--- OA_place: repository OA_type: green _id: '21056' abstract: - lang: eng text: "In this work, we introduce and study what we believe is an intriguing, and, to the best of our knowledge, previously unknown connection between two fundamental areas in computational topology, namely topological data analysis (TDA) and knot theory. Given a function from a topological space to ℝ, TDA provides tools to simplify and study the importance of topological features: in particular, the \U0001D459^\U0001D461⁢ℎ-dimensional persistence diagram encodes the topological changes (or \U0001D459-homology) in the sublevel set as the function value increases into a set of points in the plane. Given a continuous one parameter family of such functions, we can combine the persistence diagrams into an object known as a vineyard, which tracks the evolution of points in the persistence diagram as the function changes. If we further restrict that family of functions to be periodic, we identify the two ends of the vineyard, yielding a closed vineyard. This allows the study of monodromy, which in this context means that following the family of functions for a period permutes the set of points in a non-trivial way. Recent work has studied monodromy in the directional persistent homology transform, demonstrating some interesting connections between an input shape and monodromy in the persistent homology transform for 0-dimensional homology embedded in ℝ^2.\r\nIn this work, given a link and a value \U0001D459, we construct a topological space (based on the given link) and periodic family of functions on this space (based on the Euclidean distance function), such that the closed \U0001D459-vineyard contains this link. This shows that vineyards are topologically as rich as one could possibly hope, suggesting many future directions of work. Importantly, it has at least two immediate consequences we explicitly point out:\r\n1.\tMonodromy of any periodicity can occur in a \U0001D459-vineyard for any \U0001D459. This answers a variant of a question by Arya and collaborators. To exhibit this as a consequence of our first main result we also reformulate monodromy in a more geometric way, which may be of interest in itself.\r\n2.\tTopologically distinguishing closed vineyards is likely to be difficult (from a complexity theory as well as from a practical perspective) because of the difficulty of knot and link recognition, which have strong connections to many NP-hard problems." acknowledgement: We thank the reviewers for both SODA and ATMCS for their comments, whichimproved the exposition. We thank Kate Turner for discussion and Clément Maria for pointing out thatAlexander’s theorem was already (well) known. Mathijs Wintraecken would like to express his gratitude tothe administrative support he received from University of Notre Dame during his visit and from Sophie Honnoratand Stephanie Verdonck at Inria in general.This work has been supported by the ANR grant StratMesh, ANR-24-CE48-1899, by NSF award 2444309, andthe welcome package from IDEX of the Université Côte d’Azur, ANR-15-IDEX-01. article_processing_charge: No arxiv: 1 author: - first_name: Erin W. full_name: Chambers, Erin W. last_name: Chambers - first_name: Christopher D full_name: Fillmore, Christopher D id: 35638A5C-AAC7-11E9-B0BF-5503E6697425 last_name: Fillmore - first_name: Elizabeth R full_name: Stephenson, Elizabeth R id: 2D04F932-F248-11E8-B48F-1D18A9856A87 last_name: Stephenson orcid: 0000-0002-6862-208X - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: 'Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. Braiding Vineyards. In: Green Larsen K, Saha B, eds. Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms. Philadelphia, PA, United States: Society for Industrial and Applied Mathematics; 2026:6240-6263. doi:10.1137/1.9781611978971.225' apa: 'Chambers, E. W., Fillmore, C. D., Stephenson, E. R., & Wintraecken, M. (2026). Braiding Vineyards. In K. Green Larsen & B. Saha (Eds.), Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 6240–6263). Philadelphia, PA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611978971.225' chicago: 'Chambers, Erin W., Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “Braiding Vineyards.” In Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, edited by Kasper Green Larsen and Barna Saha, 6240–63. Philadelphia, PA, United States: Society for Industrial and Applied Mathematics, 2026. https://doi.org/10.1137/1.9781611978971.225.' ieee: 'E. W. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “Braiding Vineyards,” in Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, K. Green Larsen and B. Saha, Eds. Philadelphia, PA, United States: Society for Industrial and Applied Mathematics, 2026, pp. 6240–6263.' ista: 'Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. 2026.Braiding Vineyards. In: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms. , 6240–6263.' mla: Chambers, Erin W., et al. “Braiding Vineyards.” Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, edited by Kasper Green Larsen and Barna Saha, Society for Industrial and Applied Mathematics, 2026, pp. 6240–63, doi:10.1137/1.9781611978971.225. short: E.W. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, K. Green Larsen, B. Saha (Eds.), Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, Philadelphia, PA, United States, 2026, pp. 6240–6263. date_created: 2026-01-28T12:58:16Z date_published: 2026-01-07T00:00:00Z date_updated: 2026-02-16T08:06:23Z day: '07' department: - _id: HeEd doi: 10.1137/1.9781611978971.225 editor: - first_name: Kasper full_name: Green Larsen, Kasper last_name: Green Larsen - first_name: Barna full_name: Saha, Barna last_name: Saha external_id: arxiv: - '2504.11203' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2504.11203 month: '01' oa: 1 oa_version: Preprint page: 6240-6263 place: Philadelphia, PA, United States publication: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - '9781611978971' publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '21051' relation: earlier_version status: public status: public title: Braiding Vineyards type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: gold _id: '21113' abstract: - lang: eng text: 'Causal discovery from i.i.d. observational data is known to be generally ill-posed. We demonstrate that if we have access to the distribution induced by a structural causal model, and additional data from (in the best case) only two environments that sufficiently differ in the noise statistics, the unique causal graph is identifiable. Notably, this is the first result in the literature that guarantees the entire causal graph recovery with a constant number of environments and arbitrary nonlinear mechanisms. Our only constraint is the Gaussianity of the noise terms; however, we propose potential ways to relax this requirement. Of interest on its own, we expand on the well-known duality between independent component analysis (ICA) and causal discovery; recent advancements have shown that nonlinear ICA can be solved from multiple environments, at least as many as the number of sources: we show that the same can be achieved for causal discovery while having access to much less auxiliary information.' article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Montagna, Francesco id: 353afc8e-19f4-11f0-9db9-811f1723c83f last_name: Montagna citation: ama: 'Montagna F. On the identifiability of causal graphs with multiple environments. In: The 14th International Conference on Learning Representations. OpenReview.' apa: 'Montagna, F. (n.d.). On the identifiability of causal graphs with multiple environments. In The 14th International Conference on Learning Representations. Rio de Janeiro, Brazil: OpenReview.' chicago: Montagna, Francesco. “On the Identifiability of Causal Graphs with Multiple Environments.” In The 14th International Conference on Learning Representations. OpenReview, n.d. ieee: F. Montagna, “On the identifiability of causal graphs with multiple environments,” in The 14th International Conference on Learning Representations, Rio de Janeiro, Brazil. ista: 'Montagna F. On the identifiability of causal graphs with multiple environments. The 14th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Montagna, Francesco. “On the Identifiability of Causal Graphs with Multiple Environments.” The 14th International Conference on Learning Representations, OpenReview. short: F. Montagna, in:, The 14th International Conference on Learning Representations, OpenReview, n.d. conference: end_date: 2026-04-27 location: Rio de Janeiro, Brazil name: 'ICLR: International Conference on Learning Representations' start_date: 2026-04-23 corr_author: '1' date_created: 2026-01-30T08:16:25Z date_published: 2026-02-11T00:00:00Z date_updated: 2026-02-16T08:15:11Z day: '11' ddc: - '000' department: - _id: FrLo external_id: arxiv: - '2510.13583' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2510.13583 month: '02' oa: 1 oa_version: Published Version publication: The 14th International Conference on Learning Representations publication_status: accepted publisher: OpenReview status: public title: On the identifiability of causal graphs with multiple environments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21115' abstract: - lang: eng text: Quantifying cell morphology is central to understanding cellular regulation, fate, and heterogeneity, yet conventional image-based analyses often struggle with diverse or irregular shapes. We present a computational framework that uses topological data analysis to characterise and compare single-cell morphologies from fluorescence microscopy. Each cell is represented by its contour together with the position of its nucleus, from which we construct a filtration based on a radial distance function and derive a persistence diagram encoding the shape’s topological evolution. The similarity between two cells is quantified using the 2-Wasserstein distance between their diagrams, yielding a shape distance we call the PH distance. We apply this method to two representative experimental systems—primary human mesenchymal stem cells (hMSCs) and HeLa cells—and show that PH distances enable the detection of outliers in those systems, the identification of sub-populations, and the quantification of shape heterogeneity. We benchmark PH against three established contour-based distances (aspect ratio, Fourier descriptors, and elastic shape analysis) and show that PH offers better separation between cell types and greater robustness when clustering heterogeneous populations. Together, these results demonstrate that persistent-homology-based signatures provide a principled and sensitive approach for analysing cell morphology in settings where traditional geometric or image-based descriptors are insufficient. acknowledgement: We thank Stephan Huckemann, Katharine Turner, Benjamin Eltzner, Stephan Tillmann, Fariza Rashid, Vanessa Robins, and Lamiae Azizi for many useful discussions at various stages of this project. FR and PY gratefully acknowledge Matthias Weiss (Experimental Physics I, University of Bayreuth, Germany) for granting access to cell culture and laboratories, as well as funding consumables and the fruitful discussion that contributed to this work. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. article_number: e1013890 article_processing_charge: Yes article_type: original author: - first_name: Yossi full_name: Bleile, Yossi id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2 last_name: Bleile orcid: 0000-0002-4861-9174 - first_name: Pooja full_name: Yadav, Pooja last_name: Yadav - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl - first_name: Florian full_name: Rehfeldt, Florian last_name: Rehfeldt citation: ama: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population. PLoS Computational Biology. 2026;22. doi:10.1371/journal.pcbi.1013890' apa: 'Bokor Bleile, Y., Yadav, P., Koehl, P., & Rehfeldt, F. (2026). Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1013890' chicago: 'Bokor Bleile, Yossi, Pooja Yadav, Patrice Koehl, and Florian Rehfeldt. “Persistence Diagrams as Morphological Signatures of Cells: A Method to Measure and Compare Cells within a Population.” PLoS Computational Biology. Public Library of Science, 2026. https://doi.org/10.1371/journal.pcbi.1013890.' ieee: 'Y. Bokor Bleile, P. Yadav, P. Koehl, and F. Rehfeldt, “Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population,” PLoS Computational Biology, vol. 22. Public Library of Science, 2026.' ista: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. 2026. Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population. PLoS Computational Biology. 22, e1013890.' mla: 'Bokor Bleile, Yossi, et al. “Persistence Diagrams as Morphological Signatures of Cells: A Method to Measure and Compare Cells within a Population.” PLoS Computational Biology, vol. 22, e1013890, Public Library of Science, 2026, doi:10.1371/journal.pcbi.1013890.' short: Y. Bokor Bleile, P. Yadav, P. Koehl, F. Rehfeldt, PLoS Computational Biology 22 (2026). corr_author: '1' date_created: 2026-01-30T10:36:32Z date_published: 2026-01-28T00:00:00Z date_updated: 2026-06-11T11:51:13Z day: '28' ddc: - '000' department: - _id: HeEd doi: 10.1371/journal.pcbi.1013890 external_id: pmid: - '41604421' file: - access_level: open_access checksum: 3899d929ee9be0453c95524e49992d72 content_type: application/pdf creator: dernst date_created: 2026-02-10T07:13:06Z date_updated: 2026-02-10T07:13:06Z file_id: '21204' file_name: 2026_PloSCompBio_Bleile.pdf file_size: 8908746 relation: main_file success: 1 file_date_updated: 2026-02-10T07:13:06Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/yossibokorbleile/correa scopus_import: '1' status: public title: 'Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2026' ... --- _id: '21116' abstract: - lang: eng text: Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes. article_processing_charge: No author: - first_name: Lorena Alexandra full_name: Layana Franco, Lorena Alexandra id: 02814589-eb8f-11eb-b029-a70074f3f18f last_name: Layana Franco orcid: 0000-0002-1253-6297 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” 2026. doi:10.15479/AT-ISTA-21116 apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21116 chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21116. ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science and Technology Austria, 2026. ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21116. mla: Layana Franco, Lorena Alexandra, et al. Research Data for “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21116. short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026). corr_author: '1' date_created: 2026-01-30T11:04:14Z date_published: 2026-01-02T00:00:00Z date_updated: 2026-02-12T12:58:00Z day: '2' department: - _id: BeVi doi: 10.15479/AT-ISTA-21116 file: - access_level: open_access checksum: 0b79be6229f2ad9ac117ef00fc4f5c0e content_type: text/plain creator: llayanaf date_created: 2026-01-30T11:00:24Z date_updated: 2026-01-30T11:00:24Z file_id: '21117' file_name: README.txt file_size: 1201 relation: main_file success: 1 - access_level: open_access checksum: a3cda72e4177fa1e5d3f0f6a88f8a79b content_type: application/zip creator: llayanaf date_created: 2026-01-30T11:00:36Z date_updated: 2026-01-30T11:00:36Z file_id: '21118' file_name: Supplementary_Tables.zip file_size: 572403 relation: main_file success: 1 - access_level: open_access checksum: efb5b64698d6ca9e7b675204f6fc1c29 content_type: application/zip creator: llayanaf date_created: 2026-01-30T11:00:48Z date_updated: 2026-01-30T11:00:48Z file_id: '21119' file_name: Supplementary_Datasets.zip file_size: 19054553 relation: main_file success: 1 - access_level: open_access checksum: 254e050f648e9783ba8fe11adb3b49db content_type: application/zip creator: llayanaf date_created: 2026-01-30T11:00:56Z date_updated: 2026-01-30T11:00:56Z file_id: '21120' file_name: Perl_scripts.zip file_size: 4575 relation: main_file success: 1 file_date_updated: 2026-01-30T11:00:56Z has_accepted_license: '1' keyword: - Schizophora - sex chromosomes - sex-chromosome turnover - Diptera - genomic features - out-of-X movement. month: '01' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Research Data for "Causes and consequences of sex-chromosome turnovers in Diptera" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: repository OA_type: green _id: '21132' abstract: - lang: eng text: We unify the variational hypocoercivity framework established by D. Albritton, S. Armstrong, J.-C. Mourrat, and M. Novack [2], with the notion of second-order lifts of reversible diffusion processes, recently introduced by A. Eberle and the second author [30]. We give an abstract, yet fully constructive, presentation of the theory, so that it can be applied to a large class of linear kinetic equations. As this hypocoercivity technique does not twist the reference norm, we can recover accurate and sharp convergence rates in various models. Among those, adaptive Langevin dynamics (ALD) is discussed in full detail and we show that for near-quadratic potentials, with suitable choices of parameters, it is a near-optimal second-order lift of the overdamped Langevin dynamics. As a further consequence, we observe that the Generalised Langevin Equation (GLE) is also a second-order lift, as the standard (kinetic) Langevin dynamics are, of the overdamped Langevin dynamics. Then, convergence of (GLE) cannot exceed ballistic speed, i.e. the square root of the rate of the overdamped regime. We illustrate this phenomenon with explicit computations in a benchmark Gaussian case. acknowledgement: "We would like to thank Andreas Eberle and Gabriel Stoltz for many helpful discussions. GB\r\nhas received funding from the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101034413. FL wurde gefördert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Länder – GZ2047/1, Projekt-ID 390685813. LW is supported by the National Science Foundation via grant DMS-2407166. He is also indebted to the Mathematical Sciences department at Carnegie Mellon University for partly supporting his visit to Europe in July 2024. Part of this work was completed when GB and LW were visiting the Institute for Applied Mathematics in Bonn. GB and LW would like to thank IAM for their hospitality." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Giovanni full_name: Brigati, Giovanni id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1 last_name: Brigati - first_name: Francis full_name: Lörler, Francis last_name: Lörler - first_name: Lihan full_name: Wang, Lihan last_name: Wang citation: ama: Brigati G, Lörler F, Wang L. Hypocoercivity meets lifts. Kinetic and Related Models. 2026;20:34-55. doi:10.3934/krm.2025020 apa: Brigati, G., Lörler, F., & Wang, L. (2026). Hypocoercivity meets lifts. Kinetic and Related Models. American Institute of Mathematical Sciences. https://doi.org/10.3934/krm.2025020 chicago: Brigati, Giovanni, Francis Lörler, and Lihan Wang. “Hypocoercivity Meets Lifts.” Kinetic and Related Models. American Institute of Mathematical Sciences, 2026. https://doi.org/10.3934/krm.2025020. ieee: G. Brigati, F. Lörler, and L. Wang, “Hypocoercivity meets lifts,” Kinetic and Related Models, vol. 20. American Institute of Mathematical Sciences, pp. 34–55, 2026. ista: Brigati G, Lörler F, Wang L. 2026. Hypocoercivity meets lifts. Kinetic and Related Models. 20, 34–55. mla: Brigati, Giovanni, et al. “Hypocoercivity Meets Lifts.” Kinetic and Related Models, vol. 20, American Institute of Mathematical Sciences, 2026, pp. 34–55, doi:10.3934/krm.2025020. short: G. Brigati, F. Lörler, L. Wang, Kinetic and Related Models 20 (2026) 34–55. date_created: 2026-02-01T23:01:43Z date_published: 2026-02-01T00:00:00Z date_updated: 2026-02-16T10:02:47Z day: '01' department: - _id: JaMa doi: 10.3934/krm.2025020 ec_funded: 1 external_id: arxiv: - '2412.10890' intvolume: ' 20' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2412.10890 month: '02' oa: 1 oa_version: Preprint page: 34-55 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Kinetic and Related Models publication_identifier: eissn: - 1937-5077 issn: - 1937-5093 publication_status: epub_ahead publisher: American Institute of Mathematical Sciences quality_controlled: '1' scopus_import: '1' status: public title: Hypocoercivity meets lifts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2026' ... --- OA_place: publisher OA_type: gold _id: '21133' abstract: - lang: eng text: "Data structures based on trees and tree traversals are ubiquitous in computer systems. Many low-level programs, including some implementations of critical systems like page tables and the web browser DOM, rely on generic tree-traversal functions that traverse tree nodes in a pre-determined order, applying a client-provided operation to each visited node. Developing a general approach to specifying and verifying such traversals is tricky since the client-provided per-node operation can be stateful and may potentially depend on or modify the structure of the tree being traversed.\r\nIn this paper, we present a recipe for (semi-)automated verification of such generic, stateful tree traversals. Our recipe is (a) general: it applies to a range of tree traversals, in particular, pre-, post- and in-order depth-first traversals; (b) modular: parts of a traversal’s proof can be reused in verifying other similar traversals; (c) expressive: using the specification of a tree traversal, we can verify clients that use the traversal in a variety of different ways; and (d) automatable: many proof obligations can be discharged automatically.\r\nAt the heart of our recipe is a novel use of tree zippers to represent a logical abstraction of the tree traversal state, and zipper transitions as an abstraction of traversal steps. We realize our recipe in the RefinedC framework in Rocq, which allows us to verify a number of different tree traversals and their clients written in C." acknowledgement: We thank the anonymous reviewers for their insightful suggestions. This research is supported in part by generous awards from Android Security’s ASPIRE program and from Google Research. The third author is supported, in part, by ERC grant COCONUT (grant no. 101171349), funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. article_processing_charge: No author: - first_name: Laila full_name: Elbeheiry, Laila last_name: Elbeheiry - first_name: Michael Joachim full_name: Sammler, Michael Joachim id: 510d3901-2a03-11ee-914d-d9ae9011f0a7 last_name: Sammler - first_name: Robbert full_name: Krebbers, Robbert last_name: Krebbers - first_name: Derek full_name: Dreyer, Derek last_name: Dreyer - first_name: Deepak full_name: Garg, Deepak last_name: Garg citation: ama: 'Elbeheiry L, Sammler MJ, Krebbers R, Dreyer D, Garg D. A recipe for modular verification of generic tree traversals. In: Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs. Association for Computing Machinery; 2026:339-352. doi:10.1145/3779031.3779110' apa: 'Elbeheiry, L., Sammler, M. J., Krebbers, R., Dreyer, D., & Garg, D. (2026). A recipe for modular verification of generic tree traversals. In Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs (pp. 339–352). Rennes, France: Association for Computing Machinery. https://doi.org/10.1145/3779031.3779110' chicago: Elbeheiry, Laila, Michael Joachim Sammler, Robbert Krebbers, Derek Dreyer, and Deepak Garg. “A Recipe for Modular Verification of Generic Tree Traversals.” In Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs, 339–52. Association for Computing Machinery, 2026. https://doi.org/10.1145/3779031.3779110. ieee: L. Elbeheiry, M. J. Sammler, R. Krebbers, D. Dreyer, and D. Garg, “A recipe for modular verification of generic tree traversals,” in Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs, Rennes, France, 2026, pp. 339–352. ista: 'Elbeheiry L, Sammler MJ, Krebbers R, Dreyer D, Garg D. 2026. A recipe for modular verification of generic tree traversals. Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs. CPP: Conference on Certified Programs and Proofs, 339–352.' mla: Elbeheiry, Laila, et al. “A Recipe for Modular Verification of Generic Tree Traversals.” Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs, Association for Computing Machinery, 2026, pp. 339–52, doi:10.1145/3779031.3779110. short: L. Elbeheiry, M.J. Sammler, R. Krebbers, D. Dreyer, D. Garg, in:, Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs, Association for Computing Machinery, 2026, pp. 339–352. conference: end_date: 2026-01-13 location: Rennes, France name: 'CPP: Conference on Certified Programs and Proofs' start_date: 2026-01-12 date_created: 2026-02-01T23:01:43Z date_published: 2026-01-08T00:00:00Z date_updated: 2026-02-16T08:43:24Z day: '08' ddc: - '000' department: - _id: MiSa doi: 10.1145/3779031.3779110 file: - access_level: open_access checksum: 7df99991493e907d83a197151f378e3e content_type: application/pdf creator: dernst date_created: 2026-02-16T08:40:29Z date_updated: 2026-02-16T08:40:29Z file_id: '21225' file_name: 2026_CPP_Elbeheiry.pdf file_size: 811872 relation: main_file success: 1 file_date_updated: 2026-02-16T08:40:29Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 339-352 publication: Proceedings of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs publication_identifier: isbn: - '9798400723414' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: A recipe for modular verification of generic tree traversals tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: repository OA_type: green _id: '21134' abstract: - lang: eng text: "The Nakamoto consensus protocol underlying the Bitcoin blockchain uses proof of work as a voting mechanism. Honest miners who contribute hashing power towards securing the chain try to extend the longest chain they are aware of. Despite its simplicity, Nakamoto consensus achieves meaningful security guarantees assuming that at any point in time, a majority of the hashing power is controlled by honest parties. This also holds under “resource variability”, i.e., if the total hashing power varies greatly over time.\r\nProofs of space (PoSpace) have been suggested as a more sustainable replacement for proofs of work. Unfortunately, no construction of a “longest-chain” blockchain based on PoSpace, that is secure under dynamic availability, is known. In this work, we prove that without additional assumptions no such protocol exists. We exactly quantify this impossibility result by proving a bound on the length of the fork required for double spending as a function of the adversarial capabilities. This bound holds for any chain selection rule, and we also show a chain selection rule (albeit a very strange one) that almost matches this bound.\r\nThe Nakamoto consensus protocol underlying the Bitcoin blockchain uses proof of work as a voting mechanism. Honest miners who contribute hashing power towards securing the chain try to extend the longest chain they are aware of. Despite its simplicity, Nakamoto consensus achieves meaningful security guarantees assuming that at any point in time, a majority of the hashing power is controlled by honest parties. This also holds under “resource variability”, i.e., if the total hashing power varies greatly over time.\r\n\r\nProofs of space (PoSpace) have been suggested as a more sustainable replacement for proofs of work. Unfortunately, no construction of a “longest-chain” blockchain based on PoSpace, that is secure under dynamic availability, is known. In this work, we prove that without additional assumptions no such protocol exists. We exactly quantify this impossibility result by proving a bound on the length of the fork required for double spending as a function of the adversarial capabilities. This bound holds for any chain selection rule, and we also show a chain selection rule (albeit a very strange one) that almost matches this bound.\r\n\r\nConcretely, we consider a security game in which the honest parties at any point control 0 > 1\r\n times more space than the adversary. The adversary can change the honest space by a factor 1+- E with every block (dynamic availability), and “replotting” the space (which allows answering two challenges using the same space) takes as much time as p blocks.\r\nWe prove that no matter what chain selection rule is used, in this game the adversary can create a fork of length o^2 . p/E that will be picked as the winner by the chain selection rule.\r\nWe also provide an upper bound that matches the lower bound up to a factor o. There exists a chain selection rule (albeit a very strange one) which in the above game requires forks of length at least o . p/E\r\nOur results show the necessity of additional assumptions to create a secure PoSpace based longest-chain blockchain. The Chia network in addition to PoSpace uses a verifiable delay function. Our bounds show that an additional primitive like that is necessary." acknowledgement: This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/F85. alternative_title: - LNCS article_processing_charge: No arxiv: 1 author: - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Baig MA, Pietrzak KZ. On the (in)security of Proofs-of-space based longest-chain blockchains. In: 29th International Conference on Financial Cryptography and Data Security. Vol 15752. Springer Nature; 2026:127-142. doi:10.1007/978-3-032-07035-7_8' apa: 'Baig, M. A., & Pietrzak, K. Z. (2026). On the (in)security of Proofs-of-space based longest-chain blockchains. In 29th International Conference on Financial Cryptography and Data Security (Vol. 15752, pp. 127–142). Miyakojima, Japan: Springer Nature. https://doi.org/10.1007/978-3-032-07035-7_8' chicago: Baig, Mirza Ahad, and Krzysztof Z Pietrzak. “On the (in)Security of Proofs-of-Space Based Longest-Chain Blockchains.” In 29th International Conference on Financial Cryptography and Data Security, 15752:127–42. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-07035-7_8. ieee: M. A. Baig and K. Z. Pietrzak, “On the (in)security of Proofs-of-space based longest-chain blockchains,” in 29th International Conference on Financial Cryptography and Data Security, Miyakojima, Japan, 2026, vol. 15752, pp. 127–142. ista: 'Baig MA, Pietrzak KZ. 2026. On the (in)security of Proofs-of-space based longest-chain blockchains. 29th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 15752, 127–142.' mla: Baig, Mirza Ahad, and Krzysztof Z. Pietrzak. “On the (in)Security of Proofs-of-Space Based Longest-Chain Blockchains.” 29th International Conference on Financial Cryptography and Data Security, vol. 15752, Springer Nature, 2026, pp. 127–42, doi:10.1007/978-3-032-07035-7_8. short: M.A. Baig, K.Z. Pietrzak, in:, 29th International Conference on Financial Cryptography and Data Security, Springer Nature, 2026, pp. 127–142. conference: end_date: 2025-04-18 location: Miyakojima, Japan name: 'FC: Financial Cryptography and Data Security' start_date: 2025-04-14 corr_author: '1' date_created: 2026-02-01T23:01:43Z date_published: 2026-01-01T00:00:00Z date_updated: 2026-04-15T08:45:18Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-032-07035-7_8 external_id: arxiv: - '2505.14891' intvolume: ' 15752' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2505.14891 month: '01' oa: 1 oa_version: Preprint page: 127-142 project: - _id: 34a34d57-11ca-11ed-8bc3-a2688a8724e1 grant_number: F8509 name: Security and Privacy by Design for Complex Systems publication: 29th International Conference on Financial Cryptography and Data Security publication_identifier: eissn: - 1611-3349 isbn: - '9783032070340' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '21651' relation: dissertation_contains status: public scopus_import: '1' status: public title: On the (in)security of Proofs-of-space based longest-chain blockchains type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15752 year: '2026' ... --- OA_place: repository OA_type: green _id: '21135' abstract: - lang: eng text: Three-dimensional (3D) microscopy data is often anisotropic with significantly lower resolution (up to 8x) along the z axis than along the xy axes. Computationally generating plausible isotropic resolution from anisotropic imaging data would benefit the visual analysis of large-scale volumes. This paper proposes niiv, a self-supervised method for isotropic reconstruction of 3D microscopy data that can quickly produce images at arbitrary output resolutions. The representation embeds a learned latent code within a neural field that describes the implicit higher-resolution isotropic image region. We use an attention-guided latent interpolation approach, which allows flexible information exchange over a local latent neighborhood. Under isotropic volume assumptions, we self-supervise this representation on low-/high-resolution lateral image pairs to reconstruct an isotropic volume from low-resolution axial images. We evaluate our method on simulated and real anisotropic electron (EM) and light microscopy (LM) data. Compared to diffusion-based baselines, niiv shows improved reconstruction quality (+1 dB PSNR) and is over three orders of magnitude faster (1,000x) to infer. Specifically, niiv reconstructs a 128^3 voxel volume in 2/10th of a second, renderable at varying (continuous) high resolutions for display. Our code is available at https://github.com/jakobtroidl/niiv-miccai. acknowledgement: This work was supported by NIH grants 1U01NS132158 and R01HD104969. We thank the reviewers for their constructive feedback. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jakob full_name: Troidl, Jakob last_name: Troidl - first_name: Yiqing full_name: Liang, Yiqing last_name: Liang - first_name: Johanna full_name: Beyer, Johanna last_name: Beyer - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Markus full_name: Hadwiger, Markus last_name: Hadwiger - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: James full_name: Tompkin, James last_name: Tompkin citation: ama: 'Troidl J, Liang Y, Beyer J, et al. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In: 1st International Workshop on Efficient Medical Artificial Intelligence. Vol 16318. Springer Nature; 2026:257-267. doi:10.1007/978-3-032-13961-0_26' apa: 'Troidl, J., Liang, Y., Beyer, J., Tavakoli, M., Danzl, J. G., Hadwiger, M., … Tompkin, J. (2026). niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In 1st International Workshop on Efficient Medical Artificial Intelligence (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature. https://doi.org/10.1007/978-3-032-13961-0_26' chicago: 'Troidl, Jakob, Yiqing Liang, Johanna Beyer, Mojtaba Tavakoli, Johann G Danzl, Markus Hadwiger, Hanspeter Pfister, and James Tompkin. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” In 1st International Workshop on Efficient Medical Artificial Intelligence, 16318:257–67. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-13961-0_26.' ieee: 'J. Troidl et al., “niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction,” in 1st International Workshop on Efficient Medical Artificial Intelligence, Daejeon, South Korea, 2026, vol. 16318, pp. 257–267.' ista: 'Troidl J, Liang Y, Beyer J, Tavakoli M, Danzl JG, Hadwiger M, Pfister H, Tompkin J. 2026. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. 1st International Workshop on Efficient Medical Artificial Intelligence. EMA4MICCAI: Efficient Medical Artificial Intelligence, LNCS, vol. 16318, 257–267.' mla: 'Troidl, Jakob, et al. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” 1st International Workshop on Efficient Medical Artificial Intelligence, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:10.1007/978-3-032-13961-0_26.' short: J. Troidl, Y. Liang, J. Beyer, M. Tavakoli, J.G. Danzl, M. Hadwiger, H. Pfister, J. Tompkin, in:, 1st International Workshop on Efficient Medical Artificial Intelligence, Springer Nature, 2026, pp. 257–267. conference: end_date: 2025-09-23 location: Daejeon, South Korea name: 'EMA4MICCAI: Efficient Medical Artificial Intelligence' start_date: 2025-09-23 date_created: 2026-02-01T23:01:44Z date_published: 2026-01-03T00:00:00Z date_updated: 2026-02-16T08:50:50Z day: '03' department: - _id: JoDa doi: 10.1007/978-3-032-13961-0_26 intvolume: ' 16318' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.09.07.611785 month: '01' oa: 1 oa_version: Preprint page: 257-267 publication: 1st International Workshop on Efficient Medical Artificial Intelligence publication_identifier: eissn: - 1611-3349 isbn: - '9783032139603' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/jakobtroidl/niiv-miccai scopus_import: '1' status: public title: 'niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16318 year: '2026' ... --- OA_place: repository _id: '21137' acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: ScienComp - _id: LifeSc acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H. article_processing_charge: No author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 citation: ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137 apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137 chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137. ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026. ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137. mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137. short: S. Naik, (2026). contributor: - contributor_type: researcher first_name: Yann-Edwin last_name: Keta - contributor_type: supervisor first_name: 'Silke ' last_name: Henkes - contributor_type: supervisor first_name: Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - contributor_type: supervisor first_name: Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 corr_author: '1' date_created: 2026-02-04T16:38:02Z date_published: 2026-03-24T00:00:00Z date_updated: 2026-06-10T09:44:10Z day: '24' department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-21137 ec_funded: 1 file: - access_level: open_access checksum: 5d1fda7e410f24c311fcf6bcf725698f content_type: application/zip creator: snaik date_created: 2026-03-16T11:51:10Z date_updated: 2026-03-16T11:51:10Z description: 'Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. ' file_id: '21461' file_name: cells-main.zip file_size: 725916 relation: main_file title: Cell git repository - access_level: open_access checksum: ee350c8eaed99f3ca348c47c8b190d3c content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-18T14:52:02Z date_updated: 2026-03-18T14:52:02Z file_id: '21464' file_name: DevBranchDataRepo.zip file_size: 282168895 relation: main_file success: 1 - access_level: open_access checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f content_type: text/markdown creator: snaik date_created: 2026-03-18T15:01:32Z date_updated: 2026-03-18T15:01:32Z file_id: '21466' file_name: ReadMe.md file_size: 2231 relation: main_file success: 1 - access_level: open_access checksum: da9a4687e5144b61a64ca341f922046a content_type: image/svg+xml creator: snaik date_created: 2026-03-18T15:12:57Z date_updated: 2026-03-18T15:12:57Z file_id: '21467' file_name: PaperSchematics.svg file_size: 1951210 relation: main_file success: 1 - access_level: open_access checksum: 9ac1054b16c212c6f34d402dce2c80e0 content_type: application/octet-stream creator: snaik date_created: 2026-03-21T03:37:43Z date_updated: 2026-03-21T03:37:43Z file_id: '21468' file_name: maxwell_sketch.tex file_size: 1897 relation: main_file success: 1 - access_level: open_access checksum: 7c9ecf78e2593b3830d96fa94baa08df content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-24T07:21:43Z date_updated: 2026-03-24T07:21:43Z file_id: '21495' file_name: DataRepo.zip file_size: 749368723 relation: main_file success: 1 file_date_updated: 2026-03-24T07:21:43Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '3' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 252C3B08-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1250-B20 name: Nano-Analytics of Cellular Systems publisher: Institute of Science and Technology Austria status: public title: 'Data associated with Keratins coordinate tissue spreading ' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: repository OA_type: green _id: '21140' abstract: - lang: eng text: 'We consider several problems related to packing forests in graphs. The first one is to find k edge-disjoint forests in a directed graph G of maximal size such that the indegree of each vertex in these forests is at most k. We describe a min-max characterization for this problem and show that it can be solved in almost linear time for fixed k, extending the algorithm of [Gabow, 1995]. Specifically, the complexity is O(kδm log n), where n, m are the number of vertices and edges in G respectively, and δ = max{1, k − kG}, where kG is the edge connectivity of the graph. Using our solution to this problem, we improve complexities for two existing applications:(1) k-forest problem: find k forests in an undirected graph G maximizing the number of edges in their union. We show how to solve this problem in O(k3 min{kn, m} log2 n + k · MAXFLOW(m, m) log n) time, breaking the Ok(n3/2) complexity barrier of previously known approaches.(2) Directed edge-connectivity augmentation problem: find a smallest set of directed edges whose addition to the given directed graph makes it strongly k-connected. We improve the deterministic complexity for this problem from O(kδ(m + δn) log n) [Gabow, STOC 1994] to O(kδm log n). A similar approach with the same complexity also works for the undirected version of the problem.' article_processing_charge: No arxiv: 1 author: - first_name: Pavel full_name: Arkhipov, Pavel id: b25f2ab2-1fed-11ee-8599-fe02d211784f last_name: Arkhipov - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Arkhipov P, Kolmogorov V. Faster algorithms for packing forests in graphs and related problems. In: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2026:4023-4042. doi:10.1137/1.9781611978971.148' apa: 'Arkhipov, P., & Kolmogorov, V. (2026). Faster algorithms for packing forests in graphs and related problems. In Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4023–4042). Vancouver, Canada: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611978971.148' chicago: Arkhipov, Pavel, and Vladimir Kolmogorov. “Faster Algorithms for Packing Forests in Graphs and Related Problems.” In Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, 4023–42. Society for Industrial and Applied Mathematics, 2026. https://doi.org/10.1137/1.9781611978971.148. ieee: P. Arkhipov and V. Kolmogorov, “Faster algorithms for packing forests in graphs and related problems,” in Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, Vancouver, Canada, 2026, pp. 4023–4042. ista: 'Arkhipov P, Kolmogorov V. 2026. Faster algorithms for packing forests in graphs and related problems. Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4023–4042.' mla: Arkhipov, Pavel, and Vladimir Kolmogorov. “Faster Algorithms for Packing Forests in Graphs and Related Problems.” Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2026, pp. 4023–42, doi:10.1137/1.9781611978971.148. short: P. Arkhipov, V. Kolmogorov, in:, Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2026, pp. 4023–4042. conference: end_date: 2026-01-14 location: Vancouver, Canada name: 'SODA: Symposium on Discrete Algorithms' start_date: 2026-01-11 corr_author: '1' date_created: 2026-02-05T10:51:34Z date_published: 2026-01-07T00:00:00Z date_updated: 2026-02-16T09:18:33Z day: '07' department: - _id: VlKo doi: 10.1137/1.9781611978971.148 external_id: arxiv: - '2409.20314' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.20314 month: '01' oa: 1 oa_version: Preprint page: 4023-4042 publication: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - '9781611978971' publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' status: public title: Faster algorithms for packing forests in graphs and related problems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- _id: '21145' abstract: - lang: eng text: 'Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. ' acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011." article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot citation: ama: Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:10.15479/AT-ISTA-21145 apa: Becker, L. M., Schanda, P., & Chipot, C. (2026). Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21145 chicago: Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21145. ieee: L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. ista: Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21145. mla: Becker, Lea Marie, et al. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21145. short: L.M. Becker, P. Schanda, C. Chipot, (2026). contributor: - contributor_type: researcher first_name: Haohao last_name: Fu - contributor_type: researcher first_name: Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - contributor_type: researcher first_name: Matthias last_name: Dreydoppel - contributor_type: researcher first_name: Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - contributor_type: researcher first_name: Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - contributor_type: researcher first_name: Ulrich last_name: Weininger - contributor_type: researcher first_name: Sylvain last_name: Engilberge corr_author: '1' date_created: 2026-02-05T13:54:39Z date_published: 2026-02-09T00:00:00Z date_updated: 2026-06-10T08:25:16Z day: '09' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-21145 file: - access_level: open_access checksum: 02a419cce8cea450bc952f35488d2df5 content_type: text/plain creator: lbecker date_created: 2026-02-05T13:52:37Z date_updated: 2026-02-05T13:52:37Z file_id: '21146' file_name: README.txt file_size: 4263 relation: table_of_contents - access_level: open_access checksum: b0b82b1aa73985b0b308a3fa52d21aea content_type: application/zip creator: lbecker date_created: 2026-02-05T13:52:41Z date_updated: 2026-02-05T13:52:41Z file_id: '21147' file_name: Research_Data.zip file_size: 50647107 relation: main_file success: 1 file_date_updated: 2026-02-05T13:52:41Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publisher: Institute of Science and Technology Austria related_material: record: - id: '20641' relation: earlier_version status: public status: public title: Additional Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21149' abstract: - lang: eng text: We present a general theoretical framework for helical dichroism (HD), establishing an explicit link between chiral resolution and orbital angular momentum (OAM) exchange in light–matter interaction. Tracing microscopic mechanisms of the OAM transfer, we derive rotational selection rules, which establish that HD emerges only from the spin–orbit coupling of light, even for beams without the far-field OAM. Our findings refine the conditions for observing HD, provide a tool to re-examine the outcome of prior experiments, and guide future designs for chiral sensing with structured light. acknowledgement: This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. article_number: '053204' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Mateja full_name: Hrast, Mateja id: 48dbb294-2a9c-11ef-905d-f56be71f0e5d last_name: Hrast - first_name: Georgios full_name: Koutentakis, Georgios id: d7b23d3a-9e21-11ec-b482-f76739596b95 last_name: Koutentakis - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Hrast M, Koutentakis G, Maslov M, Lemeshko M. Bottom-up analysis of rovibrational helical dichroism. Physical Review Letters. 2026;136(5). doi:10.1103/fkf1-1jml apa: Hrast, M., Koutentakis, G., Maslov, M., & Lemeshko, M. (2026). Bottom-up analysis of rovibrational helical dichroism. Physical Review Letters. American Physical Society. https://doi.org/10.1103/fkf1-1jml chicago: Hrast, Mateja, Georgios Koutentakis, Mikhail Maslov, and Mikhail Lemeshko. “Bottom-up Analysis of Rovibrational Helical Dichroism.” Physical Review Letters. American Physical Society, 2026. https://doi.org/10.1103/fkf1-1jml. ieee: M. Hrast, G. Koutentakis, M. Maslov, and M. Lemeshko, “Bottom-up analysis of rovibrational helical dichroism,” Physical Review Letters, vol. 136, no. 5. American Physical Society, 2026. ista: Hrast M, Koutentakis G, Maslov M, Lemeshko M. 2026. Bottom-up analysis of rovibrational helical dichroism. Physical Review Letters. 