_name":"Zava, Nicolò","orcid":"0000-0001-8686-1888","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","last_name":"Zava"}],"arxiv":1,"oa":1,"article_type":"original","acknowledgement":"The author was supported by the FWF Grant, Project number I4245-N35. The author would like to thank Thomas Weighill for the helpful discussions around Theorem 3.10, and Takamitsu Yamauchi for bringing to my attention the fundamental reference [35]. Furthermore, the author\r\nis thankful for the detailed and helpful comments of the reviewer of this manuscript.","issue":"8","doi":"10.2140/agt.2025.25.5153","title":"Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff space into Hilbert spaces","has_accepted_license":"1","date_created":"2025-12-29T12:09:09Z","year":"2025","intvolume":" 25","external_id":{"arxiv":["2303.04730"]},"publication_identifier":{"eissn":["1472-2739"],"issn":["1472-2747"]},"ddc":["500"],"file_date_updated":"2026-01-05T12:16:38Z","citation":{"ista":"Zava N. 2025. Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff space into Hilbert spaces. Algebraic & Geometric Topology. 25(8), 5153–5174.","ieee":"N. Zava, “Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff space into Hilbert spaces,” Algebraic & Geometric Topology, vol. 25, no. 8. Mathematical Sciences Publishers, pp. 5153–5174, 2025.","apa":"Zava, N. (2025). Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff space into Hilbert spaces. Algebraic & Geometric Topology. Mathematical Sciences Publishers. https://doi.org/10.2140/agt.2025.25.5153","chicago":"Zava, Nicolò. “Coarse and Bi-Lipschitz Embeddability of Subspaces of the Gromov–Hausdorff Space into Hilbert Spaces.” Algebraic & Geometric Topology. Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/agt.2025.25.5153.","short":"N. Zava, Algebraic & Geometric Topology 25 (2025) 5153–5174.","ama":"Zava N. Coarse and bi-Lipschitz embeddability of subspaces of the Gromov–Hausdorff space into Hilbert spaces. Algebraic & Geometric Topology. 2025;25(8):5153-5174. doi:10.2140/agt.2025.25.5153","mla":"Zava, Nicolò. “Coarse and Bi-Lipschitz Embeddability of Subspaces of the Gromov–Hausdorff Space into Hilbert Spaces.” Algebraic & Geometric Topology, vol. 25, no. 8, Mathematical Sciences Publishers, 2025, pp. 5153–74, doi:10.2140/agt.2025.25.5153."},"article_processing_charge":"No","file":[{"content_type":"application/pdf","success":1,"file_name":"2025_AlgebraicGeomTopology_Zava.pdf","creator":"dernst","file_size":574389,"date_updated":"2026-01-05T12:16:38Z","date_created":"2026-01-05T12:16:38Z","file_id":"20943","access_level":"open_access","checksum":"1e05b4f17a44500ae1ae1e21bc636f6a","relation":"main_file"}],"publisher":"Mathematical Sciences Publishers","publication":"Algebraic & Geometric Topology","project":[{"_id":"26AD5D90-B435-11E9-9278-68D0E5697425","name":"Algebraic Footprints of Geometric Features in Homology","grant_number":"I04245","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"OA_place":"publisher","type":"journal_article","department":[{"_id":"HeEd"}],"scopus_import":"1","corr_author":"1","date_updated":"2026-01-05T12:19:09Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"diamond","month":"11","publication_status":"published","volume":25,"_id":"20867","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"5153-5174","quality_controlled":"1","PlanS_conform":"1"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83xc"}],"title":"The neural basis of species-specific defensive behaviour in Peromyscus mice","status":"public","date_updated":"2026-01-05T11:38:41Z","month":"06","year":"2025","date_created":"2025-12-30T07:36:29Z","OA_type":"hybrid","oa_version":"Submitted Version","_id":"20883","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publisher":"Dryad","related_material":{"record":[{"status":"public","id":"20101","relation":"used_in_publication"}]},"citation":{"ista":"Felix B, Reinhard K, Nuttin B, Sans Dublanc A, Liu C, Tong V, Murmann JS, Wierda K, Farrow K, Hoekstra H. 2025. The neural basis of species-specific defensive behaviour in Peromyscus mice, Dryad, 10.5061/DRYAD.Q2BVQ83XC.","ieee":"B. Felix et al., “The neural basis of species-specific defensive behaviour in Peromyscus mice.” Dryad, 2025.","apa":"Felix, B., Reinhard, K., Nuttin, B., Sans Dublanc, A., Liu, C., Tong, V., … Hoekstra, H. (2025). The neural basis of species-specific defensive behaviour in Peromyscus mice. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83XC","chicago":"Felix, Baier, Katja Reinhard, Bram Nuttin, Arnau Sans Dublanc, Chen Liu, Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” Dryad, 2025. https://doi.org/10.5061/DRYAD.Q2BVQ83XC.","short":"B. Felix, K. Reinhard, B. Nuttin, A. Sans Dublanc, C. Liu, V. Tong, J.S. Murmann, K. Wierda, K. Farrow, H. Hoekstra, (2025).","ama":"Felix B, Reinhard K, Nuttin B, et al. The neural basis of species-specific defensive behaviour in Peromyscus mice. 2025. doi:10.5061/DRYAD.Q2BVQ83XC","mla":"Felix, Baier, et al. The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice. Dryad, 2025, doi:10.5061/DRYAD.Q2BVQ83XC."},"day":"23","abstract":[{"text":"Evading imminent predator threat is critical for survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours is still poorly understood. Here we find that two sister species of deer mice (genus Peromyscus) show different responses to the same looming stimulus: P. maniculatus, which occupies densely vegetated habitats, predominantly escapes, while the open field specialist, P. polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal gray (dPAG) in driving behaviour differs. While dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not P. polionotus, while their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain.","lang":"eng"}],"oa":1,"author":[{"last_name":"Felix","first_name":"Baier","full_name":"Felix, Baier"},{"last_name":"Reinhard","first_name":"Katja","full_name":"Reinhard, Katja"},{"full_name":"Nuttin, Bram","first_name":"Bram","last_name":"Nuttin"},{"full_name":"Sans Dublanc, Arnau","first_name":"Arnau","last_name":"Sans Dublanc"},{"last_name":"Liu","first_name":"Chen","full_name":"Liu, Chen"},{"first_name":"Victoria","full_name":"Tong, Victoria","last_name":"Tong"},{"first_name":"Julie Stefanie","full_name":"Murmann, Julie Stefanie","last_name":"Murmann","id":"1d390868-f128-11eb-9611-a0ca5f7833b5"},{"last_name":"Wierda","full_name":"Wierda, Keimpe","first_name":"Keimpe"},{"first_name":"Karl","full_name":"Farrow, Karl","last_name":"Farrow"},{"first_name":"Hopi","full_name":"Hoekstra, Hopi","last_name":"Hoekstra"}],"date_published":"2025-06-23T00:00:00Z","department":[{"_id":"GradSch"}],"OA_place":"repository","type":"research_data_reference","doi":"10.5061/DRYAD.Q2BVQ83XC"},{"date_created":"2026-01-02T10:46:47Z","year":"2025","publication_identifier":{"issn":["2663-337X"]},"title":"Theory and applications of verifiable delay functions","has_accepted_license":"1","citation":{"apa":"Hoffmann, C. (2025). Theory and applications of verifiable delay functions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20920","chicago":"Hoffmann, Charlotte. “Theory and Applications of Verifiable Delay Functions.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20920.","ieee":"C. Hoffmann, “Theory and applications of verifiable delay functions,” Institute of Science and Technology Austria, 2025.","ista":"Hoffmann C. 2025. Theory and applications of verifiable delay functions. Institute of Science and Technology Austria.","mla":"Hoffmann, Charlotte. Theory and Applications of Verifiable Delay Functions. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20920.","ama":"Hoffmann C. Theory and applications of verifiable delay functions. 2025. doi:10.15479/AT-ISTA-20920","short":"C. Hoffmann, Theory and Applications of Verifiable Delay Functions, Institute of Science and Technology Austria, 2025."