136(5), 053204. mla: Hrast, Mateja, et al. “Bottom-up Analysis of Rovibrational Helical Dichroism.” Physical Review Letters, vol. 136, no. 5, 053204, American Physical Society, 2026, doi:10.1103/fkf1-1jml. short: M. Hrast, G. Koutentakis, M. Maslov, M. Lemeshko, Physical Review Letters 136 (2026). corr_author: '1' date_created: 2026-02-06T10:53:17Z date_published: 2026-02-05T00:00:00Z date_updated: 2026-02-10T11:30:37Z day: '05' ddc: - '530' department: - _id: MiLe doi: 10.1103/fkf1-1jml external_id: arxiv: - '2505.16393' file: - access_level: open_access checksum: 805c929fff9fd4d0e733293eaace67b8 content_type: application/pdf creator: dernst date_created: 2026-02-10T11:25:46Z date_updated: 2026-02-10T11:25:46Z file_id: '21210' file_name: 2026_PhysicalReviewLetters_Hrast.pdf file_size: 511312 relation: main_file success: 1 file_date_updated: 2026-02-10T11:25:46Z has_accepted_license: '1' intvolume: ' 136' issue: '5' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3 grant_number: F100403 name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Bottom-up analysis of rovibrational helical dichroism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21158' abstract: - lang: eng text: Vernalization-regulated flowering is vital for wheat yield and geographical distribution, and the diversity of flowering time genes is essential for the breeding of climate-resilient varieties. Sugars have long been recognized in regulating flowering; however, the intrinsic connection between carbohydrate metabolism and vernalization response remains largely unexplored. Here, we identify a fructose 1,6-bisphosphate aldolase (FBA) encoding gene, HtL1/FBA10, as a modulator of heading time variation based on a genome-wide association study utilizing wheat core germplasm collections. Evolutionary analysis shows a decrease in the proportion of haplotype-2 of HtL1, which is linked to delayed flowering, in Chinese and American wheat varieties compared to landraces. Vernalization reduces HtL1/FBA10 phosphorylation levels and increases its O-GlcNAcylation, which in turn enhances its enzymatic activity and facilitates VERNALIZATION 1 (VRN1) transcription by regulating histone acetylation at the VRN1 locus. Our findings provide mechanistic insights into the interplay between glucose metabolism and the epigenetic regulation of vernalization in winter wheat. acknowledgement: This work was supported by the Basic Science Center Project of National Natural Science Foundation of China (32388201) to K.C and the National Natural Science Foundation of China (31970331) to L.X. We thank Dr. Zhuang Lu, Dr. Bin Han and Ms. Jingquan Li (Plant Science Facility of the Institute of Botany, Chinese Academy of Sciences) for their technical assistance in LC-MS/MS assay, small molecule compound analysis and the subcellular localization assay, respectively. We thank Dr. Wei Luo and Dr. Dongfeng Liu for helpful discussions. article_number: '999' article_processing_charge: Yes article_type: original author: - first_name: Pengfang full_name: Yang, Pengfang last_name: Yang - first_name: Yangyang full_name: Liu, Yangyang last_name: Liu - first_name: Qi full_name: Dong, Qi last_name: Dong - first_name: Yuting full_name: Miao, Yuting last_name: Miao - first_name: Jianlong full_name: Zhang, Jianlong last_name: Zhang - first_name: Shujuan full_name: Xu, Shujuan id: 9724dd9d-f591-11ee-bd51-e97ed0652286 last_name: Xu - first_name: Hong full_name: Zhao, Hong last_name: Zhao - first_name: Yuda full_name: Niu, Yuda last_name: Niu - first_name: Xueyong full_name: Zhang, Xueyong last_name: Zhang - first_name: Yunyuan full_name: Xu, Yunyuan last_name: Xu - first_name: Zifeng full_name: Guo, Zifeng last_name: Guo - first_name: Lijing full_name: Xing, Lijing last_name: Xing - first_name: Kang full_name: Chong, Kang last_name: Chong citation: ama: Yang P, Liu Y, Dong Q, et al. O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering. Nature Communications. 2026;17. doi:10.1038/s41467-025-67734-0 apa: Yang, P., Liu, Y., Dong, Q., Miao, Y., Zhang, J., Xu, S., … Chong, K. (2026). O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-67734-0 chicago: Yang, Pengfang, Yangyang Liu, Qi Dong, Yuting Miao, Jianlong Zhang, Shujuan Xu, Hong Zhao, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10 Regulate Wheat Vernalization for Flowering.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-025-67734-0. ieee: P. Yang et al., “O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering,” Nature Communications, vol. 17. Springer Nature, 2026. ista: Yang P, Liu Y, Dong Q, Miao Y, Zhang J, Xu S, Zhao H, Niu Y, Zhang X, Xu Y, Guo Z, Xing L, Chong K. 2026. O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering. Nature Communications. 17, 999. mla: Yang, Pengfang, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10 Regulate Wheat Vernalization for Flowering.” Nature Communications, vol. 17, 999, Springer Nature, 2026, doi:10.1038/s41467-025-67734-0. short: P. Yang, Y. Liu, Q. Dong, Y. Miao, J. Zhang, S. Xu, H. Zhao, Y. Niu, X. Zhang, Y. Xu, Z. Guo, L. Xing, K. Chong, Nature Communications 17 (2026). date_created: 2026-02-08T23:02:48Z date_published: 2026-01-27T00:00:00Z date_updated: 2026-02-12T14:34:24Z day: '27' ddc: - '580' department: - _id: XiFe doi: 10.1038/s41467-025-67734-0 external_id: pmid: - '41455723' file: - access_level: open_access checksum: 9ae170ec70ba1ab56b6f1ffe67d1de7f content_type: application/pdf creator: dernst date_created: 2026-02-12T14:33:14Z date_updated: 2026-02-12T14:33:14Z file_id: '21223' file_name: 2026_NatureComm_Yang.pdf file_size: 4685882 relation: main_file success: 1 file_date_updated: 2026-02-12T14:33:14Z has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21159' abstract: - lang: eng text: "One of the foundational theorems of extremal graph theory is Dirac’s theorem, which\r\nsays that if an n-vertex graph G has minimum degree at least n/2, then G has a\r\nHamilton cycle, and therefore a perfect matching (if n is even). Later work by Sárközy,\r\nSelkow and Szemerédi showed that in fact Dirac graphs have many Hamilton cycles\r\nand perfect matchings, culminating in a result of Cuckler and Kahn that gives a precise\r\ndescription of the numbers of Hamilton cycles and perfect matchings in a Dirac graph\r\nG (in terms of an entropy-like parameter of G). In this paper we extend Cuckler\r\nand Kahn’s result to perfect matchings in hypergraphs. For positive integers d < k,\r\nand for n divisible by k, let md (k, n) be the minimum d-degree that ensures the\r\nexistence of a perfect matching in an n-vertex k-uniform hypergraph. In general, it is\r\nan open question to determine (even asymptotically) the values of md (k, n), but we are\r\nnonetheless able to prove an analogue of the Cuckler–Kahn theorem, showing that if\r\nan n-vertex k-uniform hypergraph G has minimum d-degree at least (1+γ )md (k, n)\r\n(for any constantγ > 0), then the number of perfect matchings in G is controlled by\r\nan entropy-like parameter of G. This strengthens cruder estimates arising from work\r\nof Kang–Kelly–Kühn–Osthus–Pfenninger and Pham–Sah–Sawhney–Simkin." acknowledgement: We would like to thank the referees for a number of helpful comments and suggestions, which have substantially improved the paper. Open access funding provided by Institute of Science and Technology (IST Austria). article_number: '5' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Roodabeh full_name: Safavi Hemami, Roodabeh id: 72ed2640-8972-11ed-ae7b-f9c81ec75154 last_name: Safavi Hemami - first_name: Yiting full_name: Wang, Yiting id: 1917d194-076e-11ed-97cd-837255f88785 last_name: Wang orcid: 0000-0002-2856-767X citation: ama: Kwan MA, Safavi Hemami R, Wang Y. Counting perfect matchings in Dirac hypergraphs. Combinatorica. 2026;46. doi:10.1007/s00493-025-00194-8 apa: Kwan, M. A., Safavi Hemami, R., & Wang, Y. (2026). Counting perfect matchings in Dirac hypergraphs. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-025-00194-8 chicago: Kwan, Matthew Alan, Roodabeh Safavi Hemami, and Yiting Wang. “Counting Perfect Matchings in Dirac Hypergraphs.” Combinatorica. Springer Nature, 2026. https://doi.org/10.1007/s00493-025-00194-8. ieee: M. A. Kwan, R. Safavi Hemami, and Y. Wang, “Counting perfect matchings in Dirac hypergraphs,” Combinatorica, vol. 46. Springer Nature, 2026. ista: Kwan MA, Safavi Hemami R, Wang Y. 2026. Counting perfect matchings in Dirac hypergraphs. Combinatorica. 46, 5. mla: Kwan, Matthew Alan, et al. “Counting Perfect Matchings in Dirac Hypergraphs.” Combinatorica, vol. 46, 5, Springer Nature, 2026, doi:10.1007/s00493-025-00194-8. short: M.A. Kwan, R. Safavi Hemami, Y. Wang, Combinatorica 46 (2026). corr_author: '1' date_created: 2026-02-08T23:02:49Z date_published: 2026-02-01T00:00:00Z date_updated: 2026-02-16T09:55:17Z day: '01' ddc: - '510' department: - _id: MaKw - _id: MoHe doi: 10.1007/s00493-025-00194-8 external_id: arxiv: - '2408.09589' file: - access_level: open_access checksum: 47b0031d90b0e6b9a843f422a1486089 content_type: application/pdf creator: dernst date_created: 2026-02-16T09:52:38Z date_updated: 2026-02-16T09:52:38Z file_id: '21228' file_name: 2026_Combinatorica_Kwan.pdf file_size: 539646 relation: main_file success: 1 file_date_updated: 2026-02-16T09:52:38Z has_accepted_license: '1' intvolume: ' 46' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Combinatorica publication_identifier: eissn: - 1439-6912 issn: - 0209-9683 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Counting perfect matchings in Dirac hypergraphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2026' ... --- OA_place: publisher OA_type: diamond PlanS_conform: '1' _id: '21160' abstract: - lang: eng text: "Context. AM Canum Venaticorum (AM CVn) stars are ultra-compact binary systems composed of a white dwarf primary accreting from a hydrogen-deficient donor. They play a crucial role in astrophysics as potential progenitors of Type Ia supernovae and as laboratories for gravitational wave studies. However, their formation and evolutionary history remain incomplete. Three formation channels have been discussed in the literature: the white dwarf, He-star, and cataclysmic variable channels.\r\n\r\nAims. The chemical composition of the accretor atmosphere reflects the material transferred from the donor. In this work we took the first accurate measurements of the fundamental parameters of the accreting white dwarf in ZTF J225237.05−051917.4, including the abundances of key elements such as carbon, nitrogen, and silicon, by analysing ultraviolet spectra obtained with the Hubble Space Telescope (HST). These measurements provide new insight into the evolutionary history of the system and, together with existing optical observations, establish it as a benchmark to develop our pipeline, paving the way for its application to a larger sample of AM CVn systems.\r\n\r\nMethods. We determined the binary parameters through photometric analysis and constrained the atmospheric parameters of the white dwarf accretor, including its effective temperature, surface gravity, and chemical abundances, by fitting the HST ultraviolet spectrum with synthetic spectral models. We then inferred the system’s formation channel by comparing the results with theoretical evolutionary models.\r\n\r\nResults. According to our measurements, the accretor’s effective temperature (Teff) is 23 300 ± 600 K and the surface gravity (log g) is 8.4 ± 0.3, which imply an accretor mass (MWD) of 0.86 ± 0.16 M⊙. We find a high nitrogen-to-carbon abundance ratio by mass of > 153.