},"file":[{"date_created":"2026-01-02T10:39:16Z","file_name":"2025_Hoffmann_Charlotte_Source.zip","creator":"choffman","content_type":"application/x-zip-compressed","date_updated":"2026-01-02T10:39:16Z","file_size":8355494,"relation":"source_file","checksum":"8a099fbf54963bd0be38f7ce73658682","access_level":"closed","file_id":"20921"},{"date_created":"2026-01-02T10:39:26Z","file_size":2258804,"date_updated":"2026-01-02T10:39:26Z","success":1,"file_name":"2025_Hoffmann_Charlotte_Thesis.pdf","creator":"choffman","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"9521c07bfb2bb5b14a49c09fcfc96474","file_id":"20922"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file_date_updated":"2026-01-02T10:39:26Z","ddc":["004"],"date_published":"2025-12-31T00:00:00Z","author":[{"id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","last_name":"Hoffmann","full_name":"Hoffmann, Charlotte","first_name":"Charlotte","orcid":"0000-0003-2027-5549"}],"oa":1,"abstract":[{"lang":"eng","text":"Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality.\r\n\r\nThe only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).\r\nThe iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \\pi. Given \\pi, the output of VDF can be verified in time much less than T.\r\n\r\nWe first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications.\r\n\r\nSecondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources.\r\n\r\nWe then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions).\r\n\r\nFinally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory.\r\n\r\nTogether, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications."}],"day":"31","doi":"10.15479/AT-ISTA-20920","degree_awarded":"PhD","publication_status":"published","month":"12","status":"public","date_updated":"2026-04-16T09:11:08Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"related_material":{"record":[{"status":"public","id":"13143","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"20701"},{"relation":"part_of_dissertation","status":"public","id":"12176"},{"relation":"earlier_version","status":"public","id":"20556"},{"id":"19778","status":"public","relation":"part_of_dissertation"}]},"page":"116","_id":"20920","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"OA_place":"publisher","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"KrPi"}]},{"has_accepted_license":"1","pmid":1,"title":"Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination","external_id":{"pmid":["41455105"]},"publication_identifier":{"eissn":["2666-1667"]},"year":"2025","date_created":"2026-01-04T23:01:33Z","intvolume":" 7","ddc":["570"],"article_processing_charge":"Yes","publisher":"Elsevier","DOAJ_listed":"1","citation":{"ista":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2025. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7, 104295.","ieee":"W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana, “Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination,” STAR Protocols, vol. 7. Elsevier, 2025.","apa":"Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., & Tachibana, K. (2025). Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2025.104295","chicago":"Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” STAR Protocols. Elsevier, 2025. https://doi.org/10.1016/j.xpro.2025.104295.","short":"W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2025).","ama":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 2025;7. doi:10.1016/j.xpro.2025.104295","mla":"Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” STAR Protocols, vol. 7, 104295, Elsevier, 2025, doi:10.1016/j.xpro.2025.104295."},"day":"26","abstract":[{"text":"Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.\r\nFor complete details on the use and execution of this protocol, please refer to Michael et al.1","lang":"eng"}],"author":[{"first_name":"Wataru","full_name":"Kobayashi, Wataru","last_name":"Kobayashi"},{"orcid":"0000-0002-6080-839X","first_name":"Alicia","full_name":"Michael, Alicia","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"full_name":"Ruangroengkulrith, Siwat","first_name":"Siwat","last_name":"Ruangroengkulrith"},{"first_name":"Maximilian","full_name":"Kümmecke, Maximilian","last_name":"Kümmecke"},{"last_name":"Tachibana","full_name":"Tachibana, Kikuë","first_name":"Kikuë"}],"oa":1,"date_published":"2025-12-26T00:00:00Z","acknowledgement":"We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).","article_type":"original","doi":"10.1016/j.xpro.2025.104295","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.xpro.2025.104295"}],"status":"public","date_updated":"2026-06-18T18:27:57Z","publication_status":"epub_ahead","month":"12","volume":7,"OA_type":"gold","_id":"20924","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","PlanS_conform":"1","article_number":"104295","quality_controlled":"1","project":[{"grant_number":"101162145","name":"Circadian structural transitions of chromatin","_id":"9136c684-16d5-11f0-9cad-91c0177b365f"}],"publication":"STAR Protocols","language":[{"iso":"eng"}],"department":[{"_id":"AlMi"}],"OA_place":"publisher","type":"journal_article","corr_author":"1","scopus_import":"1"},{"language":[{"iso":"eng"}],"publication":"Letters in Mathematical Physics","project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"ec_funded":1,"scopus_import":"1","corr_author":"1","type":"journal_article","OA_place":"publisher","department":[{"_id":"LaEr"}],"OA_type":"hybrid","month":"12","volume":116,"publication_status":"epub_ahead","date_updated":"2026-01-05T11:22:25Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.1007/s11005-025-02037-5","open_access":"1"}],"quality_controlled":"1","article_number":"5","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20925","oa_version":"Published Version","date_published":"2025-12-26T00:00:00Z","oa":1,"author":[{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"last_name":"Vogel","id":"1cd0554a-ea28-11f0-9f40-ff76440883cd","full_name":"Vogel, Cornelia","first_name":"Cornelia"}],"abstract":[{"text":"We prove normal typicality and dynamical typicality for a (centered) random block-band matrix model with block-dependent variances. A key feature of our model is that we achieve intermediate equilibration times, an aspect that has not been proven rigorously in any model before. Our proof builds on recently established concentration estimates for products of resolvents of Wigner type random matrices (Erdős and Riabov in Commun Math Phys 405(12): 282, 2024) and an intricate analysis of the deterministic approximation.","lang":"eng"}],"day":"26","doi":"10.1007/s11005-025-02037-5","article_type":"original","acknowledgement":"L.E. and J.H. are supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. Moreover, J.H. acknowledges (partial) financial support by the ERC Consolidator Grant “ProbQuant” (jointly with the Swiss State Secretariat for Education, Research and Innovation). C.V. was (partially) supported by the German Academic Scholarship Foundation and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – TRR 352 – Project-ID 470903074. Moreover, C.V. acknowledges (partial) financial support by the ERC Starting Grant “FermiMath\" No. 101040991 and the ERC Consolidator Grant “RAMBAS” No. 10104424, funded by the European Union. Open access funding provided by Institute of Science and Technology (IST Austria).","intvolume":" 116","date_created":"2026-01-04T23:01:33Z","year":"2025","publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"external_id":{"pmid":["41459414"]},"pmid":1,"title":"Normal typicality and dynamical typicality for a random block-band matrix model","has_accepted_license":"1","citation":{"ista":"Erdös L, Henheik SJ, Vogel C. 2025. Normal typicality and dynamical typicality for a random block-band matrix model. Letters in Mathematical Physics. 116, 5.","ieee":"L. Erdös, S. J. Henheik, and C. Vogel, “Normal typicality and dynamical typicality for a random block-band matrix model,” Letters in Mathematical Physics, vol. 116. Springer Nature, 2025.","chicago":"Erdös, László, Sven Joscha Henheik, and Cornelia Vogel. “Normal Typicality and Dynamical Typicality for a Random Block-Band Matrix Model.” Letters in Mathematical Physics. Springer Nature, 2025. https://doi.org/10.1007/s11005-025-02037-5.","apa":"Erdös, L., Henheik, S. J., & Vogel, C. (2025). Normal typicality and dynamical typicality for a random block-band matrix model. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-025-02037-5","short":"L. Erdös, S.J. Henheik, C. Vogel, Letters in Mathematical Physics 116 (2025).","ama":"Erdös L, Henheik SJ, Vogel C. Normal typicality and dynamical typicality for a random block-band matrix model. Letters in Mathematical Physics. 2025;116. doi:10.1007/s11005-025-02037-5","mla":"Erdös, László, et al. “Normal Typicality and Dynamical Typicality for a Random Block-Band Matrix Model.” Letters in Mathematical Physics, vol. 116, 5, Springer Nature, 2025, doi:10.1007/s11005-025-02037-5."},"article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","ddc":["510"]},{"doi":"10.1021/acs.jctc.5c01400","article_type":"original","acknowledgement":"Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating discussions.","issue":"24","date_published":"2025-12-10T00:00:00Z","arxiv":1,"author":[{"full_name":"Kim, Dongjin","first_name":"Dongjin","last_name":"Kim"},{"first_name":"Xiaoyu","full_name":"Wang, Xiaoyu","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","last_name":"Wang"},{"full_name":"Vargas, Santiago","first_name":"Santiago","last_name":"Vargas"},{"full_name":"Zhong, Peichen","first_name":"Peichen","last_name":"Zhong"},{"first_name":"Daniel S.","full_name":"King, Daniel S.","last_name":"King"},{"full_name":"Inizan, Theo Jaffrelot","first_name":"Theo Jaffrelot","last_name":"Inizan"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"oa":1,"abstract":[{"text":"Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs.","lang":"eng"}],"day":"10","citation":{"ama":"Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400","mla":"Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24, doi:10.1021/acs.jctc.5c01400.","short":"D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 12709–12724.","chicago":"Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King, Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400.","apa":"Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., & Cheng, B. (2025). A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400","ista":"Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724.","ieee":"D. Kim et al., “A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials,” Journal of Chemical Theory and Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724, 2025."},"publisher":"American Chemical Society","article_processing_charge":"No","year":"2025","date_created":"2026-01-04T23:01:33Z","intvolume":" 21","external_id":{"pmid":["41368735 "],"arxiv":["2507.14302"]},"publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"title":"A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials","pmid":1,"scopus_import":"1","corr_author":"1","type":"journal_article","OA_place":"repository","department":[{"_id":"GradSch"},{"_id":"BiCh"}],"language":[{"iso":"eng"}],"publication":"Journal of Chemical Theory and Computation","quality_controlled":"1","_id":"20926","page":"12709-12724","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","publication_status":"published","month":"12","volume":21,"status":"public","date_updated":"2026-01-05T11:34:21Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2507.14302","open_access":"1"}]},{"language":[{"iso":"eng"}],"publication":"Physical Review B","scopus_import":"1","type":"journal_article","OA_place":"repository","department":[{"_id":"MaIb"},{"_id":"JoFi"}],"OA_type":"green","publication_status":"published","month":"12","volume":112,"status":"public","date_updated":"2026-01-05T10:07:04Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2512.05236"}],"article_number":"214443","quality_controlled":"1","related_material":{"record":[{"id":"20940","status":"public","relation":"research_data"}]},"_id":"20927","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-12-19T00:00:00Z","author":[{"first_name":"Supriya","full_name":"Mandal, Supriya","last_name":"Mandal"},{"first_name":"Krishnendu","full_name":"Maji, Krishnendu","id":"76bc9e9f-ba0b-11ee-8184-90edabd17a58","last_name":"Maji"},{"last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","orcid":"0000-0001-8319-2148","first_name":"Lucky","full_name":"Kapoor, Lucky"},{"last_name":"Sasmal","full_name":"Sasmal, Souvik","first_name":"Souvik"},{"last_name":"Manni","first_name":"Soham","full_name":"Manni, Soham"},{"last_name":"Jesudasan","full_name":"Jesudasan, John","first_name":"John"},{"last_name":"Raychaudhuri","first_name":"Pratap","full_name":"Raychaudhuri, Pratap"},{"full_name":"Thamizhavel, Arumugam","first_name":"Arumugam","last_name":"Thamizhavel"},{"last_name":"Deshmukh","full_name":"Deshmukh, Mandar M.","first_name":"Mandar M."}],"arxiv":1,"oa":1,"abstract":[{"text":"Cavity-magnon polaritons are hybrid excitations from the interaction between cavity photons and magnons, the quanta of collective spin oscillations. Along with the tunability of the magnon-photon coupling strength, fast information transfer and conversion speed are desired in hybrid devices. This can be achieved utilizing the propagating nature of spin waves with nonzero momentum for their ultrafast time dynamics and reduced ohmic dissipation. Antiferromagnets are particularly interesting as hosts for magnons since stray-field interactions are minimized and they support multiple modes with distinctive magnetic-field behavior across the phase diagram. Chromium trichloride (CrCl3) is a van der Waals layered antiferromagnet having a strong easy-plane anisotropy and a weak in-plane easy-axis anisotropy. Despite some magnetic resonance studies, the impact of magnetic reorientation of spins in CrCl3 on the cavity-magnon-polariton interaction strength as a function of magnetic field remains largely unexplored. In this study, we investigate the coupling between magnons in CrCl3 and photons in a coplanar waveguide resonator as a function of magnetic field. In particular, we find that the magnon-photon coupling strength varies nonmonotonically and distinctly with the magnetic field for the acoustic and the optical magnons, which can be utilized to tune the magnon-photon coupling strength using an external magnetic field as a knob. We find the signature of spin-flop transition in the two harmonics of the cavity due to a stronger dispersive coupling between optical magnons and cavity photons at lower fields. Additionally, we find standing modes formed by spin waves with nonzero momentum associated with the two hybrid magnons when the external field is applied at an angle with the crystal plane. These modes do not undergo substantial coupling with the cavity mode unlike the antiferromagnetic modes and can be used as low-loss propagation channels in hybrid devices.","lang":"eng"}],"day":"19","doi":"10.1103/bdd1-b8ys","article_type":"original","acknowledgement":"We thank R. Vijayaraghavan, V. Singh, A. Kamra, A. Barman, M. Patankar, S. Kundu, S. Hazra, S. Sahu, A. Riswadkar, A. Bhattacharjee, and S. Das for helpful discussions and experimental assistance. We acknowledge the Swarnajayanti Fellowship of the Department of Science and Technology (for M.M.D.), DST Nanomission Grant No. SR/NM/NS-45/2016, SERB SUPRA Grant No. SPR/2019/001247, ONRG Grant No. N62909–18-1–2058, and the Department of Atomic Energy of the Government of India Grant No. 12-R&D-TFR5.10–0100 for support.","issue":"21","year":"2025","date_created":"2026-01-04T23:01:34Z","intvolume":" 112","external_id":{"arxiv":["2512.05236"]},"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"title":"Cavity based sensing of antiferromagnetic canting and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system","citation":{"ama":"Mandal S, Maji K, Kapoor L, et al. Cavity based sensing of antiferromagnetic canting and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system. Physical Review B. 2025;112(21). doi:10.1103/bdd1-b8ys","mla":"Mandal, Supriya, et al. “Cavity Based Sensing of Antiferromagnetic Canting and Nonzero-Momentum Spin Waves in a van Der Waals Cavity-Magnon-Polariton System.” Physical Review B, vol. 112, no. 21, 214443, American Physical Society, 2025, doi:10.1103/bdd1-b8ys.","short":"S. Mandal, K. Maji, L. Kapoor, S. Sasmal, S. Manni, J. Jesudasan, P. Raychaudhuri, A. Thamizhavel, M.M. Deshmukh, Physical Review B 112 (2025).","chicago":"Mandal, Supriya, Krishnendu Maji, Lucky Kapoor, Souvik Sasmal, Soham Manni, John Jesudasan, Pratap Raychaudhuri, Arumugam Thamizhavel, and Mandar M. Deshmukh. “Cavity Based Sensing of Antiferromagnetic Canting and Nonzero-Momentum Spin Waves in a van Der Waals Cavity-Magnon-Polariton System.” Physical Review B. American Physical Society, 2025. https://doi.org/10.1103/bdd1-b8ys.","apa":"Mandal, S., Maji, K., Kapoor, L., Sasmal, S., Manni, S., Jesudasan, J., … Deshmukh, M. M. (2025). Cavity based sensing of antiferromagnetic canting and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system. Physical Review B. American Physical Society. https://doi.org/10.1103/bdd1-b8ys","ista":"Mandal S, Maji K, Kapoor L, Sasmal S, Manni S, Jesudasan J, Raychaudhuri P, Thamizhavel A, Deshmukh MM. 2025. Cavity based sensing of antiferromagnetic canting and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system. Physical Review B. 112(21), 214443.","ieee":"S. Mandal et al., “Cavity based sensing of antiferromagnetic canting and nonzero-momentum spin waves in a van der Waals cavity-magnon-polariton system,” Physical Review B, vol. 112, no. 21. American Physical Society, 2025."},"article_processing_charge":"No","publisher":"American Physical Society"},{"doi":"10.1038/s41467-025-66409-0","article_type":"original","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).","date_published":"2025-12-11T00:00:00Z","oa":1,"author":[{"last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat","full_name":"Artan, Murat"},{"last_name":"Schön","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","first_name":"Hanna","full_name":"Schön, Hanna"},{"orcid":"0000-0001-8347-0443","first_name":"Mario","full_name":"De Bono, Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"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"}],"day":"11","citation":{"ieee":"M. Artan, H. Schön, and M. de Bono, “Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins,” Nature Communications, 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.","chicago":"Artan, Murat, Hanna Schön, and Mario de Bono. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory Proteins.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-66409-0.","apa":"Artan, M., Schön, H., & de Bono, M. (2025). Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-66409-0","short":"M. Artan, H. Schön, M. de Bono, Nature Communications 16 (2025).","ama":"Artan M, Schön H, de Bono M. Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins. Nature Communications. 2025;16. doi:10.1038/s41467-025-66409-0","mla":"Artan, Murat, et al. “Proximity Labeling of DAF-16 FOXO Highlights Aging Regulatory Proteins.” Nature Communications, vol. 16, 11355, Springer Nature, 2025, doi:10.1038/s41467-025-66409-0."},"DOAJ_listed":"1","file":[{"date_updated":"2026-01-05T10:58:28Z","file_size":1642352,"content_type":"application/pdf","success":1,"file_name":"2025_NatureComm_Artan.pdf","creator":"dernst","date_created":"2026-01-05T10:58:28Z","file_id":"20941","access_level":"open_access","checksum":"748e2e003b878b85b6048d51621d6aae","relation":"main_file"}],"publisher":"Springer Nature","article_processing_charge":"Yes","ddc":["570"],"file_date_updated":"2026-01-05T10:58:28Z","intvolume":" 16","date_created":"2026-01-04T23:01:34Z","year":"2025","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"pmid":["41381452"]},"pmid":1,"title":"Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","corr_author":"1","OA_place":"publisher","type":"journal_article","APC_amount":"7068 EUR","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"publication":"Nature Communications","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"}],"quality_controlled":"1","article_number":"11355","PlanS_conform":"1","oa_version":"Published Version","_id":"20929","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"}],"OA_type":"gold","month":"12","volume":16,"publication_status":"published","date_updated":"2026-05-20T08:10:18Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"language":[{"iso":"eng"}],"publication":"Astronomy & Astrophysics","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"ec_funded":1,"scopus_import":"1","OA_place":"publisher","type":"journal_article","department":[{"_id":"LiBu"}],"OA_type":"diamond","publication_status":"published","month":"12","volume":704,"status":"public","date_updated":"2026-02-16T12:15:07Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"A237","quality_controlled":"1","PlanS_conform":"1","_id":"20930","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-12-01T00:00:00Z","author":[{"first_name":"J. L.","full_name":"Gragera-Más, J. L.","last_name":"Gragera-Más"},{"last_name":"Torres Rodriguez","id":"a8df4360-4328-11ee-8f1a-e502d0c83fc2","orcid":"0000-0002-3150-8988","first_name":"Santiago","full_name":"Torres Rodriguez, Santiago"},{"last_name":"Mustill","full_name":"Mustill, A. J.","first_name":"A. J."},{"last_name":"Villaver","full_name":"Villaver, E.","first_name":"E."}],"arxiv":1,"oa":1,"abstract":[{"lang":"eng","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."}],"day":"01","doi":"10.1051/0004-6361/202555940","article_type":"original","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.","year":"2025","date_created":"2026-01-04T23:01:34Z","intvolume":" 704","external_id":{"arxiv":["2510.02509"]},"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"title":"A kinematic history of stellar encounters with Beta Pictoris","has_accepted_license":"1","DOAJ_listed":"1","citation":{"chicago":"Gragera-Más, J. L., Santiago Torres Rodriguez, A. J. Mustill, and E. Villaver. “A Kinematic History of Stellar Encounters with Beta Pictoris.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202555940.","apa":"Gragera-Más, J. L., Torres Rodriguez, S., Mustill, A. J., & Villaver, E. (2025). A kinematic history of stellar encounters with Beta Pictoris. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202555940","ieee":"J. L. Gragera-Más, S. Torres Rodriguez, A. J. Mustill, and E. Villaver, “A kinematic history of stellar encounters with Beta Pictoris,” Astronomy & Astrophysics, 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 & Astrophysics. 704, A237.","ama":"Gragera-Más JL, Torres Rodriguez S, Mustill AJ, Villaver E. A kinematic history of stellar encounters with Beta Pictoris. Astronomy & Astrophysics. 2025;704. doi:10.1051/0004-6361/202555940","mla":"Gragera-Más, J. L., et al. “A Kinematic History of Stellar Encounters with Beta Pictoris.” Astronomy & Astrophysics, vol. 704, A237, EDP Sciences, 2025, doi:10.1051/0004-6361/202555940.","short":"J.L. Gragera-Más, S. Torres Rodriguez, A.J. Mustill, E. Villaver, Astronomy & Astrophysics 704 (2025)."},"file":[{"content_type":"application/pdf","creator":"dernst","file_name":"2025_AstronomyAstrophysics_GrageraMas.pdf","success":1,"file_size":11021467,"date_updated":"2026-01-05T11:06:16Z","date_created":"2026-01-05T11:06:16Z","file_id":"20942","access_level":"open_access","checksum":"2fb4d5a1603043aa7931a31f2c180877","relation":"main_file"}],"article_processing_charge":"No","publisher":"EDP Sciences","ddc":["520"],"file_date_updated":"2026-01-05T11:06:16Z"},{"has_accepted_license":"1","title":"Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields","external_id":{"arxiv":["2511.09617"]},"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"date_created":"2026-01-04T23:01:35Z","year":"2025","intvolume":" 704","file_date_updated":"2026-01-05T08:36:28Z","ddc":["520"],"publisher":"EDP Sciences","article_processing_charge":"No","file":[{"date_updated":"2026-01-05T08:36:28Z","file_size":2620909,"content_type":"application/pdf","file_name":"2025_AstronomyAstrophysics_Mombarg.pdf","creator":"dernst","success":1,"date_created":"2026-01-05T08:36:28Z","file_id":"20937","checksum":"d838b4783920c43b7cc866e9cf08b383","access_level":"open_access","relation":"main_file"}],"DOAJ_listed":"1","citation":{"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 & Astrophysics 704 (2025).","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.” Astronomy & Astrophysics, vol. 704, A336, EDP Sciences, 2025, doi:10.1051/0004-6361/202557247.","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. Astronomy & Astrophysics. 2025;704. doi:10.1051/0004-6361/202557247","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 & Astrophysics. 704, A336.","ieee":"J. S. G. Mombarg et al., “Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? Implications for measurements of rotation and internal magnetic fields,” Astronomy & Astrophysics, vol. 704. EDP Sciences, 2025.","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. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202557247","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.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202557247."},"day":"19","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."}],"arxiv":1,"author":[{"first_name":"J. S.G.","full_name":"Mombarg, J. S.G.","last_name":"Mombarg"},{"full_name":"Vanlaer, V.","first_name":"V.","last_name":"Vanlaer"},{"last_name":"Das","id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","orcid":"0000-0003-0896-7972","full_name":"Das, Srijan B","first_name":"Srijan B"},{"last_name":"Rieutord","full_name":"Rieutord, M.","first_name":"M."},{"last_name":"Aerts","full_name":"Aerts, C.","first_name":"C."},{"last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle"},{"last_name":"Mathis","first_name":"S.","full_name":"Mathis, S."},{"last_name":"Reese","first_name":"D. R.","full_name":"Reese, D. R."},{"last_name":"Ballot","first_name":"J.","full_name":"Ballot, J."}],"oa":1,"date_published":"2025-12-19T00:00:00Z","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.","article_type":"original","doi":"10.1051/0004-6361/202557247","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-02-16T12:14:36Z","status":"public","month":"12","volume":704,"publication_status":"published","OA_type":"diamond","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20931","oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"20936","status":"public"}]},"PlanS_conform":"1","article_number":"A336","quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"_id":"914d8549-16d5-11f0-9cad-bbe6324c93a9","name":"Unveiling the mysteries of stellar dynamics: a pioneering journey in magnetoasteroseismology","grant_number":"101165631"}],"publication":"Astronomy & Astrophysics","language":[{"iso":"eng"}],"department":[{"_id":"LiBu"}],"type":"journal_article","OA_place":"publisher","scopus_import":"1","ec_funded":1},{"publication":"Astronomy & Astrophysics","language":[{"iso":"eng"}],"department":[{"_id":"JoMa"}],"OA_place":"publisher","type":"journal_article","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-02-16T12:14:52Z","status":"public","publication_status":"published","month":"12","volume":704,"OA_type":"diamond","_id":"20932","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","quality_controlled":"1","article_number":"A328","day":"01","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."}],"oa":1,"arxiv":1,"author":[{"first_name":"Y.","full_name":"Liu, Y.","last_name":"Liu"},{"last_name":"Mascia","id":"edaf889c-c7cd-11ef-ab1b-bb28c431bd29","full_name":"Mascia, Sara","first_name":"Sara"},{"full_name":"Pentericci, L.","first_name":"L.","last_name":"Pentericci"},{"last_name":"Watson","first_name":"P.","full_name":"Watson, P."},{"last_name":"Alavi","full_name":"Alavi, A.","first_name":"A."},{"first_name":"P.","full_name":"Bergamini, P.","last_name":"Bergamini"},{"first_name":"M.","full_name":"Bradač, M.","last_name":"Bradač"},{"last_name":"Calabrò","full_name":"Calabrò, A.","first_name":"A."},{"first_name":"K.","full_name":"Glazebrook, K.","last_name":"Glazebrook"},{"last_name":"Henry","full_name":"Henry, A.","first_name":"A."},{"first_name":"M.","full_name":"Llerena, M.","last_name":"Llerena"},{"last_name":"Merlin","full_name":"Merlin, E.","first_name":"E."},{"first_name":"B.","full_name":"Metha, B.","last_name":"Metha"},{"last_name":"Nanayakkara","first_name":"T.","full_name":"Nanayakkara, T."},{"first_name":"L.","full_name":"Napolitano, L.","last_name":"Napolitano"},{"last_name":"Roy","first_name":"N.","full_name":"Roy, N."},{"last_name":"Siana","full_name":"Siana, B.","first_name":"B."},{"last_name":"Vanzella","full_name":"Vanzella, E.","first_name":"E."},{"last_name":"Vulcani","full_name":"Vulcani, B.","first_name":"B."},{"full_name":"Wang, X.","first_name":"X.","last_name":"Wang"}],"date_published":"2025-12-01T00:00:00Z","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.","article_type":"original","doi":"10.1051/0004-6361/202556410","has_accepted_license":"1","title":"A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"external_id":{"arxiv":["2507.11045"]},"intvolume":" 704","year":"2025","date_created":"2026-01-04T23:01:35Z","ddc":["520"],"file_date_updated":"2026-01-05T09:26:17Z","file":[{"access_level":"open_access","checksum":"3e6061f3c4bfb521b3333ea4913c241a","relation":"main_file","file_id":"20938","date_created":"2026-01-05T09:26:17Z","date_updated":"2026-01-05T09:26:17Z","file_size":4642530,"content_type":"application/pdf","creator":"dernst","success":1,"file_name":"2025_AstronomyAstrophysics_Liu.pdf"}],"article_processing_charge":"No","publisher":"EDP Sciences","citation":{"mla":"Liu, Y., et al. “A Lyman Continuum Analysis of ∼100 Galaxies at z Spec∼ 3 in the Abell 2744 Cluster Field.” Astronomy & Astrophysics, vol. 704, A328, EDP Sciences, 2025, doi:10.1051/0004-6361/202556410.","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. Astronomy & Astrophysics. 2025;704. doi:10.1051/0004-6361/202556410","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 & Astrophysics 704 (2025).","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. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202556410","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.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202556410.","ieee":"Y. Liu et al., “A Lyman continuum analysis of ∼100 galaxies at z spec∼ 3 in the Abell 2744 cluster field,” Astronomy & Astrophysics, 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 & Astrophysics. 704, A328."},"DOAJ_listed":"1"},{"language":[{"iso":"eng"}],"publication":"Angewandte Chemie International Edition","project":[{"_id":"7bf494dc-9f16-11ee-852c-9fe37e3f50f0","name":"Integrating Molecular Photoswitches with PH-Feedback Mechanisms: Towards Life-like Materials","grant_number":"713490"}],"scopus_import":"1","OA_place":"publisher","type":"journal_article","department":[{"_id":"RaKl"}],"OA_type":"hybrid","month":"12","publication_status":"epub_ahead","status":"public","date_updated":"2026-01-05T09:42:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.1002/anie.202523447","open_access":"1"}],"article_number":"e23447","quality_controlled":"1","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20933","oa_version":"Published Version","date_published":"2025-12-23T00:00:00Z","author":[{"last_name":"Meteling","first_name":"Henning Jörn","full_name":"Meteling, Henning Jörn"},{"last_name":"Gemen","first_name":"Julius","full_name":"Gemen, Julius"},{"last_name":"Häkkinen","full_name":"Häkkinen, Satu","first_name":"Satu"},{"first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"},{"last_name":"Priimagi","first_name":"Arri","full_name":"Priimagi, Arri"}],"oa":1,"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"}],"day":"23","doi":"10.1002/anie.202523447","article_type":"original","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.","year":"2025","date_created":"2026-01-04T23:01:35Z","external_id":{"pmid":["41437660"]},"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"title":"Sensitized disequilibration of water-soluble azopolymers","pmid":1,"has_accepted_license":"1","citation":{"apa":"Meteling, H. J., Gemen, J., Häkkinen, S., Klajn, R., & Priimagi, A. (2025). Sensitized disequilibration of water-soluble azopolymers. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202523447","chicago":"Meteling, Henning Jörn, Julius Gemen, Satu Häkkinen, Rafal Klajn, and Arri Priimagi. “Sensitized Disequilibration of Water-Soluble Azopolymers.” Angewandte Chemie International Edition. Wiley, 2025. https://doi.org/10.1002/anie.202523447.","ista":"Meteling HJ, Gemen J, Häkkinen S, Klajn R, Priimagi A. 2025. Sensitized disequilibration of water-soluble azopolymers. Angewandte Chemie International Edition., e23447.","ieee":"H. J. Meteling, J. Gemen, S. Häkkinen, R. Klajn, and A. Priimagi, “Sensitized disequilibration of water-soluble azopolymers,” Angewandte Chemie International Edition. Wiley, 2025.","mla":"Meteling, Henning Jörn, et al. “Sensitized Disequilibration of Water-Soluble Azopolymers.” Angewandte Chemie International Edition, e23447, Wiley, 2025, doi:10.1002/anie.202523447.","ama":"Meteling HJ, Gemen J, Häkkinen S, Klajn R, Priimagi A. Sensitized disequilibration of water-soluble azopolymers. Angewandte Chemie International Edition. 2025. doi:10.1002/anie.202523447","short":"H.J. Meteling, J. Gemen, S. Häkkinen, R. Klajn, A. Priimagi, Angewandte Chemie International Edition (2025)."},"publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","ddc":["540"]},{"publication":"Transactions on Machine Learning Research","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"OA_place":"publisher","type":"journal_article","corr_author":"1","scopus_import":"1","alternative_title":["TMLR"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-01-05T09:54:59Z","status":"public","month":"12","publication_status":"published","OA_type":"gold","_id":"20934","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://github.com/francescomontagna/learning-to-induce.git","relation":"software"}]},"PlanS_conform":"1","quality_controlled":"1","day":"18","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."}],"arxiv":1,"author":[{"last_name":"Montagna","id":"353afc8e-19f4-11f0-9db9-811f1723c83f","full_name":"Montagna, Francesco","first_name":"Francesco"},{"last_name":"Cairney-Leeming","id":"2214a80c-31f8-11ee-a48d-cf52cc58759b","full_name":"Cairney-Leeming, Maximilian T","first_name":"Maximilian T"},{"last_name":"Sridhar","full_name":"Sridhar, Dhanya","first_name":"Dhanya"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"}],"oa":1,"date_published":"2025-12-18T00:00:00Z","article_type":"original","has_accepted_license":"1","title":"Demystifying amortized causal discovery with transformers","external_id":{"arxiv":["2405.16924"]},"publication_identifier":{"eissn":["2835-8856"]},"date_created":"2026-01-04T23:01:35Z","year":"2025","ddc":["000"],"file_date_updated":"2026-01-05T09:51:28Z","article_processing_charge":"No","file":[{"date_created":"2026-01-05T09:51:28Z","creator":"dernst","success":1,"file_name":"2025_PMLR_Montagna.pdf","content_type":"application/pdf","date_updated":"2026-01-05T09:51:28Z","file_size":1030280,"relation":"main_file","access_level":"open_access","checksum":"968c471bb1f682cf823b2d4cadea8a3f","file_id":"20939"}],"publisher":"ML Research Press","citation":{"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.” Transactions on Machine Learning Research, ML Research Press, 2025.","ama":"Montagna F, Cairney-Leeming MT, Sridhar D, Locatello F. Demystifying amortized causal discovery with transformers. Transactions on Machine Learning Research. 2025.","ieee":"F. Montagna, M. T. Cairney-Leeming, D. Sridhar, and F. Locatello, “Demystifying amortized causal discovery with transformers,” Transactions on Machine Learning Research. 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.","chicago":"Montagna, Francesco, Maximilian T Cairney-Leeming, Dhanya Sridhar, and Francesco Locatello. “Demystifying Amortized Causal Discovery with Transformers.” Transactions on Machine Learning Research. ML Research Press, 2025.","apa":"Montagna, F., Cairney-Leeming, M. T., Sridhar, D., & Locatello, F. (2025). Demystifying amortized causal discovery with transformers. Transactions on Machine Learning Research. ML Research Press."}},{"oa_version":"Published Version","_id":"20935","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2025.11.029","open_access":"1"}],"date_updated":"2026-01-05T08:32:47Z","status":"public","publication_status":"inpress","month":"12","OA_type":"hybrid","department":[{"_id":"AlMi"}],"OA_place":"publisher","type":"journal_article","scopus_import":"1","publication":"Molecular Cell","language":[{"iso":"eng"}],"ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","citation":{"ama":"Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. doi:10.1016/j.molcel.2025.11.029","mla":"Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell, Elsevier, doi:10.1016/j.molcel.2025.11.029.","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.).","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.” Molecular Cell. Elsevier, n.d. https://doi.org/10.1016/j.molcel.2025.11.029.","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. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2025.11.029","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 et al., “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell. Elsevier."},"title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"date_created":"2026-01-04T23:01:36Z","year":"2025","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.","article_type":"original","doi":"10.1016/j.molcel.2025.11.029","day":"19","abstract":[{"lang":"eng","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."}],"author":[{"last_name":"Kelley","first_name":"Ron","full_name":"Kelley, Ron"},{"first_name":"Sagar","full_name":"Khavnekar, Sagar","last_name":"Khavnekar"},{"first_name":"Ricardo D.","full_name":"Righetto, Ricardo D.","last_name":"Righetto"},{"full_name":"Heebner, Jessica","first_name":"Jessica","last_name":"Heebner"},{"orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","first_name":"Xianjun","full_name":"Zhang, Xianjun"},{"full_name":"Chakraborty, Saikat","first_name":"Saikat","last_name":"Chakraborty"},{"full_name":"Tagiltsev, Grigory","first_name":"Grigory","last_name":"Tagiltsev"},{"first_name":"Alicia","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Van Dorst, Sofie","first_name":"Sofie","last_name":"Van Dorst"},{"first_name":"Florent","full_name":"Waltz, Florent","last_name":"Waltz"},{"last_name":"Mccafferty","full_name":"Mccafferty, Caitlyn L.","first_name":"Caitlyn L."},{"full_name":"Lamm, Lorenz","first_name":"Lorenz","last_name":"Lamm"},{"first_name":"Simon","full_name":"Zufferey, Simon","last_name":"Zufferey"},{"last_name":"Van Der Stappen","first_name":"Philippe","full_name":"Van Der Stappen, Philippe"},{"last_name":"Van Den Hoek","first_name":"Hugo","full_name":"Van Den Hoek, Hugo"},{"last_name":"Wietrzynski","full_name":"Wietrzynski, Wojciech","first_name":"Wojciech"},{"last_name":"Harar","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","orcid":"0000-0001-5206-1794","full_name":"Harar, Pavol","first_name":"Pavol"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"last_name":"Briggs","first_name":"John A.G.","full_name":"Briggs, John A.G."},{"last_name":"Plitzko","full_name":"Plitzko, Jürgen M.","first_name":"Jürgen M."},{"full_name":"Engel, Benjamin D.","first_name":"Benjamin D.","last_name":"Engel"},{"first_name":"Abhay","full_name":"Kotecha, Abhay","last_name":"Kotecha"}],"oa":1,"date_published":"2025-12-19T00:00:00Z"},{"citation":{"mla":"Mombarg, Joey, et al. Is a 1D Perturbative Method Sufficient for Asteroseismic Modelling of β Cephei Pulsators? Zenodo, 2025, doi:10.5281/ZENODO.17580178.","ama":"Mombarg J, Vanlaer V, Das SB, et al. Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators? 2025. doi:10.5281/ZENODO.17580178","short":"J. Mombarg, V. Vanlaer, S.B. Das, M. Rieutord, C. Aerts, L.A. Bugnet, S. Mathis, D. Reese, J. Ballot, (2025).","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. https://doi.org/10.5281/ZENODO.17580178.","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. https://doi.org/10.5281/ZENODO.17580178","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, 10.5281/ZENODO.17580178.","ieee":"J. Mombarg et al., “Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators?” Zenodo, 2025."},"publisher":"Zenodo","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"20931","relation":"used_in_publication"}]},"_id":"20936","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","ddc":["520"],"date_created":"2026-01-05T08:39:33Z","year":"2025","OA_type":"gold","month":"11","title":"Is a 1D perturbative method sufficient for asteroseismic modelling of β Cephei pulsators?","date_updated":"2026-02-16T12:14:36Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.17580178","open_access":"1"}],"doi":"10.5281/ZENODO.17580178","OA_place":"repository","type":"research_data_reference","department":[{"_id":"LiBu"}],"date_published":"2025-11-11T00:00:00Z","oa":1,"author":[{"full_name":"Mombarg, Joey","first_name":"Joey","last_name":"Mombarg"},{"last_name":"Vanlaer","first_name":"Vincent","full_name":"Vanlaer, Vincent"},{"id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","last_name":"Das","full_name":"Das, Srijan B","first_name":"Srijan B","orcid":"0000-0003-0896-7972"},{"first_name":"Michel","full_name":"Rieutord, Michel","last_name":"Rieutord"},{"first_name":"Conny","full_name":"Aerts, Conny","last_name":"Aerts"},{"orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"full_name":"Mathis, Stephane","first_name":"Stephane","last_name":"Mathis"},{"last_name":"Reese","first_name":"Daniel","full_name":"Reese, Daniel"},{"last_name":"Ballot","full_name":"Ballot, Jerome","first_name":"Jerome"}],"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)"}],"day":"11"},{"oa":1,"author":[{"last_name":"Mandal","full_name":"Mandal, Supriya","first_name":"Supriya"},{"full_name":"Maji, Krishnendu","first_name":"Krishnendu","last_name":"Maji","id":"76bc9e9f-ba0b-11ee-8184-90edabd17a58"},{"orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky","first_name":"Lucky","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"first_name":"Souvik","full_name":"Sasmal, Souvik","last_name":"Sasmal"},{"first_name":"Soham","full_name":"Manni, Soham","last_name":"Manni"},{"last_name":"Jesudasan","full_name":"Jesudasan, John","first_name":"John"},{"full_name":"Raychaudhuri, Pratap","first_name":"Pratap","last_name":"Raychaudhuri"},{"last_name":"Thamizhavel","full_name":"Thamizhavel, Arumugam","first_name":"Arumugam"},{"full_name":"Deshmukh, Mandar M.","first_name":"Mandar M.","last_name":"Deshmukh"}],"date_published":"2025-05-02T00:00:00Z","day":"02","abstract":[{"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.","lang":"eng"}],"doi":"10.5281/ZENODO.15321721","department":[{"_id":"MaIb"},{"_id":"JoFi"}],"type":"research_data_reference","OA_place":"repository","month":"05","OA_type":"green","date_created":"2026-01-05T10:00:06Z","year":"2025","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.15321721","open_access":"1"}],"title":"Mode dispersion with magnetic field in a cavity-magnonics system","status":"public","date_updated":"2026-01-05T10:07:04Z","article_processing_charge":"No","publisher":"Zenodo","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20927"}]},"citation":{"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. https://doi.org/10.5281/ZENODO.15321721.","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. https://doi.org/10.5281/ZENODO.15321721","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, 10.5281/ZENODO.15321721.","ieee":"S. Mandal et al., “Mode dispersion with magnetic field in a cavity-magnonics system.” Zenodo, 2025.","ama":"Mandal S, Maji K, Kapoor L, et al. Mode dispersion with magnetic field in a cavity-magnonics system. 2025. doi:10.5281/ZENODO.15321721","mla":"Mandal, Supriya, et al. Mode Dispersion with Magnetic Field in a Cavity-Magnonics System. Zenodo, 2025, doi:10.5281/ZENODO.15321721.","short":"S. Mandal, K. Maji, L. Kapoor, S. Sasmal, S. Manni, J. Jesudasan, P. Raychaudhuri, A. Thamizhavel, M.M. Deshmukh, (2025)."},"_id":"20940","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Wiley","article_processing_charge":"Yes (in subscription journal)","extern":"1","citation":{"ista":"Loos M, Xu F, Mandal PK, Chakrabortty T, Douat C, Konrad DB, Cabbar M, Singer J, Corvaglia V, Carell T, Huc I. 2025. Interfacing B‐DNA and DNA mimic foldamers. Angewandte Chemie International Edition. 64(31), e202505273.","ieee":"M. Loos et al., “Interfacing B‐DNA and DNA mimic foldamers,” Angewandte Chemie International Edition, vol. 64, no. 31. Wiley, 2025.","apa":"Loos, M., Xu, F., Mandal, P. K., Chakrabortty, T., Douat, C., Konrad, D. B., … Huc, I. (2025). Interfacing B‐DNA and DNA mimic foldamers. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202505273","chicago":"Loos, Manuel, Felix Xu, Pradeep K Mandal, Tulika Chakrabortty, Céline Douat, David B. Konrad, Melis Cabbar, et al. “Interfacing B‐DNA and DNA Mimic Foldamers.” Angewandte Chemie International Edition. Wiley, 2025. https://doi.org/10.1002/anie.202505273.","short":"M. Loos, F. Xu, P.K. Mandal, T. Chakrabortty, C. Douat, D.B. Konrad, M. Cabbar, J. Singer, V. Corvaglia, T. Carell, I. Huc, Angewandte Chemie International Edition 64 (2025).","mla":"Loos, Manuel, et al. “Interfacing B‐DNA and DNA Mimic Foldamers.” Angewandte Chemie International Edition, vol. 64, no. 31, e202505273, Wiley, 2025, doi:10.1002/anie.202505273.","ama":"Loos M, Xu F, Mandal PK, et al. Interfacing B‐DNA and DNA mimic foldamers. Angewandte Chemie International Edition. 2025;64(31). doi:10.1002/anie.202505273"},"ddc":["540"],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"external_id":{"pmid":["40346004"]},"intvolume":" 64","date_created":"2026-01-08T07:04:48Z","year":"2025","has_accepted_license":"1","pmid":1,"title":"Interfacing B‐DNA and DNA mimic foldamers","doi":"10.1002/anie.202505273","issue":"31","article_type":"original","oa":1,"author":[{"last_name":"Loos","first_name":"Manuel","full_name":"Loos, Manuel"},{"first_name":"Felix","full_name":"Xu, Felix","last_name":"Xu"},{"id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","last_name":"Mandal","full_name":"Mandal, Pradeep K","first_name":"Pradeep K","orcid":"0000-0001-5996-956X"},{"last_name":"Chakrabortty","full_name":"Chakrabortty, Tulika","first_name":"Tulika"},{"full_name":"Douat, Céline","first_name":"Céline","last_name":"Douat"},{"last_name":"Konrad","full_name":"Konrad, David B.","first_name":"David B."},{"first_name":"Melis","full_name":"Cabbar, Melis","last_name":"Cabbar"},{"full_name":"Singer, Johannes","first_name":"Johannes","last_name":"Singer"},{"last_name":"Corvaglia","first_name":"Valentina","full_name":"Corvaglia, Valentina"},{"last_name":"Carell","full_name":"Carell, Thomas","first_name":"Thomas"},{"first_name":"Ivan","full_name":"Huc, Ivan","last_name":"Huc"}],"date_published":"2025-07-28T00:00:00Z","day":"28","abstract":[{"lang":"eng","text":"A linker unit was designed and synthesized that can serve both as a hairpin turn in a DNA duplex and anchor point for an aromatic helical foldamer mimicking the shape and surface properties of B‐DNA. Methods were developed to synthesize natural/non‐natural chimeric molecules combining foldamer and DNA segments. The ability of the linker to position the foldamer helix and the duplex DNA so that their rims and grooves are in register, despite their completely different chemical nature, was demonstrated using single crystal X‐ray diffraction, circular dichroism and molecular models. Bio‐layer interferometry confirmed that artificial hairpin DNA duplexes keep their ability to bind to DNA binding proteins. The chimeric molecules may pave the way to competitive inhibitors of protein‐DNA interactions involving sequence‐selective DNA‐binding proteins."}],"PlanS_conform":"1","quality_controlled":"1","article_number":"e202505273","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20960","oa_version":"Published Version","month":"07","publication_status":"published","volume":64,"OA_type":"hybrid","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.1002/anie.202505273","open_access":"1"}],"status":"public","date_updated":"2026-01-19T11:07:53Z","scopus_import":"1","type":"journal_article","OA_place":"publisher","language":[{"iso":"eng"}],"publication":"Angewandte Chemie International Edition"},{"day":"22","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"}],"arxiv":1,"author":[{"last_name":"Patel","full_name":"Patel, Lipi","first_name":"Lipi"},{"id":"221708e1-1ff6-11ee-9fa6-85146607433e","last_name":"Hawaldar","full_name":"Hawaldar, Samarth","first_name":"Samarth","orcid":"0000-0002-1965-4309"},{"first_name":"Aditya","full_name":"Panikkar, Aditya","last_name":"Panikkar"},{"last_name":"Shankar","full_name":"Shankar, Athreya","first_name":"Athreya"},{"first_name":"Baladitya","full_name":"Suri, Baladitya","last_name":"Suri"}],"oa":1,"date_published":"2025-12-22T00:00:00Z","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","article_type":"original","doi":"10.1063/5.0290636","title":"Impedance-engineered Josephson parametric amplifier with single-step lithography","external_id":{"arxiv":["2507.09298"]},"publication_identifier":{"issn":["0003-6951"],"eissn":["1077-3118"]},"year":"2025","date_created":"2026-01-11T23:01:34Z","intvolume":" 127","publisher":"AIP Publishing","article_processing_charge":"No","citation":{"ieee":"L. Patel, S. Hawaldar, A. Panikkar, A. Shankar, and B. Suri, “Impedance-engineered Josephson parametric amplifier with single-step lithography,” Applied Physics Letters, 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.","apa":"Patel, L., Hawaldar, S., Panikkar, A., Shankar, A., & Suri, B. (2025). Impedance-engineered Josephson parametric amplifier with single-step lithography. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0290636","chicago":"Patel, Lipi, Samarth Hawaldar, Aditya Panikkar, Athreya Shankar, and Baladitya Suri. “Impedance-Engineered Josephson Parametric Amplifier with Single-Step Lithography.” Applied Physics Letters. AIP Publishing, 2025. https://doi.org/10.1063/5.0290636.","short":"L. Patel, S. Hawaldar, A. Panikkar, A. Shankar, B. Suri, Applied Physics Letters 127 (2025).","mla":"Patel, Lipi, et al. “Impedance-Engineered Josephson Parametric Amplifier with Single-Step Lithography.” Applied Physics Letters, vol. 127, no. 25, 254001, AIP Publishing, 2025, doi:10.1063/5.0290636.","ama":"Patel L, Hawaldar S, Panikkar A, Shankar A, Suri B. Impedance-engineered Josephson parametric amplifier with single-step lithography. Applied Physics Letters. 2025;127(25). doi:10.1063/5.0290636"},"publication":"Applied Physics Letters","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"type":"journal_article","OA_place":"repository","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2507.09298","open_access":"1"}],"date_updated":"2026-01-12T09:57:53Z","status":"public","publication_status":"published","month":"12","volume":127,"OA_type":"green","_id":"20976","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"254001","quality_controlled":"1"},{"ddc":["570"],"file_date_updated":"2026-01-12T09:30:15Z","DOAJ_listed":"1","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. Nature Communications. 2025;16. doi:10.1038/s41467-025-66562-6","mla":"Maslarova, Anna, et al. “Spatiotemporal Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans.” Nature Communications, vol. 16, 11636, Springer Nature, 2025, doi:10.1038/s41467-025-66562-6.","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).","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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-66562-6","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.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-66562-6.","ieee":"A. Maslarova et al., “Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans,” Nature Communications, vol. 16. Springer Nature, 2025.","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."},"publisher":"Springer Nature","article_processing_charge":"Yes","file":[{"file_id":"20978","access_level":"open_access","checksum":"a8a1670e197484382e087be60f643945","relation":"main_file","date_updated":"2026-01-12T09:30:15Z","file_size":7629997,"content_type":"application/pdf","file_name":"2025_NatureComm_Maslarova.pdf","success":1,"creator":"dernst","date_created":"2026-01-12T09:30:15Z"}],"pmid":1,"title":"Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans","has_accepted_license":"1","year":"2025","date_created":"2026-01-11T23:01:35Z","intvolume":" 16","external_id":{"pmid":["39975118"]},"publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","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.).","doi":"10.1038/s41467-025-66562-6","abstract":[{"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.","lang":"eng"}],"day":"30","date_published":"2025-12-30T00:00:00Z","author":[{"first_name":"Anna","full_name":"Maslarova, Anna","last_name":"Maslarova"},{"full_name":"Shin, Jiyun N.","first_name":"Jiyun N.","last_name":"Shin"},{"full_name":"Navas Olivé, Andrea C","first_name":"Andrea C","orcid":"0000-0002-9280-8597","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","last_name":"Navas Olivé"},{"last_name":"Vöröslakos","first_name":"Mihály","full_name":"Vöröslakos, Mihály"},{"last_name":"Hamer","first_name":"Hajo","full_name":"Hamer, Hajo"},{"first_name":"Arnd","full_name":"Doerfler, Arnd","last_name":"Doerfler"},{"last_name":"Henin","full_name":"Henin, Simon","first_name":"Simon"},{"last_name":"Buzsáki","full_name":"Buzsáki, György","first_name":"György"},{"full_name":"Liu, Anli","first_name":"Anli","last_name":"Liu"}],"oa":1,"_id":"20977","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_number":"11636","quality_controlled":"1","date_updated":"2026-01-12T09:31:56Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"OA_type":"gold","volume":16,"publication_status":"published","month":"12","OA_place":"publisher","type":"journal_article","department":[{"_id":"PeJo"}],"scopus_import":"1","publication":"Nature Communications","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"language":[{"iso":"eng"}]}]