\r\n\r\nConclusions. The accretor is significantly hotter than previous estimates based on simplified blackbody fits to the spectral energy distribution, underscoring the importance of detailed spectral modelling for accurately determining system parameters. Our results show that ultraviolet spectroscopy is well suited to constraining the formation channels of AM CVn systems. Of the three proposed formation channels, the He-star channel can be excluded given the high nitrogen-to-carbon ratio. Our results are consistent with both the white dwarf and cataclysmic variable channels." acknowledgement: "We thank Lars Bildsten for valuable insights and discussions. We acknowledge with thanks the variable star observations from the\r\nAAVSO International Database contributed by observers worldwide and used in this research. We thank the members of the Spanish Observers of Supernovae\r\n(ObSN) group for their valuable photometric contributions. This research was\r\nsupported by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2121 “Quantum Universe”\r\n– 390833306. Co-funded by the European Union (ERC, CompactBINARIES,\r\n101078773). Views and opinions expressed are however those of the author(s)\r\nonly and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority\r\ncan be held responsible for them. DB acknowledges support from the São Paulo\r\nResearch Foundation (FAPESP), Brazil, Process Numbers #2024/03736-2 and\r\n#2025/00817-4. MRS is supported by Fondecyt (grant 1221059). MJG acknowledges support from the European Research Council through ERC Advanced\r\nGrant No. 101054731, from the National Aeronautics and Space Administration under grants 80NSSC24K0436, 80NSSC22K0479, and 80NSSC24K0380,\r\nand from the National Science Foundation under grant AST-2205736. PJG\r\nis supported by NRF SARChI grant 111692. PR-G acknowledges support by\r\nthe Agencia Estatal de Investigación del Ministerio de Ciencia e Innovación\r\n(MCIN/AEI) and the European Regional Development Fund (ERDF) under grant\r\nPID2021–124879NB–I00. DS is supported by the UK Science and Technology Facilities Council (STFC, grant numbers ST/T007184/1, ST/T003103/1,\r\nand ST/T000406/1). OT acknowledges Proyectos Internos USM 2025, PI-LII2025-03. GT was supported by grants IN109723 from the Programa de Apoyo a\r\nProyectos de Investigación e Innovación Tecnológica (PAPIIT). This project has\r\nreceived funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101020057)." article_number: A14 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: W. full_name: Yu, W. last_name: Yu - first_name: A. F. full_name: Pala, A. F. last_name: Pala - first_name: T. full_name: Kupfer, T. last_name: Kupfer - first_name: B. T. full_name: Gänsicke, B. T. last_name: Gänsicke - first_name: D. full_name: Koester, D. last_name: Koester - first_name: D. full_name: Belloni, D. last_name: Belloni - first_name: T. L.S. full_name: Wong, T. L.S. last_name: Wong - first_name: M. R. full_name: Schreiber, M. R. last_name: Schreiber - first_name: Joannes C full_name: van Roestel, Joannes C id: 4d122fc8-6083-11f0-87a5-97d68b860333 last_name: van Roestel - first_name: A. J. full_name: Brown, A. J. last_name: Brown - first_name: E. O. full_name: Waagen, E. O. last_name: Waagen - first_name: J. L. full_name: González-Carballo, J. L. last_name: González-Carballo - first_name: S. full_name: Bednarz, S. last_name: Bednarz - first_name: K. full_name: Bernacki, K. last_name: Bernacki - first_name: D. full_name: De Martino, D. last_name: De Martino - first_name: E. full_name: Fernández Mañanes, E. last_name: Fernández Mañanes - first_name: R. full_name: González Farfán, R. last_name: González Farfán - first_name: M. J. full_name: Green, M. J. last_name: Green - first_name: P. J. full_name: Groot, P. J. last_name: Groot - first_name: F. J. full_name: Hambsch, F. J. last_name: Hambsch - first_name: C. full_name: Knigge, C. last_name: Knigge - first_name: J. L. full_name: Martin-Velasco, J. L. last_name: Martin-Velasco - first_name: M. full_name: Morales-Aimar, M. last_name: Morales-Aimar - first_name: G. full_name: Myers, G. last_name: Myers - first_name: R. full_name: Naves Nogues, R. last_name: Naves Nogues - first_name: R. full_name: Poggiani, R. last_name: Poggiani - first_name: A. full_name: Popowicz, A. last_name: Popowicz - first_name: G. full_name: Ramsay, G. last_name: Ramsay - first_name: E. full_name: Reina-Lorenz, E. last_name: Reina-Lorenz - first_name: P. full_name: Rodríguez-Gil, P. last_name: Rodríguez-Gil - first_name: J. L. full_name: Salto-González, J. L. last_name: Salto-González - first_name: E. M. full_name: Sion, E. M. last_name: Sion - first_name: D. full_name: Steeghs, D. last_name: Steeghs - first_name: P. full_name: Szkody, P. last_name: Szkody - first_name: O. full_name: Toloza, O. last_name: Toloza - first_name: G. full_name: Tovmassian, G. last_name: Tovmassian citation: ama: 'Yu W, Pala AF, Kupfer T, et al. The evolutionary history of ultra-compact accreting binaries: I. Chemical abundances and the formation channel of the eclipsing AM CVn system ZTF J225237.05-051917.4 from HST spectroscopy. Astronomy and Astrophysics. 2026;706. doi:10.1051/0004-6361/202557568' apa: 'Yu, W., Pala, A. F., Kupfer, T., Gänsicke, B. T., Koester, D., Belloni, D., … Tovmassian, G. (2026). The evolutionary history of ultra-compact accreting binaries: I. Chemical abundances and the formation channel of the eclipsing AM CVn system ZTF J225237.05-051917.4 from HST spectroscopy. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202557568' chicago: 'Yu, W., A. F. Pala, T. Kupfer, B. T. Gänsicke, D. Koester, D. Belloni, T. L.S. Wong, et al. “The Evolutionary History of Ultra-Compact Accreting Binaries: I. Chemical Abundances and the Formation Channel of the Eclipsing AM CVn System ZTF J225237.05-051917.4 from HST Spectroscopy.” Astronomy and Astrophysics. EDP Sciences, 2026. https://doi.org/10.1051/0004-6361/202557568.' ieee: 'W. Yu et al., “The evolutionary history of ultra-compact accreting binaries: I. Chemical abundances and the formation channel of the eclipsing AM CVn system ZTF J225237.05-051917.4 from HST spectroscopy,” Astronomy and Astrophysics, vol. 706. EDP Sciences, 2026.' ista: 'Yu W, Pala AF, Kupfer T, Gänsicke BT, Koester D, Belloni D, Wong TLS, Schreiber MR, van Roestel JC, Brown AJ, Waagen EO, González-Carballo JL, Bednarz S, Bernacki K, De Martino D, Fernández Mañanes E, González Farfán R, Green MJ, Groot PJ, Hambsch FJ, Knigge C, Martin-Velasco JL, Morales-Aimar M, Myers G, Naves Nogues R, Poggiani R, Popowicz A, Ramsay G, Reina-Lorenz E, Rodríguez-Gil P, Salto-González JL, Sion EM, Steeghs D, Szkody P, Toloza O, Tovmassian G. 2026. The evolutionary history of ultra-compact accreting binaries: I. Chemical abundances and the formation channel of the eclipsing AM CVn system ZTF J225237.05-051917.4 from HST spectroscopy. Astronomy and Astrophysics. 706, A14.' mla: 'Yu, W., et al. “The Evolutionary History of Ultra-Compact Accreting Binaries: I. Chemical Abundances and the Formation Channel of the Eclipsing AM CVn System ZTF J225237.05-051917.4 from HST Spectroscopy.” Astronomy and Astrophysics, vol. 706, A14, EDP Sciences, 2026, doi:10.1051/0004-6361/202557568.' short: W. Yu, A.F. Pala, T. Kupfer, B.T. Gänsicke, D. Koester, D. Belloni, T.L.S. Wong, M.R. Schreiber, J.C. van Roestel, A.J. Brown, E.O. Waagen, J.L. González-Carballo, S. Bednarz, K. Bernacki, D. De Martino, E. Fernández Mañanes, R. González Farfán, M.J. Green, P.J. Groot, F.J. Hambsch, C. Knigge, J.L. Martin-Velasco, M. Morales-Aimar, G. Myers, R. Naves Nogues, R. Poggiani, A. Popowicz, G. Ramsay, E. Reina-Lorenz, P. Rodríguez-Gil, J.L. Salto-González, E.M. Sion, D. Steeghs, P. Szkody, O. Toloza, G. Tovmassian, Astronomy and Astrophysics 706 (2026). date_created: 2026-02-08T23:02:49Z date_published: 2026-02-01T00:00:00Z date_updated: 2026-02-16T09:36:24Z day: '01' ddc: - '520' department: - _id: IlCa doi: 10.1051/0004-6361/202557568 external_id: arxiv: - '2512.04147' file: - access_level: open_access checksum: 2faec710fd04f927aa43deb57e35c9b2 content_type: application/pdf creator: dernst date_created: 2026-02-16T09:33:56Z date_updated: 2026-02-16T09:33:56Z file_id: '21227' file_name: 2026_AstronomyAstrophysics_Yu.pdf file_size: 4020466 relation: main_file success: 1 file_date_updated: 2026-02-16T09:33:56Z has_accepted_license: '1' intvolume: ' 706' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Astronomy and Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'The evolutionary history of ultra-compact accreting binaries: I. Chemical abundances and the formation channel of the eclipsing AM CVn system ZTF J225237.05-051917.4 from HST spectroscopy' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 706 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21161' abstract: - lang: eng text: In many species, sex-biased expression is widespread and thought to contribute to sexual dimorphism. While bulk RNA-sequencing has been instrumental in identifying strongly sex-biased genes, it lacks resolution to assess variation across cell-types and tissue compartments. Using single-nucleus expression data from the Fly Cell Atlas, we investigate sex differences in adult Drosophila melanogaster. We find that differences in cell-type composition between the sexes are not a major source of sex-bias, as for the vast majority of genes, the degree of sex-bias is similar regardless of whether sex differences in cell-type composition are controlled for or not. Our analysis confirms a deficit of X-linked male-biased genes in the body’s somatic tissues that is widespread across cell-types. We also find the excess of X-linked female-biased genes to be associated with nervous system cells in the head but with epithelial cells in the body’s somatic tissues, showing that single-nucleus data crucially resolves sex-bias at the cell-type level. We investigate dosage compensation (DC) across 15 tissues and 17 cell-types. We observe that it varies throughout the body. Surprisingly, we observe a lack of DC in a cluster of main cells within the male accessory glands. This result highlights the importance of understanding context-dependent DC. acknowledged_ssus: - _id: ScienComp - _id: Bio acknowledgement: This work was partly funded by an Austrian Science Foundation FWF ESPRIT fellowship (10.55776/ESP6331524) to C.B. We would like to thank the Vicoso group for their invaluable input and discussions throughout this work. We thank Filip Ruzicka for his insightful comments on the manuscript. All computational resources were provided by the Scientific Computing Unit at ISTA. This research was also supported through resources provided by the Imaging & Optics Facility (IOF) at ISTA. article_number: '20252471' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Carolina full_name: De Castro Barbosa Rodrigues Barata, Carolina id: 20565186-803f-11ed-ab7e-96a4ff7694ef last_name: De Castro Barbosa Rodrigues Barata orcid: 0000-0003-1945-2245 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: de Castro Barbosa Rodrigues Barata C, Vicoso B. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings of the Royal Society B Biological Sciences. 2026;293(2063). doi:10.1098/rspb.2025.2471 apa: de Castro Barbosa Rodrigues Barata, C., & Vicoso, B. (2026). Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings of the Royal Society B Biological Sciences. Royal Society of London. https://doi.org/10.1098/rspb.2025.2471 chicago: Castro Barbosa Rodrigues Barata, Carolina de, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” Proceedings of the Royal Society B Biological Sciences. Royal Society of London, 2026. https://doi.org/10.1098/rspb.2025.2471. ieee: C. de Castro Barbosa Rodrigues Barata and B. Vicoso, “Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster,” Proceedings of the Royal Society B Biological Sciences, vol. 293, no. 2063. Royal Society of London, 2026. ista: de Castro Barbosa Rodrigues Barata C, Vicoso B. 2026. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings of the Royal Society B Biological Sciences. 293(2063), 20252471. mla: de Castro Barbosa Rodrigues Barata, Carolina, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” Proceedings of the Royal Society B Biological Sciences, vol. 293, no. 2063, 20252471, Royal Society of London, 2026, doi:10.1098/rspb.2025.2471. short: C. de Castro Barbosa Rodrigues Barata, B. Vicoso, Proceedings of the Royal Society B Biological Sciences 293 (2026). corr_author: '1' date_created: 2026-02-08T23:02:49Z date_published: 2026-01-28T00:00:00Z date_updated: 2026-02-16T09:27:33Z day: '28' ddc: - '570' department: - _id: BeVi doi: 10.1098/rspb.2025.2471 external_id: pmid: - '41592777' file: - access_level: open_access checksum: d76afebca0a6f112df0146ae2d929f36 content_type: application/pdf creator: dernst date_created: 2026-02-16T09:26:02Z date_updated: 2026-02-16T09:26:02Z file_id: '21226' file_name: 2026_RoyalSocPubProceedingsB_Barata.pdf file_size: 2230841 relation: main_file success: 1 file_date_updated: 2026-02-16T09:26:02Z has_accepted_license: '1' intvolume: ' 293' issue: '2063' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 90ef7108-16d5-11f0-9cad-e6e116913473 grant_number: ESP 6331524 name: Does genetic drift set a limit on the adaptive evolution of sex-biased expression? publication: Proceedings of the Royal Society B Biological Sciences publication_identifier: eissn: - 1471-2954 publication_status: published publisher: Royal Society of London quality_controlled: '1' scopus_import: '1' status: public title: Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 293 year: '2026' ... --- _id: '21164' abstract: - lang: eng text: 'Global emission inventories often fail to capture the complexities of vehicular pollution in regions with unique fuel mixes, such as Brazil’s extensive biofuel use, leading to significant uncertainties in atmospheric modeling. This study presents a century-long (1960–2100) bottom-up vehicular emission inventory for Brazil, leveraging locally derived emission factors. Our estimates reveal substantial discrepancies in magnitude, timing, and speciation of non-CO2 pollutants (CO, NMHC, PM2.5) compared to leading global inventories (EDGAR, CEDS, CAMS), highlighting critical inaccuracies in widely used data sets. More critically, future projections under Shared Socioeconomic Pathways (SSPs) uncover a novel positive feedback mechanism: rising temperatures significantly enhance vehicular evaporative nonmethane hydrocarbon (NMHC) emissions. This temperature-dependent increase and subsequent NMHC oxidation to CO2 suggest an overlooked pathway that could amplify climate warming and air pollution globally, particularly after a breakpoint around 2050 (p < 0.05). While historical emissions peaked in the 1990s–2000s, nonexhaust PM becomes increasingly important. Air quality simulations using our inventory in the MUSICA model show good regional PM2.5 agreement but highlight challenges in resolving local primary pollutant peaks. This comprehensive inventory provides crucial data for Brazil and uncovers globally relevant climate–chemistry interactions, urging a re-evaluation of regional specificities in global emission assessments.' acknowledgement: Part of this material is based upon work supported by the NSF National Center for Atmospheric Research, which is a major facility sponsored by the National Science Foundation under Cooperative Agreement No. 1852977. Casallas was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. E. D. Freitas thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 313210/2022–5). Silva gratefully acknowledges the financial support from the National Council for Scientific and Technological Development (CNPq), process number 140512/2021–7. P. Lichtig was supported by base funding from the National Commission for Atomic Energy (CNEA, Arg.) and by NSF NCAR. R.Y. Ynoue thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 406728/2022–4). M. A. Franco thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 407752/2023–4). G. M. Pereira thanks the support by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Process numbers 2018/07848–9, 2016/18438–0, and 2019/01316–80) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES; Process number 88887.103225/2025–00). M.F. Andrade thanks the support by FAPESP (Process number 2016/18438–0) and CNPQ (Klimapolis INCT). article_number: 5c08400 article_processing_charge: No article_type: original author: - first_name: Sergio full_name: Ibarra-Espinosa, Sergio last_name: Ibarra-Espinosa - first_name: Edmilson full_name: Dias de Freitas, Edmilson last_name: Dias de Freitas - first_name: Benjamin full_name: Gaubert, Benjamin last_name: Gaubert - first_name: Pablo full_name: Lichtig, Pablo last_name: Lichtig - first_name: Karl full_name: Ropkins, Karl last_name: Ropkins - first_name: Iara full_name: da Silva, Iara last_name: da Silva - first_name: Guilherme full_name: Martins Pereira, Guilherme last_name: Martins Pereira - first_name: Daniel full_name: Schuch, Daniel last_name: Schuch - first_name: Janaina full_name: Nascimento, Janaina last_name: Nascimento - first_name: Leonardo full_name: Hoinaski, Leonardo last_name: Hoinaski - first_name: Leila Droprinchinski full_name: Martins, Leila Droprinchinski last_name: Martins - first_name: Mario full_name: Gavidia-Calderón, Mario last_name: Gavidia-Calderón - first_name: Angel full_name: Vara-Vela, Angel last_name: Vara-Vela - first_name: Taciana full_name: Toledo de Almeida Albuquerque, Taciana last_name: Toledo de Almeida Albuquerque - first_name: Rita Yuri full_name: Ynoue, Rita Yuri last_name: Ynoue - first_name: Sebastian full_name: Diez, Sebastian last_name: Diez - first_name: Zamir full_name: Mera, Zamir last_name: Mera - first_name: Alejandro full_name: Casallas Garcia, Alejandro id: 92081129-2d75-11ef-a48d-b04dd7a2385a last_name: Casallas Garcia orcid: 0000-0002-1988-5035 - first_name: Fidel full_name: Vallejo, Fidel last_name: Vallejo - first_name: Valeria full_name: Diaz, Valeria last_name: Diaz - first_name: Rizzieri full_name: Pedruzzi, Rizzieri last_name: Pedruzzi - first_name: Rosana full_name: Abrutzky, Rosana last_name: Abrutzky - first_name: Marco A. full_name: Franco, Marco A. last_name: Franco - first_name: Nicolas full_name: Huneeus, Nicolas last_name: Huneeus - first_name: Hector full_name: Jorquera, Hector last_name: Jorquera - first_name: Luis Carlos full_name: Belalcázar-Cerón, Luis Carlos last_name: Belalcázar-Cerón - first_name: Néstor Y. full_name: Rojas, Néstor Y. last_name: Rojas - first_name: Maria full_name: de Fatima Andrade, Maria last_name: de Fatima Andrade - first_name: Louisa full_name: Emmons, Louisa last_name: Emmons - first_name: Guy full_name: Brasseur, Guy last_name: Brasseur citation: ama: 'Ibarra-Espinosa S, Dias de Freitas E, Gaubert B, et al. A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science &amp; Technology. 2026. doi:10.1021/acs.est.5c08400' apa: 'Ibarra-Espinosa, S., Dias de Freitas, E., Gaubert, B., Lichtig, P., Ropkins, K., da Silva, I., … Brasseur, G. (2026). A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science &amp; Technology. American Chemical Society. https://doi.org/10.1021/acs.est.5c08400' chicago: 'Ibarra-Espinosa, Sergio, Edmilson Dias de Freitas, Benjamin Gaubert, Pablo Lichtig, Karl Ropkins, Iara da Silva, Guilherme Martins Pereira, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” Environmental Science &amp; Technology. American Chemical Society, 2026. https://doi.org/10.1021/acs.est.5c08400.' ieee: 'S. Ibarra-Espinosa et al., “A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality,” Environmental Science &amp; Technology. American Chemical Society, 2026.' ista: 'Ibarra-Espinosa S, Dias de Freitas E, Gaubert B, Lichtig P, Ropkins K, da Silva I, Martins Pereira G, Schuch D, Nascimento J, Hoinaski L, Martins LD, Gavidia-Calderón M, Vara-Vela A, Toledo de Almeida Albuquerque T, Ynoue RY, Diez S, Mera Z, Casallas Garcia A, Vallejo F, Diaz V, Pedruzzi R, Abrutzky R, Franco MA, Huneeus N, Jorquera H, Belalcázar-Cerón LC, Rojas NY, de Fatima Andrade M, Emmons L, Brasseur G. 2026. A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science &amp; Technology., 5c08400.' mla: 'Ibarra-Espinosa, Sergio, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” Environmental Science &amp; Technology, 5c08400, American Chemical Society, 2026, doi:10.1021/acs.est.5c08400.' short: S. Ibarra-Espinosa, E. Dias de Freitas, B. Gaubert, P. Lichtig, K. Ropkins, I. da Silva, G. Martins Pereira, D. Schuch, J. Nascimento, L. Hoinaski, L.D. Martins, M. Gavidia-Calderón, A. Vara-Vela, T. Toledo de Almeida Albuquerque, R.Y. Ynoue, S. Diez, Z. Mera, A. Casallas Garcia, F. Vallejo, V. Diaz, R. Pedruzzi, R. Abrutzky, M.A. Franco, N. Huneeus, H. Jorquera, L.C. Belalcázar-Cerón, N.Y. Rojas, M. de Fatima Andrade, L. Emmons, G. Brasseur, Environmental Science &amp; Technology (2026). date_created: 2026-02-09T06:54:10Z date_published: 2026-02-04T00:00:00Z date_updated: 2026-02-16T10:33:07Z day: '04' ddc: - '550' department: - _id: CaMu doi: 10.1021/acs.est.5c08400 ec_funded: 1 external_id: pmid: - '41636708' has_accepted_license: '1' language: - iso: eng month: '02' oa_version: None pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Environmental Science & Technology publication_identifier: eissn: - 1520-5851 issn: - 0013-936X publication_status: epub_ahead publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: 'A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: repository OA_type: free access _id: '21174' abstract: - lang: eng text: UTe2 exhibits the remarkable phenomenon of re-entrant superconductivity, whereby the zero-resistance state reappears above 40 tesla after being suppressed with a field of around 10 tesla. One potential pairing mechanism, invoked in the related re-entrant superconductors UCoGe and URhGe, involves transverse fluctuations of a ferromagnetic order parameter. However, the requisite ferromagnetic order - present in both UCoGe and URhGe - is absent in UTe2, and magnetization measurements show no sign of strong fluctuations. Here, we measure the magnetotropic susceptibility of UTe2 across two field-angle planes. This quantity is sensitive to the magnetic susceptibility in a direction transverse to the applied magnetic field - a quantity that is not accessed in conventional magnetization measurements. We observe a very large decrease in the magnetotropic susceptibility over a broad range of field orientations, indicating a large increase in the transverse magnetic susceptibility. The three superconducting phases of UTe2, including the high-field re-entrant phase, surround this region of enhanced susceptibility in the field-angle phase diagram. The strongest transverse susceptibility is found near the critical end point of the high-field metamagnetic transition, suggesting that quantum critical fluctuations of a field-induced magnetic order parameter may be responsible for the large transverse susceptibility, and may provide a pairing mechanism for field-induced superconductivity in UTe2. acknowledged_ssus: - _id: NanoFab acknowledgement: Thanks to Salvatore Bagiante, Evgeniia Volobueva, Lubuna Shafeek, Ali Bangura and Zoltan Kollo. article_processing_charge: Yes author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 citation: ama: Modic KA. Research data for “Giant transverse magnetic fluctuations at the edge of re-entrant superconductivity in UTe2.” 2026. doi:10.15479/AT-ISTA-21174 apa: Modic, K. A. (2026). Research data for “Giant transverse magnetic fluctuations at the edge of re-entrant superconductivity in UTe2.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21174 chicago: Modic, Kimberly A. “Research Data for ‘Giant Transverse Magnetic Fluctuations at the Edge of Re-Entrant Superconductivity in UTe2.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21174. ieee: K. A. Modic, “Research data for ‘Giant transverse magnetic fluctuations at the edge of re-entrant superconductivity in UTe2.’” Institute of Science and Technology Austria, 2026. ista: Modic KA. 2026. Research data for ‘Giant transverse magnetic fluctuations at the edge of re-entrant superconductivity in UTe2’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21174. mla: Modic, Kimberly A. Research Data for “Giant Transverse Magnetic Fluctuations at the Edge of Re-Entrant Superconductivity in UTe2.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21174. short: K.A. Modic, (2026). contributor: - contributor_type: project_member first_name: Valeska id: 467ed36b-dc96-11ea-b7c8-b043a380b282 last_name: Zambra orcid: 0000-0002-8806-5719 corr_author: '1' date_created: 2026-02-09T12:04:20Z date_published: 2026-02-19T00:00:00Z date_updated: 2026-05-11T06:35:59Z day: '19' ddc: - '530' department: - _id: KiMo doi: 10.15479/AT-ISTA-21174 file: - access_level: open_access checksum: 53157d908fba663275c2b8dc6ee84fdb content_type: text/plain creator: kmodic date_created: 2026-02-19T07:38:15Z date_updated: 2026-02-19T07:38:15Z file_id: '21332' file_name: README.txt file_size: 1347 relation: main_file success: 1 - access_level: open_access checksum: b2c8ca5620ee9c181a42082068d3d73c content_type: application/zip creator: kmodic date_created: 2026-02-19T07:39:03Z date_updated: 2026-02-19T07:39:03Z file_id: '21333' file_name: processed_data_bc_plane_Fig2d.zip file_size: 534853 relation: main_file success: 1 - access_level: open_access checksum: 976bf113da4b1133313f0b292e71289f content_type: application/zip creator: kmodic date_created: 2026-02-19T07:39:07Z date_updated: 2026-02-19T07:39:07Z file_id: '21334' file_name: processed_data_ac_plane_Fig2c.zip file_size: 427144 relation: main_file success: 1 file_date_updated: 2026-02-19T07:39:07Z has_accepted_license: '1' keyword: - transverse magnetic susceptibility - magnetotropic - superconductivity - magnetic fluctuations month: '02' oa: 1 oa_version: Published Version project: - _id: bd968c70-d553-11ed-ba76-cde40b0aba64 grant_number: '101078696' name: Gaining leverage with spin liquids and superconductors publisher: Institute of Science and Technology Austria related_material: link: - relation: preprint url: https://arxiv.org/pdf/2506.08984 record: - id: '21845' relation: used_in_publication status: public status: public title: Research data for "Giant transverse magnetic fluctuations at the edge of re-entrant superconductivity in UTe2" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher _id: '21198' abstract: - lang: eng text: "In recent years there has been a massive increase in the amount of data generated in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones, have become\r\nubiquitous in most societies on earth. Through text typed, photos taken and apps used,\r\nthese devices, which we refer to as clients, generate enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of these devices means the data they generate is often\r\nsensitive and privacy concerns prevent it being gathered and stored in a central location. This\r\npresents a challenge to the modern machine learning paradigm that requires central access\r\nto large amounts of data. Federated learning (FL) has emerged as one of the answers to\r\nthis problem. Rather than bringing the data to the model, FL sends the model to the data.\r\nModel training takes place on device, with periodically synchronized updates, allowing data to\r\nremain locally stored. While this approach offers significant privacy advantages it comes with\r\nits own set of unique challenges. These include: data heterogeneity, the notion that different\r\ndevices generate data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity, meaning that different devices may have differing hardware specifications; high\r\ncommunication costs, which are induced by the repeated transferring of models over the\r\nnetwork and low device computational power, which limits the use of larger models on device.\r\nIn this thesis we present a range of methods for federated learning. We focus primarily on\r\nthe challenge of data heterogeneity, though the methods presented are designed to be well\r\nadapted to the other challenges of a federated setting, such as the constraints of limited\r\ncompute and communication overhead. We first present a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates clients as samples from a certain probability\r\ndistribution and infers the parameters of this distribution from the available training clients.\r\nThis learned distribution then represents the heterogeneity present among the clients and can\r\nbe sampled from in order to create new simulated clients that are similar to the real clients we\r\nhave observed so far. Following this we present two methods for directly dealing with data\r\nheterogeneity through personalization. Highly heterogeneous client data distributions can mean\r\nthat learning a single global model becomes suboptimal, and some form of personalization of\r\nmodels to each individual client is required. Our approaches are based around hypernetworks,\r\nwhich we use to generate personalized model parameters without the need for additional\r\ntraining or finetuning. In the first approach we focus on generating full parameterizations of\r\nclient models using learned embeddings of client data and labels, with a hypernetwork located\r\non the central server. In the second approach we address the more challenging scenario where\r\nwe want to generate a personalized model for a client without any label information. The\r\nhypernetwork is trained to generate a low dimensional representation of a client’s personalized\r\nmodel parameters, allowing it to be transferred to and run on the client devices. In our final\r\npresented method, we change our focus and rather than aim to directly address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected by it. This is done in the context\r\nof k-means clustering and we present a method for federated clustering with a focus on added\r\nprivacy guarantees." acknowledged_ssus: - _id: ScienComp acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12]. Furthermore, the candidate acknowledges the support from the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott citation: ama: Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:10.15479/AT-ISTA-21198 apa: Scott, J. A. (2026). Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21198 chicago: Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated Learning.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21198. ieee: J. A. Scott, “Data heterogeneity and personalization in federated learning,” Institute of Science and Technology Austria, 2026. ista: Scott JA. 2026. Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. mla: Scott, Jonathan A. Data Heterogeneity and Personalization in Federated Learning. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21198. short: J.A. Scott, Data Heterogeneity and Personalization in Federated Learning, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-02-09T14:59:53Z date_published: 2026-02-09T00:00:00Z date_updated: 2026-04-07T11:46:11Z day: '09' ddc: - '005' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/AT-ISTA-21198 file: - access_level: closed checksum: 121c1d968bd86f3630aa7e81d5bbbcb0 content_type: application/zip creator: jscott date_created: 2026-02-17T11:46:22Z date_updated: 2026-02-17T11:46:22Z file_id: '21298' file_name: 2026_Scott_Jonathan_Thesis_Source.zip file_size: 272379252 relation: source_file - access_level: open_access checksum: 6e3e08ba474bbee8511cc8a839ab2077 content_type: application/pdf creator: jscott date_created: 2026-02-27T10:25:41Z date_updated: 2026-02-27T10:25:41Z file_id: '21366' file_name: 2026_Jonathan_Scott_Thesis.pdf file_size: 15220298 relation: main_file success: 1 file_date_updated: 2026-02-27T10:25:41Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '158' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20819' relation: part_of_dissertation status: public - id: '17411' relation: part_of_dissertation status: public - id: '18120' relation: part_of_dissertation status: public - id: '21207' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Data heterogeneity and personalization in federated learning type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: repository OA_type: green _id: '21212' abstract: - lang: eng text: "Malignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma.\r\n\r\n“In-tissue” phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process." acknowledgement: "We thank Dr. Wenjie Liu for providing critical feedback on the manuscript. We also thank Dr.\r\nPat Pramoonjago at the Biorepository and Tissue Research Facility, and Hope Davis at the\r\nvivarium for their assistance on the project. These Core Facilities are supported by UVA Cancer\r\nCenter grant #P30-CA044579. We are grateful to Dr. Jonathan A. Epstein for providing the\r\nNf1GRD/+ mouse strain (https://pubmed.ncbi.nlm.nih.gov/26460546/). This work was partly\r\nsupported by the National Institute of Neurological Diseases and Stroke R21 NS125479-01A1\r\n(H.Z.), American Cancer Society Institutional Research Grant to the University of Virginia\r\n(Y.J.), the National Natural Science Foundation of China #82072787 (M.Y.), the National\r\nCancer Institute U54 CA238114 (F.W.), U01 CA284193 (K.M.N.), and U54 CA274499 (K.A.J.,\r\nM.F-S.), the National institute of General Medical Sciences R35 GM133404 (M.F-S.), the Dr.\r\nMiriam and Sheldon G. Adelson Medical Research Foundation (H.I.K., S.A.G.), the National\r\nCenter for Advancing Translational Sciences KL2TR001882 (K.S.P.), Tower Cancer Career Development Grant (K.S.P.), McKnight Neurobiology of Brain Disorders Grant (K.S.P.). The\r\ncontent is solely the responsibility of the authors and does not necessarily represent the official\r\nviews of the National Institutes of Health. Illustrations in this manuscript were created with\r\nBioRender (BioRender.com)." article_processing_charge: No author: - first_name: Ying full_name: Jiang, Ying last_name: Jiang - first_name: Ryuhjin full_name: Ahn, Ryuhjin last_name: Ahn - first_name: Arthur full_name: Huang, Arthur last_name: Huang - first_name: Phillippe P. full_name: Gonzalez, Phillippe P. last_name: Gonzalez - first_name: Jungeun full_name: Kim, Jungeun last_name: Kim - first_name: Guoxin full_name: Zhang, Guoxin last_name: Zhang - first_name: Zihao full_name: Liu, Zihao last_name: Liu - first_name: Zhenqiang full_name: He, Zhenqiang last_name: He - first_name: Lindsey full_name: Dudley, Lindsey last_name: Dudley - first_name: Kunal S. full_name: Patel, Kunal S. last_name: Patel - first_name: Godfrey A. full_name: Dzhivhuho, Godfrey A. last_name: Dzhivhuho - first_name: Sam full_name: Crowl, Sam last_name: Crowl - first_name: Piotr full_name: Przanowski, Piotr last_name: Przanowski - first_name: Luisa Quesada full_name: Camacho, Luisa Quesada last_name: Camacho - first_name: Sijie full_name: Hao, Sijie last_name: Hao - first_name: Jianhao full_name: Zeng, Jianhao last_name: Zeng - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Mohammad full_name: Fallahi-Sichani, Mohammad last_name: Fallahi-Sichani - first_name: Kevin A. full_name: Janes, Kevin A. last_name: Janes - first_name: Kristen M. full_name: Naegle, Kristen M. last_name: Naegle - first_name: Marie-Louise full_name: Hammarskjold, Marie-Louise last_name: Hammarskjold - first_name: Steven A. full_name: Goldman, Steven A. last_name: Goldman - first_name: Harley I. full_name: Kornblum, Harley I. last_name: Kornblum - first_name: Maojin full_name: Yao, Maojin last_name: Yao - first_name: Forest full_name: White, Forest last_name: White - first_name: Hui full_name: Zong, Hui last_name: Zong citation: ama: Jiang Y, Ahn R, Huang A, et al. Critical role of cell competition in gliomagenesis. bioRxiv. 2026. doi:10.64898/2026.01.15.699808 apa: Jiang, Y., Ahn, R., Huang, A., Gonzalez, P. P., Kim, J., Zhang, G., … Zong, H. (2026). Critical role of cell competition in gliomagenesis. bioRxiv. https://doi.org/10.64898/2026.01.15.699808 chicago: Jiang, Ying, Ryuhjin Ahn, Arthur Huang, Phillippe P. Gonzalez, Jungeun Kim, Guoxin Zhang, Zihao Liu, et al. “Critical Role of Cell Competition in Gliomagenesis.” BioRxiv, 2026. https://doi.org/10.64898/2026.01.15.699808. ieee: Y. Jiang et al., “Critical role of cell competition in gliomagenesis,” bioRxiv. 2026. ista: Jiang Y, Ahn R, Huang A, Gonzalez PP, Kim J, Zhang G, Liu Z, He Z, Dudley L, Patel KS, Dzhivhuho GA, Crowl S, Przanowski P, Camacho LQ, Hao S, Zeng J, Hippenmeyer S, Fallahi-Sichani M, Janes KA, Naegle KM, Hammarskjold M-L, Goldman SA, Kornblum HI, Yao M, White F, Zong H. 2026. Critical role of cell competition in gliomagenesis. bioRxiv, 10.64898/2026.01.15.699808. mla: Jiang, Ying, et al. “Critical Role of Cell Competition in Gliomagenesis.” BioRxiv, 2026, doi:10.64898/2026.01.15.699808. short: Y. Jiang, R. Ahn, A. Huang, P.P. Gonzalez, J. Kim, G. Zhang, Z. Liu, Z. He, L. Dudley, K.S. Patel, G.A. Dzhivhuho, S. Crowl, P. Przanowski, L.Q. Camacho, S. Hao, J. Zeng, S. Hippenmeyer, M. Fallahi-Sichani, K.A. Janes, K.M. Naegle, M.-L. Hammarskjold, S.A. Goldman, H.I. Kornblum, M. Yao, F. White, H. Zong, BioRxiv (2026). date_created: 2026-02-10T12:55:55Z date_published: 2026-01-16T00:00:00Z date_updated: 2026-02-16T10:12:42Z day: '16' ddc: - '570' department: - _id: SiHi doi: 10.64898/2026.01.15.699808 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.64898/2026.01.15.699808 month: '01' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: published status: public title: Critical role of cell competition in gliomagenesis tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ...