[{"abstract":[{"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.","lang":"eng"}],"date_updated":"2026-02-16T08:50:50Z","main_file_link":[{"url":"https://doi.org/10.1101/2024.09.07.611785","open_access":"1"}],"date_created":"2026-02-01T23:01:44Z","author":[{"full_name":"Troidl, Jakob","first_name":"Jakob","last_name":"Troidl"},{"full_name":"Liang, Yiqing","last_name":"Liang","first_name":"Yiqing"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","first_name":"Mojtaba"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"last_name":"Hadwiger","first_name":"Markus","full_name":"Hadwiger, Markus"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"},{"full_name":"Tompkin, James","first_name":"James","last_name":"Tompkin"}],"title":"niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction","OA_type":"green","date_published":"2026-01-03T00:00:00Z","publication":"1st International Workshop on Efficient Medical Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","citation":{"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.","mla":"Troidl, Jakob, et al. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” <i>1st International Workshop on Efficient Medical Artificial Intelligence</i>, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:<a href=\"https://doi.org/10.1007/978-3-032-13961-0_26\">10.1007/978-3-032-13961-0_26</a>.","ieee":"J. Troidl <i>et al.</i>, “niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction,” in <i>1st International Workshop on Efficient Medical Artificial Intelligence</i>, 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.","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 <i>1st International Workshop on Efficient Medical Artificial Intelligence</i>, 16318:257–67. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/978-3-032-13961-0_26\">https://doi.org/10.1007/978-3-032-13961-0_26</a>.","ama":"Troidl J, Liang Y, Beyer J, et al. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In: <i>1st International Workshop on Efficient Medical Artificial Intelligence</i>. Vol 16318. Springer Nature; 2026:257-267. doi:<a href=\"https://doi.org/10.1007/978-3-032-13961-0_26\">10.1007/978-3-032-13961-0_26</a>","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 <i>1st International Workshop on Efficient Medical Artificial Intelligence</i> (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-032-13961-0_26\">https://doi.org/10.1007/978-3-032-13961-0_26</a>"},"quality_controlled":"1","_id":"21135","article_processing_charge":"No","oa_version":"Preprint","day":"03","intvolume":"     16318","alternative_title":["LNCS"],"department":[{"_id":"JoDa"}],"scopus_import":"1","month":"01","doi":"10.1007/978-3-032-13961-0_26","conference":{"name":"EMA4MICCAI: Efficient Medical Artificial Intelligence","location":"Daejeon, South Korea","end_date":"2025-09-23","start_date":"2025-09-23"},"related_material":{"link":[{"url":"https://github.com/jakobtroidl/niiv-miccai","relation":"software"}]},"page":"257-267","language":[{"iso":"eng"}],"year":"2026","oa":1,"status":"public","publication_identifier":{"isbn":["9783032139603"],"issn":["0302-9743"],"eissn":["1611-3349"]},"volume":16318,"OA_place":"repository","type":"conference","acknowledgement":"This work was supported by NIH grants 1U01NS132158 and R01HD104969. We thank the reviewers for their constructive feedback."},{"abstract":[{"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.","lang":"eng"}],"date_updated":"2026-02-16T09:18:33Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2409.20314"}],"external_id":{"arxiv":["2409.20314"]},"date_created":"2026-02-05T10:51:34Z","author":[{"last_name":"Arkhipov","first_name":"Pavel","full_name":"Arkhipov, Pavel","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"}],"title":"Faster algorithms for packing forests in graphs and related problems","corr_author":"1","OA_type":"green","date_published":"2026-01-07T00:00:00Z","publication":"Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","citation":{"chicago":"Arkhipov, Pavel, and Vladimir Kolmogorov. “Faster Algorithms for Packing Forests in Graphs and Related Problems.” In <i>Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 4023–42. Society for Industrial and Applied Mathematics, 2026. <a href=\"https://doi.org/10.1137/1.9781611978971.148\">https://doi.org/10.1137/1.9781611978971.148</a>.","ama":"Arkhipov P, Kolmogorov V. Faster algorithms for packing forests in graphs and related problems. In: <i>Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2026:4023-4042. doi:<a href=\"https://doi.org/10.1137/1.9781611978971.148\">10.1137/1.9781611978971.148</a>","apa":"Arkhipov, P., &#38; Kolmogorov, V. (2026). Faster algorithms for packing forests in graphs and related problems. In <i>Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 4023–4042). Vancouver, Canada: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611978971.148\">https://doi.org/10.1137/1.9781611978971.148</a>","ieee":"P. Arkhipov and V. Kolmogorov, “Faster algorithms for packing forests in graphs and related problems,” in <i>Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Vancouver, Canada, 2026, pp. 4023–4042.","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.","mla":"Arkhipov, Pavel, and Vladimir Kolmogorov. “Faster Algorithms for Packing Forests in Graphs and Related Problems.” <i>Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2026, pp. 4023–42, doi:<a href=\"https://doi.org/10.1137/1.9781611978971.148\">10.1137/1.9781611978971.148</a>.","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."},"_id":"21140","oa_version":"Preprint","article_processing_charge":"No","day":"07","department":[{"_id":"VlKo"}],"arxiv":1,"month":"01","doi":"10.1137/1.9781611978971.148","conference":{"start_date":"2026-01-11","name":"SODA: Symposium on Discrete Algorithms","location":"Vancouver, Canada","end_date":"2026-01-14"},"page":"4023-4042","language":[{"iso":"eng"}],"year":"2026","oa":1,"status":"public","publication_identifier":{"eisbn":["9781611978971"]},"OA_place":"repository","type":"conference"},{"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/F1004].","type":"journal_article","OA_place":"publisher","volume":136,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"status":"public","oa":1,"year":"2026","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"creator":"dernst","access_level":"open_access","file_id":"21210","content_type":"application/pdf","checksum":"805c929fff9fd4d0e733293eaace67b8","file_size":511312,"date_updated":"2026-02-10T11:25:46Z","file_name":"2026_PhysicalReviewLetters_Hrast.pdf","relation":"main_file","date_created":"2026-02-10T11:25:46Z"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","PlanS_conform":"1","doi":"10.1103/fkf1-1jml","issue":"5","month":"02","arxiv":1,"scopus_import":"1","article_type":"original","department":[{"_id":"MiLe"}],"intvolume":"       136","day":"05","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","_id":"21149","quality_controlled":"1","citation":{"apa":"Hrast, M., Koutentakis, G., Maslov, M., &#38; Lemeshko, M. (2026). Bottom-up analysis of rovibrational helical dichroism. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/fkf1-1jml\">https://doi.org/10.1103/fkf1-1jml</a>","ama":"Hrast M, Koutentakis G, Maslov M, Lemeshko M. Bottom-up analysis of rovibrational helical dichroism. <i>Physical Review Letters</i>. 2026;136(5). doi:<a href=\"https://doi.org/10.1103/fkf1-1jml\">10.1103/fkf1-1jml</a>","chicago":"Hrast, Mateja, Georgios Koutentakis, Mikhail Maslov, and Mikhail Lemeshko. “Bottom-up Analysis of Rovibrational Helical Dichroism.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/fkf1-1jml\">https://doi.org/10.1103/fkf1-1jml</a>.","ista":"Hrast M, Koutentakis G, Maslov M, Lemeshko M. 2026. Bottom-up analysis of rovibrational helical dichroism. Physical Review Letters. 136(5), 053204.","ieee":"M. Hrast, G. Koutentakis, M. Maslov, and M. Lemeshko, “Bottom-up analysis of rovibrational helical dichroism,” <i>Physical Review Letters</i>, vol. 136, no. 5. American Physical Society, 2026.","mla":"Hrast, Mateja, et al. “Bottom-up Analysis of Rovibrational Helical Dichroism.” <i>Physical Review Letters</i>, vol. 136, no. 5, 053204, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/fkf1-1jml\">10.1103/fkf1-1jml</a>.","short":"M. Hrast, G. Koutentakis, M. Maslov, M. Lemeshko, Physical Review Letters 136 (2026)."},"ddc":["530"],"publisher":"American Physical Society","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-02-10T11:25:46Z","publication":"Physical Review Letters","date_published":"2026-02-05T00:00:00Z","OA_type":"hybrid","corr_author":"1","article_number":"053204","project":[{"_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3","grant_number":"F100403","name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions"}],"title":"Bottom-up analysis of rovibrational helical dichroism","author":[{"first_name":"Mateja","last_name":"Hrast","full_name":"Hrast, Mateja","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d"},{"last_name":"Koutentakis","first_name":"Georgios","full_name":"Koutentakis, Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95"},{"orcid":"0000-0003-4074-2570","last_name":"Maslov","first_name":"Mikhail","full_name":"Maslov, Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"date_created":"2026-02-06T10:53:17Z","external_id":{"arxiv":["2505.16393"]},"date_updated":"2026-02-10T11:30:37Z","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."}]},{"OA_place":"publisher","volume":17,"status":"public","publication_identifier":{"eissn":["2041-1723"]},"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.","type":"journal_article","month":"01","DOAJ_listed":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","date_created":"2026-02-12T14:33:14Z","date_updated":"2026-02-12T14:33:14Z","file_name":"2026_NatureComm_Yang.pdf","content_type":"application/pdf","checksum":"9ae170ec70ba1ab56b6f1ffe67d1de7f","file_size":4685882,"file_id":"21223","creator":"dernst","success":1,"access_level":"open_access"}],"language":[{"iso":"eng"}],"oa":1,"year":"2026","has_accepted_license":"1","PlanS_conform":"1","doi":"10.1038/s41467-025-67734-0","ddc":["580"],"citation":{"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.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-025-67734-0\">https://doi.org/10.1038/s41467-025-67734-0</a>.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-67734-0\">https://doi.org/10.1038/s41467-025-67734-0</a>","ama":"Yang P, Liu Y, Dong Q, et al. O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-025-67734-0\">10.1038/s41467-025-67734-0</a>","ieee":"P. Yang <i>et al.</i>, “O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","mla":"Yang, Pengfang, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10 Regulate Wheat Vernalization for Flowering.” <i>Nature Communications</i>, vol. 17, 999, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-025-67734-0\">10.1038/s41467-025-67734-0</a>.","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).","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."},"quality_controlled":"1","publisher":"Springer Nature","department":[{"_id":"XiFe"}],"intvolume":"        17","scopus_import":"1","article_type":"original","article_processing_charge":"Yes","oa_version":"Published Version","_id":"21158","day":"27","author":[{"first_name":"Pengfang","last_name":"Yang","full_name":"Yang, Pengfang"},{"last_name":"Liu","first_name":"Yangyang","full_name":"Liu, Yangyang"},{"full_name":"Dong, Qi","last_name":"Dong","first_name":"Qi"},{"last_name":"Miao","first_name":"Yuting","full_name":"Miao, Yuting"},{"full_name":"Zhang, Jianlong","first_name":"Jianlong","last_name":"Zhang"},{"first_name":"Shujuan","last_name":"Xu","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","full_name":"Xu, Shujuan"},{"full_name":"Zhao, Hong","first_name":"Hong","last_name":"Zhao"},{"full_name":"Niu, Yuda","last_name":"Niu","first_name":"Yuda"},{"full_name":"Zhang, Xueyong","first_name":"Xueyong","last_name":"Zhang"},{"full_name":"Xu, Yunyuan","first_name":"Yunyuan","last_name":"Xu"},{"full_name":"Guo, Zifeng","first_name":"Zifeng","last_name":"Guo"},{"last_name":"Xing","first_name":"Lijing","full_name":"Xing, Lijing"},{"first_name":"Kang","last_name":"Chong","full_name":"Chong, Kang"}],"title":"O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering","external_id":{"pmid":["41455723"]},"date_created":"2026-02-08T23:02:48Z","abstract":[{"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.","lang":"eng"}],"date_updated":"2026-02-12T14:34:24Z","file_date_updated":"2026-02-12T14:33:14Z","publication":"Nature Communications","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"999","date_published":"2026-01-27T00:00:00Z","OA_type":"gold"},{"publisher":"Springer Nature","quality_controlled":"1","citation":{"mla":"Kwan, Matthew Alan, et al. “Counting Perfect Matchings in Dirac Hypergraphs.” <i>Combinatorica</i>, vol. 46, 5, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s00493-025-00194-8\">10.1007/s00493-025-00194-8</a>.","short":"M.A. Kwan, R. Safavi Hemami, Y. Wang, Combinatorica 46 (2026).","ieee":"M. A. Kwan, R. Safavi Hemami, and Y. Wang, “Counting perfect matchings in Dirac hypergraphs,” <i>Combinatorica</i>, vol. 46. Springer Nature, 2026.","ista":"Kwan MA, Safavi Hemami R, Wang Y. 2026. Counting perfect matchings in Dirac hypergraphs. Combinatorica. 46, 5.","chicago":"Kwan, Matthew Alan, Roodabeh Safavi Hemami, and Yiting Wang. “Counting Perfect Matchings in Dirac Hypergraphs.” <i>Combinatorica</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00493-025-00194-8\">https://doi.org/10.1007/s00493-025-00194-8</a>.","apa":"Kwan, M. A., Safavi Hemami, R., &#38; Wang, Y. (2026). Counting perfect matchings in Dirac hypergraphs. <i>Combinatorica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00493-025-00194-8\">https://doi.org/10.1007/s00493-025-00194-8</a>","ama":"Kwan MA, Safavi Hemami R, Wang Y. Counting perfect matchings in Dirac hypergraphs. <i>Combinatorica</i>. 2026;46. doi:<a href=\"https://doi.org/10.1007/s00493-025-00194-8\">10.1007/s00493-025-00194-8</a>"},"ddc":["510"],"day":"01","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","_id":"21159","article_type":"original","scopus_import":"1","department":[{"_id":"MaKw"},{"_id":"MoHe"}],"intvolume":"        46","date_updated":"2026-02-16T09:55:17Z","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."}],"author":[{"orcid":"0000-0002-4003-7567","last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"first_name":"Roodabeh","last_name":"Safavi Hemami","full_name":"Safavi Hemami, Roodabeh","id":"72ed2640-8972-11ed-ae7b-f9c81ec75154"},{"last_name":"Wang","first_name":"Yiting","orcid":"0000-0002-2856-767X","id":"1917d194-076e-11ed-97cd-837255f88785","full_name":"Wang, Yiting"}],"title":"Counting perfect matchings in Dirac hypergraphs","external_id":{"arxiv":["2408.09589"]},"date_created":"2026-02-08T23:02:49Z","date_published":"2026-02-01T00:00:00Z","OA_type":"hybrid","corr_author":"1","article_number":"5","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-02-16T09:52:38Z","publication":"Combinatorica","publication_identifier":{"issn":["0209-9683"],"eissn":["1439-6912"]},"status":"public","OA_place":"publisher","volume":46,"type":"journal_article","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).","arxiv":1,"month":"02","has_accepted_license":"1","PlanS_conform":"1","doi":"10.1007/s00493-025-00194-8","oa":1,"year":"2026","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2026-02-16T09:52:38Z","relation":"main_file","file_name":"2026_Combinatorica_Kwan.pdf","date_updated":"2026-02-16T09:52:38Z","checksum":"47b0031d90b0e6b9a843f422a1486089","file_size":539646,"content_type":"application/pdf","file_id":"21228","access_level":"open_access","creator":"dernst","success":1}],"language":[{"iso":"eng"}]},{"date_created":"2026-02-08T23:02:49Z","external_id":{"arxiv":["2512.04147"]},"author":[{"full_name":"Yu, W.","first_name":"W.","last_name":"Yu"},{"full_name":"Pala, A. F.","last_name":"Pala","first_name":"A. F."},{"full_name":"Kupfer, T.","first_name":"T.","last_name":"Kupfer"},{"full_name":"Gänsicke, B. T.","last_name":"Gänsicke","first_name":"B. T."},{"last_name":"Koester","first_name":"D.","full_name":"Koester, D."},{"last_name":"Belloni","first_name":"D.","full_name":"Belloni, D."},{"first_name":"T. L.S.","last_name":"Wong","full_name":"Wong, T. L.S."},{"full_name":"Schreiber, M. R.","first_name":"M. R.","last_name":"Schreiber"},{"first_name":"Joannes C","last_name":"van Roestel","id":"4d122fc8-6083-11f0-87a5-97d68b860333","full_name":"van Roestel, Joannes C"},{"full_name":"Brown, A. J.","last_name":"Brown","first_name":"A. J."},{"full_name":"Waagen, E. O.","first_name":"E. O.","last_name":"Waagen"},{"first_name":"J. L.","last_name":"González-Carballo","full_name":"González-Carballo, J. L."},{"full_name":"Bednarz, S.","last_name":"Bednarz","first_name":"S."},{"first_name":"K.","last_name":"Bernacki","full_name":"Bernacki, K."},{"full_name":"De Martino, D.","first_name":"D.","last_name":"De Martino"},{"full_name":"Fernández Mañanes, E.","last_name":"Fernández Mañanes","first_name":"E."},{"first_name":"R.","last_name":"González Farfán","full_name":"González Farfán, R."},{"full_name":"Green, M. J.","last_name":"Green","first_name":"M. J."},{"full_name":"Groot, P. J.","last_name":"Groot","first_name":"P. J."},{"full_name":"Hambsch, F. J.","last_name":"Hambsch","first_name":"F. J."},{"full_name":"Knigge, C.","last_name":"Knigge","first_name":"C."},{"full_name":"Martin-Velasco, J. L.","last_name":"Martin-Velasco","first_name":"J. L."},{"first_name":"M.","last_name":"Morales-Aimar","full_name":"Morales-Aimar, M."},{"full_name":"Myers, G.","last_name":"Myers","first_name":"G."},{"last_name":"Naves Nogues","first_name":"R.","full_name":"Naves Nogues, R."},{"first_name":"R.","last_name":"Poggiani","full_name":"Poggiani, R."},{"full_name":"Popowicz, A.","last_name":"Popowicz","first_name":"A."},{"full_name":"Ramsay, G.","first_name":"G.","last_name":"Ramsay"},{"first_name":"E.","last_name":"Reina-Lorenz","full_name":"Reina-Lorenz, E."},{"full_name":"Rodríguez-Gil, P.","first_name":"P.","last_name":"Rodríguez-Gil"},{"full_name":"Salto-González, J. L.","last_name":"Salto-González","first_name":"J. L."},{"first_name":"E. M.","last_name":"Sion","full_name":"Sion, E. M."},{"full_name":"Steeghs, D.","last_name":"Steeghs","first_name":"D."},{"last_name":"Szkody","first_name":"P.","full_name":"Szkody, P."},{"full_name":"Toloza, O.","last_name":"Toloza","first_name":"O."},{"first_name":"G.","last_name":"Tovmassian","full_name":"Tovmassian, G."}],"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","date_updated":"2026-02-16T09:36:24Z","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file_date_updated":"2026-02-16T09:33:56Z","publication":"Astronomy and Astrophysics","OA_type":"diamond","date_published":"2026-02-01T00:00:00Z","article_number":"A14","quality_controlled":"1","citation":{"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.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202557568\">https://doi.org/10.1051/0004-6361/202557568</a>.","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. <i>Astronomy and Astrophysics</i>. 2026;706. doi:<a href=\"https://doi.org/10.1051/0004-6361/202557568\">10.1051/0004-6361/202557568</a>","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. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202557568\">https://doi.org/10.1051/0004-6361/202557568</a>","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.” <i>Astronomy and Astrophysics</i>, vol. 706, A14, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202557568\">10.1051/0004-6361/202557568</a>.","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).","ieee":"W. Yu <i>et al.</i>, “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,” <i>Astronomy and Astrophysics</i>, 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."},"ddc":["520"],"publisher":"EDP Sciences","scopus_import":"1","article_type":"original","intvolume":"       706","department":[{"_id":"IlCa"}],"day":"01","_id":"21160","article_processing_charge":"No","oa_version":"Published Version","month":"02","arxiv":1,"year":"2026","oa":1,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","date_created":"2026-02-16T09:33:56Z","date_updated":"2026-02-16T09:33:56Z","file_name":"2026_AstronomyAstrophysics_Yu.pdf","checksum":"2faec710fd04f927aa43deb57e35c9b2","content_type":"application/pdf","file_size":4020466,"file_id":"21227","creator":"dernst","success":1,"access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1051/0004-6361/202557568","has_accepted_license":"1","PlanS_conform":"1","volume":706,"OA_place":"publisher","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"status":"public","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).","type":"journal_article"},{"publisher":"Royal Society of London","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"ddc":["570"],"quality_controlled":"1","citation":{"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.","ieee":"C. de Castro Barbosa Rodrigues Barata and B. Vicoso, “Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster,” <i>Proceedings of the Royal Society B Biological Sciences</i>, vol. 293, no. 2063. Royal Society of London, 2026.","short":"C. de Castro Barbosa Rodrigues Barata, B. Vicoso, Proceedings of the Royal Society B Biological Sciences 293 (2026).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” <i>Proceedings of the Royal Society B Biological Sciences</i>, vol. 293, no. 2063, 20252471, Royal Society of London, 2026, doi:<a href=\"https://doi.org/10.1098/rspb.2025.2471\">10.1098/rspb.2025.2471</a>.","apa":"de Castro Barbosa Rodrigues Barata, C., &#38; Vicoso, B. (2026). Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. <i>Proceedings of the Royal Society B Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rspb.2025.2471\">https://doi.org/10.1098/rspb.2025.2471</a>","ama":"de Castro Barbosa Rodrigues Barata C, Vicoso B. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. <i>Proceedings of the Royal Society B Biological Sciences</i>. 2026;293(2063). doi:<a href=\"https://doi.org/10.1098/rspb.2025.2471\">10.1098/rspb.2025.2471</a>","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” <i>Proceedings of the Royal Society B Biological Sciences</i>. Royal Society of London, 2026. <a href=\"https://doi.org/10.1098/rspb.2025.2471\">https://doi.org/10.1098/rspb.2025.2471</a>."},"_id":"21161","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","day":"28","intvolume":"       293","department":[{"_id":"BeVi"}],"scopus_import":"1","article_type":"original","abstract":[{"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.","lang":"eng"}],"date_updated":"2026-02-16T09:27:33Z","date_created":"2026-02-08T23:02:49Z","external_id":{"pmid":["41592777"]},"author":[{"orcid":"0000-0003-1945-2245","first_name":"Carolina","last_name":"De Castro Barbosa Rodrigues Barata","full_name":"De Castro Barbosa Rodrigues Barata, Carolina","id":"20565186-803f-11ed-ab7e-96a4ff7694ef"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"title":"Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster","project":[{"grant_number":"ESP 6331524","name":"Does genetic drift set a limit on the adaptive evolution of sex-biased expression?","_id":"90ef7108-16d5-11f0-9cad-e6e116913473"}],"article_number":"20252471","corr_author":"1","OA_type":"hybrid","date_published":"2026-01-28T00:00:00Z","file_date_updated":"2026-02-16T09:26:02Z","publication":"Proceedings of the Royal Society B Biological Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","pmid":1,"status":"public","publication_identifier":{"eissn":["1471-2954"]},"volume":293,"OA_place":"publisher","type":"journal_article","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.","month":"01","doi":"10.1098/rspb.2025.2471","issue":"2063","PlanS_conform":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","success":1,"creator":"dernst","file_id":"21226","checksum":"d76afebca0a6f112df0146ae2d929f36","content_type":"application/pdf","file_size":2230841,"date_updated":"2026-02-16T09:26:02Z","file_name":"2026_RoyalSocPubProceedingsB_Barata.pdf","date_created":"2026-02-16T09:26:02Z","relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2026","oa":1},{"month":"02","has_accepted_license":"1","doi":"10.1021/acs.est.5c08400","year":"2026","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5851"],"issn":["0013-936X"]},"ec_funded":1,"status":"public","type":"journal_article","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).","date_updated":"2026-02-16T10:33:07Z","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."}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"author":[{"last_name":"Ibarra-Espinosa","first_name":"Sergio","full_name":"Ibarra-Espinosa, Sergio"},{"first_name":"Edmilson","last_name":"Dias de Freitas","full_name":"Dias de Freitas, Edmilson"},{"full_name":"Gaubert, Benjamin","last_name":"Gaubert","first_name":"Benjamin"},{"first_name":"Pablo","last_name":"Lichtig","full_name":"Lichtig, Pablo"},{"first_name":"Karl","last_name":"Ropkins","full_name":"Ropkins, Karl"},{"full_name":"da Silva, Iara","last_name":"da Silva","first_name":"Iara"},{"full_name":"Martins Pereira, Guilherme","last_name":"Martins Pereira","first_name":"Guilherme"},{"full_name":"Schuch, Daniel","first_name":"Daniel","last_name":"Schuch"},{"first_name":"Janaina","last_name":"Nascimento","full_name":"Nascimento, Janaina"},{"first_name":"Leonardo","last_name":"Hoinaski","full_name":"Hoinaski, Leonardo"},{"full_name":"Martins, Leila Droprinchinski","first_name":"Leila Droprinchinski","last_name":"Martins"},{"full_name":"Gavidia-Calderón, Mario","first_name":"Mario","last_name":"Gavidia-Calderón"},{"full_name":"Vara-Vela, Angel","last_name":"Vara-Vela","first_name":"Angel"},{"full_name":"Toledo de Almeida Albuquerque, Taciana","first_name":"Taciana","last_name":"Toledo de Almeida Albuquerque"},{"full_name":"Ynoue, Rita Yuri","first_name":"Rita Yuri","last_name":"Ynoue"},{"full_name":"Diez, Sebastian","last_name":"Diez","first_name":"Sebastian"},{"first_name":"Zamir","last_name":"Mera","full_name":"Mera, Zamir"},{"first_name":"Alejandro","last_name":"Casallas Garcia","orcid":"0000-0002-1988-5035","full_name":"Casallas Garcia, Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a"},{"last_name":"Vallejo","first_name":"Fidel","full_name":"Vallejo, Fidel"},{"first_name":"Valeria","last_name":"Diaz","full_name":"Diaz, Valeria"},{"last_name":"Pedruzzi","first_name":"Rizzieri","full_name":"Pedruzzi, Rizzieri"},{"full_name":"Abrutzky, Rosana","first_name":"Rosana","last_name":"Abrutzky"},{"first_name":"Marco A.","last_name":"Franco","full_name":"Franco, Marco A."},{"last_name":"Huneeus","first_name":"Nicolas","full_name":"Huneeus, Nicolas"},{"full_name":"Jorquera, Hector","first_name":"Hector","last_name":"Jorquera"},{"last_name":"Belalcázar-Cerón","first_name":"Luis Carlos","full_name":"Belalcázar-Cerón, Luis Carlos"},{"full_name":"Rojas, Néstor Y.","first_name":"Néstor Y.","last_name":"Rojas"},{"last_name":"de Fatima Andrade","first_name":"Maria","full_name":"de Fatima Andrade, Maria"},{"last_name":"Emmons","first_name":"Louisa","full_name":"Emmons, Louisa"},{"first_name":"Guy","last_name":"Brasseur","full_name":"Brasseur, Guy"}],"title":"A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality","date_created":"2026-02-09T06:54:10Z","external_id":{"pmid":["41636708"]},"date_published":"2026-02-04T00:00:00Z","article_number":"5c08400","publication_status":"epub_ahead","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Environmental Science &amp; Technology","publisher":"American Chemical Society","quality_controlled":"1","citation":{"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. <i>Environmental Science &#38;amp; Technology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.est.5c08400\">https://doi.org/10.1021/acs.est.5c08400</a>","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. <i>Environmental Science &#38;amp; Technology</i>. 2026. doi:<a href=\"https://doi.org/10.1021/acs.est.5c08400\">10.1021/acs.est.5c08400</a>","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.” <i>Environmental Science &#38;amp; Technology</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.est.5c08400\">https://doi.org/10.1021/acs.est.5c08400</a>.","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 &#38;amp; Technology., 5c08400.","ieee":"S. Ibarra-Espinosa <i>et al.</i>, “A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality,” <i>Environmental Science &#38;amp; Technology</i>. American Chemical Society, 2026.","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 &#38;amp; Technology (2026).","mla":"Ibarra-Espinosa, Sergio, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” <i>Environmental Science &#38;amp; Technology</i>, 5c08400, American Chemical Society, 2026, doi:<a href=\"https://doi.org/10.1021/acs.est.5c08400\">10.1021/acs.est.5c08400</a>."},"ddc":["550"],"day":"04","oa_version":"None","article_processing_charge":"No","_id":"21164","article_type":"original","scopus_import":"1","department":[{"_id":"CaMu"}]},{"ddc":["570"],"OA_place":"repository","citation":{"ama":"Jiang Y, Ahn R, Huang A, et al. Critical role of cell competition in gliomagenesis. <i>bioRxiv</i>. 2026. doi:<a href=\"https://doi.org/10.64898/2026.01.15.699808\">10.64898/2026.01.15.699808</a>","apa":"Jiang, Y., Ahn, R., Huang, A., Gonzalez, P. P., Kim, J., Zhang, G., … Zong, H. (2026). Critical role of cell competition in gliomagenesis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.64898/2026.01.15.699808\">https://doi.org/10.64898/2026.01.15.699808</a>","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.” <i>BioRxiv</i>, 2026. <a href=\"https://doi.org/10.64898/2026.01.15.699808\">https://doi.org/10.64898/2026.01.15.699808</a>.","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, <a href=\"https://doi.org/10.64898/2026.01.15.699808\">10.64898/2026.01.15.699808</a>.","mla":"Jiang, Ying, et al. “Critical Role of Cell Competition in Gliomagenesis.” <i>BioRxiv</i>, 2026, doi:<a href=\"https://doi.org/10.64898/2026.01.15.699808\">10.64898/2026.01.15.699808</a>.","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).","ieee":"Y. Jiang <i>et al.</i>, “Critical role of cell competition in gliomagenesis,” <i>bioRxiv</i>. 2026."},"status":"public","department":[{"_id":"SiHi"}],"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","oa_version":"Preprint","type":"preprint","_id":"21212","day":"16","title":"Critical role of cell competition in gliomagenesis","author":[{"first_name":"Ying","last_name":"Jiang","full_name":"Jiang, Ying"},{"last_name":"Ahn","first_name":"Ryuhjin","full_name":"Ahn, Ryuhjin"},{"first_name":"Arthur","last_name":"Huang","full_name":"Huang, Arthur"},{"full_name":"Gonzalez, Phillippe P.","first_name":"Phillippe P.","last_name":"Gonzalez"},{"first_name":"Jungeun","last_name":"Kim","full_name":"Kim, Jungeun"},{"first_name":"Guoxin","last_name":"Zhang","full_name":"Zhang, Guoxin"},{"full_name":"Liu, Zihao","first_name":"Zihao","last_name":"Liu"},{"full_name":"He, Zhenqiang","first_name":"Zhenqiang","last_name":"He"},{"full_name":"Dudley, Lindsey","first_name":"Lindsey","last_name":"Dudley"},{"full_name":"Patel, Kunal S.","first_name":"Kunal S.","last_name":"Patel"},{"first_name":"Godfrey A.","last_name":"Dzhivhuho","full_name":"Dzhivhuho, Godfrey A."},{"full_name":"Crowl, Sam","last_name":"Crowl","first_name":"Sam"},{"first_name":"Piotr","last_name":"Przanowski","full_name":"Przanowski, Piotr"},{"full_name":"Camacho, Luisa Quesada","first_name":"Luisa Quesada","last_name":"Camacho"},{"full_name":"Hao, Sijie","last_name":"Hao","first_name":"Sijie"},{"first_name":"Jianhao","last_name":"Zeng","full_name":"Zeng, Jianhao"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"},{"full_name":"Fallahi-Sichani, Mohammad","last_name":"Fallahi-Sichani","first_name":"Mohammad"},{"full_name":"Janes, Kevin A.","last_name":"Janes","first_name":"Kevin A."},{"last_name":"Naegle","first_name":"Kristen M.","full_name":"Naegle, Kristen M."},{"first_name":"Marie-Louise","last_name":"Hammarskjold","full_name":"Hammarskjold, Marie-Louise"},{"last_name":"Goldman","first_name":"Steven A.","full_name":"Goldman, Steven A."},{"last_name":"Kornblum","first_name":"Harley I.","full_name":"Kornblum, Harley I."},{"first_name":"Maojin","last_name":"Yao","full_name":"Yao, Maojin"},{"full_name":"White, Forest","last_name":"White","first_name":"Forest"},{"first_name":"Hui","last_name":"Zong","full_name":"Zong, Hui"}],"date_created":"2026-02-10T12:55:55Z","month":"01","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.64898/2026.01.15.699808"}],"date_updated":"2026-02-16T10:12:42Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publication":"bioRxiv","language":[{"iso":"eng"}],"publication_status":"published","oa":1,"year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.64898/2026.01.15.699808","date_published":"2026-01-16T00:00:00Z","OA_type":"green"},{"abstract":[{"text":"This study investigates the mechanisms driving clustered convection and the breakdown of the Intertropical Convergence Zone (ITCZ) over the Western Pacific Warm Pool using high‐resolution cloud‐resolving simulations and machine‐learning sensitivity experiments. Results show that ITCZ breakdown episodes, marked by spatially homogeneous convection and weakened meridional moisture gradients, are triggered primarily by anomalous moisture advection linked to the equatorial Rossby‐wave activity. While large‐scale moisture advection regulates the background convective state strongly, it is the surface and low‐level meridional winds that dominate transitions between clustered and random convection. Simulations demonstrate that moisture alone can sustain convective clustering, but breakdown episodes are more persistent and widespread when coupled with southerly meridional advection. These findings confirm that wave‐driven advection acts as a regulatory mechanism, periodically disrupting convective clustering and reshaping the meridional moisture gradient. This modulation of organization by wave‐induced breakdown events is critical for understanding tropical convection variability and its implications for the climate system.","lang":"eng"}],"date_updated":"2026-02-16T10:19:52Z","main_file_link":[{"url":"https://doi.org/10.1002/qj.70131","open_access":"1"}],"date_created":"2026-02-12T10:13:02Z","title":"Moisture and wind effects of Rossby waves on Western Pacific Intertropical Convergence Zone breakdown events","author":[{"orcid":"0000-0002-1988-5035","last_name":"Casallas Garcia","first_name":"Alejandro","full_name":"Casallas Garcia, Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a"},{"full_name":"Mark Tompkins, Adrian","first_name":"Adrian","last_name":"Mark Tompkins"},{"first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"article_number":"e70131","corr_author":"1","OA_type":"hybrid","date_published":"2026-02-12T00:00:00Z","publication":"Quarterly Journal of the Royal Meteorological Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"epub_ahead","publisher":"Wiley","ddc":["550"],"quality_controlled":"1","citation":{"chicago":"Casallas Garcia, Alejandro, Adrian Mark Tompkins, and Caroline J Muller. “Moisture and Wind Effects of Rossby Waves on Western Pacific Intertropical Convergence Zone Breakdown Events.” <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley, 2026. <a href=\"https://doi.org/10.1002/qj.70131\">https://doi.org/10.1002/qj.70131</a>.","ama":"Casallas Garcia A, Mark Tompkins A, Muller CJ. Moisture and wind effects of Rossby waves on Western Pacific Intertropical Convergence Zone breakdown events. <i>Quarterly Journal of the Royal Meteorological Society</i>. 2026. doi:<a href=\"https://doi.org/10.1002/qj.70131\">10.1002/qj.70131</a>","apa":"Casallas Garcia, A., Mark Tompkins, A., &#38; Muller, C. J. (2026). Moisture and wind effects of Rossby waves on Western Pacific Intertropical Convergence Zone breakdown events. <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley. <a href=\"https://doi.org/10.1002/qj.70131\">https://doi.org/10.1002/qj.70131</a>","mla":"Casallas Garcia, Alejandro, et al. “Moisture and Wind Effects of Rossby Waves on Western Pacific Intertropical Convergence Zone Breakdown Events.” <i>Quarterly Journal of the Royal Meteorological Society</i>, e70131, Wiley, 2026, doi:<a href=\"https://doi.org/10.1002/qj.70131\">10.1002/qj.70131</a>.","short":"A. Casallas Garcia, A. Mark Tompkins, C.J. Muller, Quarterly Journal of the Royal Meteorological Society (2026).","ieee":"A. Casallas Garcia, A. Mark Tompkins, and C. J. Muller, “Moisture and wind effects of Rossby waves on Western Pacific Intertropical Convergence Zone breakdown events,” <i>Quarterly Journal of the Royal Meteorological Society</i>. Wiley, 2026.","ista":"Casallas Garcia A, Mark Tompkins A, Muller CJ. 2026. Moisture and wind effects of Rossby waves on Western Pacific Intertropical Convergence Zone breakdown events. Quarterly Journal of the Royal Meteorological Society., e70131."},"_id":"21217","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","day":"12","department":[{"_id":"CaMu"}],"scopus_import":"1","article_type":"original","month":"02","doi":"10.1002/qj.70131","has_accepted_license":"1","language":[{"iso":"eng"}],"tmp":{"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)","image":"/images/cc_by_nc.png"},"year":"2026","oa":1,"status":"public","ec_funded":1,"publication_identifier":{"issn":["0035-9009"],"eissn":["1477-870X"]},"OA_place":"publisher","type":"journal_article","acknowledgement":"This article is based on chapter 5 of the PhD thesis of A. Casallas. The authors thank Graziano Giuliani for discussions on the boundary-condition experiments. A. Casallas was supported by a PhD fellowship awarded by the Abdus Salam International Centre for Theoretical Physics. A. Casallas also acknowledges support by the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 101034413. C. Muller acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). The authors gratefully acknowledge Daniel Hernández-Deckers, Lokahith Agasthya, Chris Holloway, and Paolina Cerlini for their valuable feedback and insightful discussions. They are especially thankful to Bety Pechacova for suggesting the use of SHAP to complement their analysis. They also thank the two anonymous reviewers for their constructive comments, which improved the quality and clarity of the article significantly. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ."},{"page":"133-153","doi":"10.1016/b978-0-443-21439-4.00036-5","language":[{"iso":"eng"}],"oa":1,"year":"2026","arxiv":1,"editor":[{"first_name":"Ilya","last_name":"Mandel","full_name":"Mandel, Ilya"}],"month":"01","type":"book_chapter","status":"public","publication_identifier":{"isbn":["9780443214400"]},"OA_place":"repository","volume":2,"date_published":"2026-01-01T00:00:00Z","OA_type":"green","publication":"Encyclopedia of Astrophysics","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Asteroseismology is the study of the interior physics and structure of stars using their pulsations. It is applicable to stars across the Hertzsprung–Russell (HR) diagram and a powerful technique not only to measure masses, radii, and ages but also directly constrain interior rotation, chemical mixing, and magnetism. This is because a star's self-excited pulsation modes are sensitive to its structure. Asteroseismology generally requires long-duration and high-precision time-series data. The method of forward asteroseismic modeling, which is the statistical comparison of observed pulsation mode frequencies to theoretically predicted pulsation frequencies calculated from a grid of models, provides precise constraints for calibrating various transport phenomena. In this introduction to asteroseismology, we provide an overview of its principles, and the typical data sets and methodologies used to constrain stellar interiors. Finally, we present key highlights of asteroseismic results from across the HR diagram, and conclude with ongoing challenges and future prospects for this ever-expanding field within stellar astrophysics.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2410.01715","open_access":"1"}],"date_updated":"2026-02-17T11:05:20Z","author":[{"full_name":"Bowman, Dominic M.","last_name":"Bowman","first_name":"Dominic M."},{"full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000"}],"title":"Asteroseismology","external_id":{"arxiv":["2410.01715"]},"date_created":"2026-02-16T10:43:01Z","oa_version":"Preprint","article_processing_charge":"No","_id":"21230","day":"01","department":[{"_id":"LiBu"}],"intvolume":"         2","scopus_import":"1","publisher":"Elsevier","citation":{"apa":"Bowman, D. M., &#38; Bugnet, L. A. (2026). Asteroseismology. In I. Mandel (Ed.), <i>Encyclopedia of Astrophysics</i> (Vol. 2, pp. 133–153). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-443-21439-4.00036-5\">https://doi.org/10.1016/b978-0-443-21439-4.00036-5</a>","ama":"Bowman DM, Bugnet LA. Asteroseismology. In: Mandel I, ed. <i>Encyclopedia of Astrophysics</i>. Vol 2. Elsevier; 2026:133-153. doi:<a href=\"https://doi.org/10.1016/b978-0-443-21439-4.00036-5\">10.1016/b978-0-443-21439-4.00036-5</a>","chicago":"Bowman, Dominic M., and Lisa Annabelle Bugnet. “Asteroseismology.” In <i>Encyclopedia of Astrophysics</i>, edited by Ilya Mandel, 2:133–53. Elsevier, 2026. <a href=\"https://doi.org/10.1016/b978-0-443-21439-4.00036-5\">https://doi.org/10.1016/b978-0-443-21439-4.00036-5</a>.","ista":"Bowman DM, Bugnet LA. 2026.Asteroseismology. In: Encyclopedia of Astrophysics. vol. 2, 133–153.","ieee":"D. M. Bowman and L. A. Bugnet, “Asteroseismology,” in <i>Encyclopedia of Astrophysics</i>, vol. 2, I. Mandel, Ed. Elsevier, 2026, pp. 133–153.","short":"D.M. Bowman, L.A. Bugnet, in:, I. Mandel (Ed.), Encyclopedia of Astrophysics, Elsevier, 2026, pp. 133–153.","mla":"Bowman, Dominic M., and Lisa Annabelle Bugnet. “Asteroseismology.” <i>Encyclopedia of Astrophysics</i>, edited by Ilya Mandel, vol. 2, Elsevier, 2026, pp. 133–53, doi:<a href=\"https://doi.org/10.1016/b978-0-443-21439-4.00036-5\">10.1016/b978-0-443-21439-4.00036-5</a>."},"quality_controlled":"1"},{"publication":"npj Systems Biology and Applications","file_date_updated":"2026-02-23T10:09:03Z","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"20","date_published":"2026-02-05T00:00:00Z","OA_type":"gold","title":"Simulation-based inference of cell migration dynamics in complex spatial environments","author":[{"full_name":"Arruda, Jonas","first_name":"Jonas","last_name":"Arruda"},{"full_name":"Alamoudi, Emad","first_name":"Emad","last_name":"Alamoudi"},{"full_name":"Mueller, Robert","last_name":"Mueller","first_name":"Robert"},{"last_name":"Vaisband","first_name":"Marc","full_name":"Vaisband, Marc"},{"full_name":"Molkenbur, Ronja","first_name":"Ronja","last_name":"Molkenbur"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack"},{"full_name":"Kiermaier, Eva","first_name":"Eva","last_name":"Kiermaier"},{"full_name":"Hasenauer, Jan","first_name":"Jan","last_name":"Hasenauer"}],"date_created":"2026-02-16T10:44:31Z","external_id":{"pmid":["41611727"]},"abstract":[{"text":"To assess cell migration in complex spatial environments, microfabricated chips, such as mazes and pillar forests, are routinely used to impose spatial and mechanical constraints, and cell trajectories are followed within these structures by advanced imaging techniques. In systems mechanobiology, computational models serve as essential tools to uncover how physical geometry influences intracellular dynamics; however, decoding such complex behaviors requires advanced inference techniques. Here, we integrated experimental observations of dendritic cell migration in a geometrically constrained microenvironment into a Cellular Potts model. We demonstrated that these spatial constraints modulate the motility dynamics, including speed and directional changes. We show that classical summary statistics, such as mean squared displacement and turning angle distributions, can resolve key mechanistic features but fail to extract richer spatiotemporal patterns, limiting accurate parameter inference. To solve this, we applied neural posterior estimation with in-the-loop learning of summary features. This learned summary representation of the data enables robust and flexible parameter inference, providing a data-driven framework for model calibration and advancing quantitative analysis of cell migration in structured microenvironments.","lang":"eng"}],"date_updated":"2026-02-23T10:10:10Z","department":[{"_id":"NanoFab"}],"intvolume":"        12","scopus_import":"1","article_type":"original","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","_id":"21231","day":"05","ddc":["570"],"citation":{"chicago":"Arruda, Jonas, Emad Alamoudi, Robert Mueller, Marc Vaisband, Ronja Molkenbur, Jack Merrin, Eva Kiermaier, and Jan Hasenauer. “Simulation-Based Inference of Cell Migration Dynamics in Complex Spatial Environments.” <i>Npj Systems Biology and Applications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41540-026-00648-9\">https://doi.org/10.1038/s41540-026-00648-9</a>.","apa":"Arruda, J., Alamoudi, E., Mueller, R., Vaisband, M., Molkenbur, R., Merrin, J., … Hasenauer, J. (2026). Simulation-based inference of cell migration dynamics in complex spatial environments. <i>Npj Systems Biology and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41540-026-00648-9\">https://doi.org/10.1038/s41540-026-00648-9</a>","ama":"Arruda J, Alamoudi E, Mueller R, et al. Simulation-based inference of cell migration dynamics in complex spatial environments. <i>npj Systems Biology and Applications</i>. 2026;12. doi:<a href=\"https://doi.org/10.1038/s41540-026-00648-9\">10.1038/s41540-026-00648-9</a>","ieee":"J. Arruda <i>et al.</i>, “Simulation-based inference of cell migration dynamics in complex spatial environments,” <i>npj Systems Biology and Applications</i>, vol. 12. Springer Nature, 2026.","short":"J. Arruda, E. Alamoudi, R. Mueller, M. Vaisband, R. Molkenbur, J. Merrin, E. Kiermaier, J. Hasenauer, Npj Systems Biology and Applications 12 (2026).","mla":"Arruda, Jonas, et al. “Simulation-Based Inference of Cell Migration Dynamics in Complex Spatial Environments.” <i>Npj Systems Biology and Applications</i>, vol. 12, 20, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41540-026-00648-9\">10.1038/s41540-026-00648-9</a>.","ista":"Arruda J, Alamoudi E, Mueller R, Vaisband M, Molkenbur R, Merrin J, Kiermaier E, Hasenauer J. 2026. Simulation-based inference of cell migration dynamics in complex spatial environments. npj Systems Biology and Applications. 12, 20."},"quality_controlled":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"file_name":"2026_npjSysBioApp_Arruda.pdf","date_updated":"2026-02-23T10:09:03Z","content_type":"application/pdf","file_size":10217687,"checksum":"99b2e6bbaaedf45f22e07751948669f5","date_created":"2026-02-23T10:09:03Z","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"file_id":"21346"}],"oa":1,"year":"2026","has_accepted_license":"1","PlanS_conform":"1","doi":"10.1038/s41540-026-00648-9","month":"02","DOAJ_listed":"1","acknowledgement":"This work was supported by the German Federal Ministry of Education and Research (BMBF) (EMUNE/031L0293C), the European Union via the ERC grant INTEGRATE, grant agreement number 101126146, and under Germany’s Excellence Strategy by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (EXC 2047—390685813, EXC 2151—390873048, FOR5775 — 533863915, and 524747443), the University of Bonn via the Schlegel Professorship of J.H., and the returning experts fellowship of the Ministry of Innovation, Science, and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069). J.M. is a member of the Nanofabrication Facility and is supported by the Institute of Science and Technology Austria. E.K. acknowledges the TRA Life and Health (University of Bonn) as part of the Excellence Strategy of the federal and state governments. The authors thank Laeschkir Würthner for his insightful comments on the implementation of the authors’ model. The views and opinions expressed are those of the authors only and do not necessarily reflect those of the funding agencies. Parts of Fig. 1 were created using BioRender. Open Access funding enabled and organized by Projekt DEAL.","type":"journal_article","OA_place":"publisher","volume":12,"status":"public","publication_identifier":{"eissn":["2056-7189"]}},{"year":"2026","oa":1,"language":[{"iso":"eng"}],"file":[{"file_name":"2026_EarthSystDynam_Yoon.pdf","date_updated":"2026-02-23T10:26:29Z","content_type":"application/pdf","file_size":2068229,"checksum":"6c3669c463731ad7c484b2990eb8ee0d","date_created":"2026-02-23T10:26:29Z","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"file_id":"21348"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","doi":"10.5194/esd-17-167-2026","page":"167-179","has_accepted_license":"1","PlanS_conform":"1","month":"02","DOAJ_listed":"1","acknowledgement":"AY acknowledges funding by the CLICCS centre of excellence subproject A3 funded by DFG. We thank the German Climate Computing Center DKRZ for providing computing resources and the Integrated Climate Data Center (ICDC), the Center for Earth System Research and Sustainability (CEN), University of Hamburg, for supporting the IMERG data. In addition, we would like to thank Jana Sillmann for suggesting the analysis of heat stress indices and Keno Riechers for providing a thorough internal review of the initial manuscript at the Max Planck Institute for Meteorology. Open Access funding is enabled and organized by Projekt DEAL. This research has been supported by the Deutsche Forschungsgemeinschaft (grant no. CLICCS 390683824 (A3)). The article processing charges for this open-access publication were covered by the Max Planck Society.","type":"journal_article","volume":17,"OA_place":"publisher","publication_identifier":{"eissn":["2190-4987"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication":"Earth System Dynamics","file_date_updated":"2026-02-23T10:26:29Z","OA_type":"gold","date_published":"2026-02-04T00:00:00Z","date_created":"2026-02-16T10:44:58Z","author":[{"first_name":"Arim","last_name":"Yoon","full_name":"Yoon, Arim"},{"full_name":"Hohenegger, Cathy","first_name":"Cathy","last_name":"Hohenegger"},{"last_name":"Bao","first_name":"Jiawei","full_name":"Bao, Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"last_name":"Brunner","first_name":"Lukas","full_name":"Brunner, Lukas"}],"title":"Extreme events in the Amazon after deforestation","date_updated":"2026-02-23T10:28:48Z","abstract":[{"text":"Potential self-perpetuating dieback of the Amazon rain forest has been a topic of concern. The concern is that initial deforestation could critically impair the forest’s water recycling capacities, further harming the remaining forest through reduced annual precipitation. Many studies have focused on annual mean precipitation changes, due to its widespread perception as a central control on the Amazon rain forest’s stability. However, the impact of deforestation goes beyond changes in the annual mean precipitation. Yet, global coarse-resolution climate models are not well suited to investigate changes in short-duration and localized events due to their coarse resolution. Here, we circumvent these issues by analyzing a full-deforestation scenario simulated by a global storm-resolving model. We focus on changes in the tail of the hourly distribution of precipitation, temperature, and wind. Hourly precipitation becomes more extreme in the absence of the forest than in an intact forest, with an increased occurrence of both no rain and intense rainfall. These changes are driven by enhanced moisture convergence that strengthens vertical velocity. On average, the near-surface temperature rises significantly by about 3.84 °C, and the daily minimum temperature after deforestation becomes similar to the daily maximum temperature before deforestation. Except for wet-bulb temperature, human heat stress indicators shift to more severe levels, with implications for health and a significant reduction in work productivity. Finally, the mean 10 m wind speed intensifies by a factor of four, with the 99th percentile wind speed doubling. To summarize, our findings, while based on an idealized case, provide a stark warning of the effects of continuing deforestation of the Amazon.","lang":"eng"}],"article_type":"original","scopus_import":"1","intvolume":"        17","department":[{"_id":"CaMu"}],"day":"04","_id":"21233","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","citation":{"chicago":"Yoon, Arim, Cathy Hohenegger, Jiawei Bao, and Lukas Brunner. “Extreme Events in the Amazon after Deforestation.” <i>Earth System Dynamics</i>. Copernicus GmbH, 2026. <a href=\"https://doi.org/10.5194/esd-17-167-2026\">https://doi.org/10.5194/esd-17-167-2026</a>.","ama":"Yoon A, Hohenegger C, Bao J, Brunner L. Extreme events in the Amazon after deforestation. <i>Earth System Dynamics</i>. 2026;17(1):167-179. doi:<a href=\"https://doi.org/10.5194/esd-17-167-2026\">10.5194/esd-17-167-2026</a>","apa":"Yoon, A., Hohenegger, C., Bao, J., &#38; Brunner, L. (2026). Extreme events in the Amazon after deforestation. <i>Earth System Dynamics</i>. Copernicus GmbH. <a href=\"https://doi.org/10.5194/esd-17-167-2026\">https://doi.org/10.5194/esd-17-167-2026</a>","short":"A. Yoon, C. Hohenegger, J. Bao, L. Brunner, Earth System Dynamics 17 (2026) 167–179.","mla":"Yoon, Arim, et al. “Extreme Events in the Amazon after Deforestation.” <i>Earth System Dynamics</i>, vol. 17, no. 1, Copernicus GmbH, 2026, pp. 167–79, doi:<a href=\"https://doi.org/10.5194/esd-17-167-2026\">10.5194/esd-17-167-2026</a>.","ieee":"A. Yoon, C. Hohenegger, J. Bao, and L. Brunner, “Extreme events in the Amazon after deforestation,” <i>Earth System Dynamics</i>, vol. 17, no. 1. Copernicus GmbH, pp. 167–179, 2026.","ista":"Yoon A, Hohenegger C, Bao J, Brunner L. 2026. Extreme events in the Amazon after deforestation. Earth System Dynamics. 17(1), 167–179."},"quality_controlled":"1","ddc":["550"],"publisher":"Copernicus GmbH"},{"month":"02","oa":1,"year":"2026","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"file_id":"21349","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2026-02-23T10:32:12Z","file_size":10606778,"checksum":"920e8edfd3b8b42f5bb6f86d4c66c54d","content_type":"application/pdf","date_updated":"2026-02-23T10:32:12Z","file_name":"2026_CellSystems_GomezPascual.pdf"}],"PlanS_conform":"1","has_accepted_license":"1","doi":"10.1016/j.cels.2025.101488","issue":"2","OA_place":"publisher","volume":17,"publication_identifier":{"issn":["2405-4712"]},"status":"public","acknowledgement":"We would like to thank the Summer School Systems Genetics of Neural Ageing for bringing us together and spurring our international collaboration. We would also like to acknowledge the funding for the Summer School 2022 from the e:Med Systems Medicine Program of the BMBF (Bundesministerium für Bildung und Forschung; German Ministry of Education and Research) to R.W.O. In addition, we would like to thank the FLI imaging core facility for their assistance. A.G.-P. is supported by Fundación Séneca, Región de Murcia, Spain (21259/FPI/19). D.E.M.d.B. is financed by a Rubicon scholarship (452021116) from the Dutch Research Council (NWO). This work was also supported by NIH NIA R01AG070913-01 (R.W.W.), R01AG075813-01 (D.G.A.), and R01AG075818 (C.K.). We acknowledge the help of Larry Mobraaten (Jackson Laboratory, Bar Harbor, MN) with the BXD strains and U. Obermüller for the help with the histology. For the purpose of open access, the authors have applied a CC BY public copyright license to all author-accepted manuscripts arising from this submission.","type":"journal_article","title":"The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus","author":[{"last_name":"Gómez-Pascual","first_name":"Alicia","full_name":"Gómez-Pascual, Alicia"},{"id":"ab8acda1-91c1-11f0-aad8-f75d3d6424d8","full_name":"Glikman, Dow M","first_name":"Dow M","last_name":"Glikman"},{"first_name":"Hui Xin","last_name":"Ng","full_name":"Ng, Hui Xin"},{"first_name":"James E.","last_name":"Tomkins","full_name":"Tomkins, James E."},{"full_name":"Lu, Lu","last_name":"Lu","first_name":"Lu"},{"first_name":"Ying","last_name":"Xu","full_name":"Xu, Ying"},{"full_name":"Ashbrook, David G.","last_name":"Ashbrook","first_name":"David G."},{"last_name":"Kaczorowski","first_name":"Catherine","full_name":"Kaczorowski, Catherine"},{"full_name":"Kempermann, Gerd","last_name":"Kempermann","first_name":"Gerd"},{"full_name":"Killmar, John","last_name":"Killmar","first_name":"John"},{"full_name":"Mozhui, Khyobeni","last_name":"Mozhui","first_name":"Khyobeni"},{"first_name":"Oliver","last_name":"Ohlenschläger","full_name":"Ohlenschläger, Oliver"},{"first_name":"Rudolf","last_name":"Aebersold","full_name":"Aebersold, Rudolf"},{"last_name":"Ingram","first_name":"Donald K.","full_name":"Ingram, Donald K."},{"full_name":"Williams, Evan G.","last_name":"Williams","first_name":"Evan G."},{"full_name":"Jucker, Mathias","last_name":"Jucker","first_name":"Mathias"},{"last_name":"Overall","first_name":"Rupert W.","full_name":"Overall, Rupert W."},{"last_name":"Williams","first_name":"Robert W.","full_name":"Williams, Robert W."},{"first_name":"Dennis E.M.","last_name":"de Bakker","full_name":"de Bakker, Dennis E.M."}],"external_id":{"pmid":["41633365"]},"date_created":"2026-02-16T10:45:10Z","date_updated":"2026-02-23T10:35:01Z","abstract":[{"text":"In aged humans and mice, hypobranched glycogen aggregates, known as polyglucosan bodies (PGBs), accumulate in hippocampal astrocytes. While PGBs are linked to cognitive decline in neurological diseases, they remain largely unstudied in the context of typical aging. We show that PGBs arise in autophagy-dysregulated astrocytes in the aged hippocampus, with substantial variation among 32 inbred BXD mouse strains. Genetic mapping through quantitative trait locus analysis identified a major locus (Pgb1) that modulates hippocampal PGB burden. Extensive transcriptomic and proteomic datasets were produced for the aged hippocampus of the BXD family to investigate the mechanism by which the Pgb1 locus modulates PGB burden. We identified that Pgb1 contains allelic Smarcal1 and Usp37 variants and influences PGB burden through trans-regulation of mRNA and protein expression levels, including abundance of glycogen-mobilizing factor PYGB. Furthermore, comprehensive phenome-wide association scans, transcriptomic analyses, and direct behavioral testing demonstrated that cognition remains intact despite age-related PGB burden. A record of this paper’s transparent peer review process is included in the supplemental information.","lang":"eng"}],"publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell Systems","file_date_updated":"2026-02-23T10:32:12Z","date_published":"2026-02-18T00:00:00Z","OA_type":"hybrid","article_number":"101488","citation":{"mla":"Gómez-Pascual, Alicia, et al. “The Smarcal1-Usp37 Locus Modulates Glycogen Aggregation in Astrocytes of the Aged Hippocampus.” <i>Cell Systems</i>, vol. 17, no. 2, 101488, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.cels.2025.101488\">10.1016/j.cels.2025.101488</a>.","short":"A. Gómez-Pascual, D.M. Glikman, H.X. Ng, J.E. Tomkins, L. Lu, Y. Xu, D.G. Ashbrook, C. Kaczorowski, G. Kempermann, J. Killmar, K. Mozhui, O. Ohlenschläger, R. Aebersold, D.K. Ingram, E.G. Williams, M. Jucker, R.W. Overall, R.W. Williams, D.E.M. de Bakker, Cell Systems 17 (2026).","ieee":"A. Gómez-Pascual <i>et al.</i>, “The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus,” <i>Cell Systems</i>, vol. 17, no. 2. Elsevier, 2026.","ista":"Gómez-Pascual A, Glikman DM, Ng HX, Tomkins JE, Lu L, Xu Y, Ashbrook DG, Kaczorowski C, Kempermann G, Killmar J, Mozhui K, Ohlenschläger O, Aebersold R, Ingram DK, Williams EG, Jucker M, Overall RW, Williams RW, de Bakker DEM. 2026. The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus. Cell Systems. 17(2), 101488.","chicago":"Gómez-Pascual, Alicia, Dow M Glikman, Hui Xin Ng, James E. Tomkins, Lu Lu, Ying Xu, David G. Ashbrook, et al. “The Smarcal1-Usp37 Locus Modulates Glycogen Aggregation in Astrocytes of the Aged Hippocampus.” <i>Cell Systems</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.cels.2025.101488\">https://doi.org/10.1016/j.cels.2025.101488</a>.","ama":"Gómez-Pascual A, Glikman DM, Ng HX, et al. The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus. <i>Cell Systems</i>. 2026;17(2). doi:<a href=\"https://doi.org/10.1016/j.cels.2025.101488\">10.1016/j.cels.2025.101488</a>","apa":"Gómez-Pascual, A., Glikman, D. M., Ng, H. X., Tomkins, J. E., Lu, L., Xu, Y., … de Bakker, D. E. M. (2026). The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2025.101488\">https://doi.org/10.1016/j.cels.2025.101488</a>"},"quality_controlled":"1","ddc":["570"],"publisher":"Elsevier","scopus_import":"1","article_type":"original","department":[{"_id":"GradSch"}],"intvolume":"        17","day":"18","article_processing_charge":"No","oa_version":"Published Version","_id":"21234"},{"issue":"1","doi":"10.2140/pjm.2026.340.179","page":"179-198","year":"2026","oa":1,"language":[{"iso":"eng"}],"arxiv":1,"month":"01","type":"journal_article","publication_identifier":{"eissn":["1945-5844"],"issn":["0030-8730"]},"status":"public","volume":340,"OA_place":"repository","OA_type":"green","date_published":"2026-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication":"Pacific Journal of Mathematics","date_updated":"2026-02-17T11:43:14Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.09256","open_access":"1"}],"abstract":[{"lang":"eng","text":"We obtain an asymptotic formula for the number of integral solutions to a system of diagonal equations. We obtain an asymptotic formula for the number of solutions with variables restricted to smooth numbers as well. We improve the required number of variables compared to previous results by incorporating recent progress on Waring’s problem and the resolution of the main conjecture in Vinogradov’s mean value theorem."}],"date_created":"2026-02-16T15:17:27Z","external_id":{"arxiv":["2406.09256"]},"title":"Integral solutions to systems of diagonal equations","author":[{"last_name":"Rome","first_name":"Nick","full_name":"Rome, Nick"},{"full_name":"Yamagishi, Shuntaro","id":"0c3fbc5c-f7a6-11ec-8d70-9485e75b416b","first_name":"Shuntaro","last_name":"Yamagishi"}],"day":"01","_id":"21242","oa_version":"Preprint","article_processing_charge":"No","article_type":"original","intvolume":"       340","department":[{"_id":"TiBr"}],"publisher":"Mathematical Sciences Publishers","citation":{"ista":"Rome N, Yamagishi S. 2026. Integral solutions to systems of diagonal equations. Pacific Journal of Mathematics. 340(1), 179–198.","ieee":"N. Rome and S. Yamagishi, “Integral solutions to systems of diagonal equations,” <i>Pacific Journal of Mathematics</i>, vol. 340, no. 1. Mathematical Sciences Publishers, pp. 179–198, 2026.","mla":"Rome, Nick, and Shuntaro Yamagishi. “Integral Solutions to Systems of Diagonal Equations.” <i>Pacific Journal of Mathematics</i>, vol. 340, no. 1, Mathematical Sciences Publishers, 2026, pp. 179–98, doi:<a href=\"https://doi.org/10.2140/pjm.2026.340.179\">10.2140/pjm.2026.340.179</a>.","short":"N. Rome, S. Yamagishi, Pacific Journal of Mathematics 340 (2026) 179–198.","apa":"Rome, N., &#38; Yamagishi, S. (2026). Integral solutions to systems of diagonal equations. <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pjm.2026.340.179\">https://doi.org/10.2140/pjm.2026.340.179</a>","ama":"Rome N, Yamagishi S. Integral solutions to systems of diagonal equations. <i>Pacific Journal of Mathematics</i>. 2026;340(1):179-198. doi:<a href=\"https://doi.org/10.2140/pjm.2026.340.179\">10.2140/pjm.2026.340.179</a>","chicago":"Rome, Nick, and Shuntaro Yamagishi. “Integral Solutions to Systems of Diagonal Equations.” <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers, 2026. <a href=\"https://doi.org/10.2140/pjm.2026.340.179\">https://doi.org/10.2140/pjm.2026.340.179</a>."},"quality_controlled":"1"},{"arxiv":1,"month":"01","issue":"1","doi":"10.1103/m8h6-1wfk","language":[{"iso":"eng"}],"oa":1,"year":"2026","status":"public","publication_identifier":{"eissn":["2469-990X"]},"OA_place":"repository","volume":11,"type":"journal_article","acknowledgement":"The authors acknowledge support from ERC project n-AQUA, Grant Agreement No. 101071937.\r\nB.C. and A.S. acknowledge support from the CFM Foundation. B.C. acknowledges support from\r\nthe NOMIS Foundation.","abstract":[{"text":"In this paper we examine how porosity fluctuations affect the hydrodynamic permeability of a porous matrix or membrane. We introduce a fluctuating Darcy model, which couples the Navier-Stokes equation to the space- and time-dependent porosity fluctuations via a Darcy friction term. Using a perturbative approach, a Dyson equation for hydrodynamic fluctuations is derived and solved to express the permeability in terms of the matrix fluctuation spectrum. Surprisingly, the model reveals strong modifications of the fluid permeability in fluctuating matrices compared to static ones. Applications to various matrix excitation models, the breathing matrix, phonons, and active forcing, highlight the significant influence of matrix fluctuations on fluid transport, offering insights for optimizing membrane design for separation applications.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2512.11368","open_access":"1"}],"date_updated":"2026-02-23T12:01:57Z","author":[{"full_name":"Dombret, Albert","last_name":"Dombret","first_name":"Albert"},{"full_name":"Sutter, Adrien","last_name":"Sutter","first_name":"Adrien"},{"first_name":"Baptiste","last_name":"Coquinot","orcid":"0000-0001-5524-596X","full_name":"Coquinot, Baptiste","id":"f8417bd4-f599-11ee-a482-b927e3ed1e8e"},{"full_name":"Kavokine, Nikita","last_name":"Kavokine","first_name":"Nikita"},{"full_name":"Coasne, Benoit","last_name":"Coasne","first_name":"Benoit"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"title":"Hydrodynamic permeability of fluctuating porous membranes","external_id":{"arxiv":["2512.11368"]},"date_created":"2026-02-17T08:10:09Z","corr_author":"1","article_number":"014201","date_published":"2026-01-21T00:00:00Z","OA_type":"green","publication":"Physical Review Fluids","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","quality_controlled":"1","citation":{"ista":"Dombret A, Sutter A, Coquinot B, Kavokine N, Coasne B, Bocquet L. 2026. Hydrodynamic permeability of fluctuating porous membranes. Physical Review Fluids. 11(1), 014201.","short":"A. Dombret, A. Sutter, B. Coquinot, N. Kavokine, B. Coasne, L. Bocquet, Physical Review Fluids 11 (2026).","mla":"Dombret, Albert, et al. “Hydrodynamic Permeability of Fluctuating Porous Membranes.” <i>Physical Review Fluids</i>, vol. 11, no. 1, 014201, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/m8h6-1wfk\">10.1103/m8h6-1wfk</a>.","ieee":"A. Dombret, A. Sutter, B. Coquinot, N. Kavokine, B. Coasne, and L. Bocquet, “Hydrodynamic permeability of fluctuating porous membranes,” <i>Physical Review Fluids</i>, vol. 11, no. 1. American Physical Society, 2026.","apa":"Dombret, A., Sutter, A., Coquinot, B., Kavokine, N., Coasne, B., &#38; Bocquet, L. (2026). Hydrodynamic permeability of fluctuating porous membranes. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/m8h6-1wfk\">https://doi.org/10.1103/m8h6-1wfk</a>","ama":"Dombret A, Sutter A, Coquinot B, Kavokine N, Coasne B, Bocquet L. Hydrodynamic permeability of fluctuating porous membranes. <i>Physical Review Fluids</i>. 2026;11(1). doi:<a href=\"https://doi.org/10.1103/m8h6-1wfk\">10.1103/m8h6-1wfk</a>","chicago":"Dombret, Albert, Adrien Sutter, Baptiste Coquinot, Nikita Kavokine, Benoit Coasne, and Lydéric Bocquet. “Hydrodynamic Permeability of Fluctuating Porous Membranes.” <i>Physical Review Fluids</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/m8h6-1wfk\">https://doi.org/10.1103/m8h6-1wfk</a>."},"oa_version":"Preprint","article_processing_charge":"No","_id":"21273","day":"21","department":[{"_id":"MiLe"}],"intvolume":"        11","article_type":"original"},{"acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 950349 and the Marie Skłodowska-Curie Grant Agreement No. 101034413. The computations in this paper were run in part on the the FASRC Cannon cluster supported by the FAS Division of Science Research Computing Group at Harvard University and the cluster of the Max Planck Institute for the Physics of Complex Systems.","type":"journal_article","OA_place":"publisher","volume":4,"publication_identifier":{"eissn":["2835-8279"]},"ec_funded":1,"status":"public","oa":1,"year":"2026","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":5857833,"content_type":"application/pdf","checksum":"df9776422862d1d02c66d98e2d620849","date_updated":"2026-02-24T06:53:05Z","file_name":"2026_PRXLife_Olmeda.pdf","relation":"main_file","date_created":"2026-02-24T06:53:05Z","success":1,"creator":"dernst","access_level":"open_access","file_id":"21351"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","PlanS_conform":"1","doi":"10.1103/89bj-79g5","month":"02","DOAJ_listed":"1","article_type":"original","department":[{"_id":"EdHa"}],"intvolume":"         4","day":"09","oa_version":"Published Version","article_processing_charge":"Yes","_id":"21275","citation":{"chicago":"Olmeda, Fabrizio, Misha Gupta, Onurcan Bektas, and Steffen Rulands. “Spatiotemporal Patterns of Active Epigenetic Turnover.” <i>PRX Life</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/89bj-79g5\">https://doi.org/10.1103/89bj-79g5</a>.","ama":"Olmeda F, Gupta M, Bektas O, Rulands S. Spatiotemporal patterns of active epigenetic turnover. <i>PRX Life</i>. 2026;4. doi:<a href=\"https://doi.org/10.1103/89bj-79g5\">10.1103/89bj-79g5</a>","apa":"Olmeda, F., Gupta, M., Bektas, O., &#38; Rulands, S. (2026). Spatiotemporal patterns of active epigenetic turnover. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/89bj-79g5\">https://doi.org/10.1103/89bj-79g5</a>","mla":"Olmeda, Fabrizio, et al. “Spatiotemporal Patterns of Active Epigenetic Turnover.” <i>PRX Life</i>, vol. 4, 013018, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/89bj-79g5\">10.1103/89bj-79g5</a>.","short":"F. Olmeda, M. Gupta, O. Bektas, S. Rulands, PRX Life 4 (2026).","ieee":"F. Olmeda, M. Gupta, O. Bektas, and S. Rulands, “Spatiotemporal patterns of active epigenetic turnover,” <i>PRX Life</i>, vol. 4. American Physical Society, 2026.","ista":"Olmeda F, Gupta M, Bektas O, Rulands S. 2026. Spatiotemporal patterns of active epigenetic turnover. PRX Life. 4, 013018."},"quality_controlled":"1","ddc":["570"],"publisher":"American Physical Society","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-02-24T06:53:05Z","publication":"PRX Life","date_published":"2026-02-09T00:00:00Z","OA_type":"gold","corr_author":"1","article_number":"013018","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"author":[{"first_name":"Fabrizio","last_name":"Olmeda","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","full_name":"Olmeda, Fabrizio"},{"full_name":"Gupta, Misha","first_name":"Misha","last_name":"Gupta"},{"first_name":"Onurcan","last_name":"Bektas","full_name":"Bektas, Onurcan"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"}],"title":"Spatiotemporal patterns of active epigenetic turnover","date_created":"2026-02-17T08:17:53Z","date_updated":"2026-02-24T06:54:32Z","abstract":[{"lang":"eng","text":"DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives rise to a biochemical cycle and active turnover of DNA methylation. While the ensuing biochemical oscillations have been implicated in the regulation of cell differentiation, their functional role and spatiotemporal dynamics are unknown. In this work, we demonstrate that chromatin-mediated coupling between these local biochemical cycles can lead to the emergence of phase-locked domains, regions of locally synchronized turnover activity, whose coarsening is arrested by genomic heterogeneity. We introduce a minimal model based on stochastic oscillators with constrained long-range and nonreciprocal interactions, shaped by the local chromatin organization. Through a combination of analytical theory and stochastic simulations, we predict both the degree of synchronization and the typical size of emergent phase-locked domains. We qualitatively test these predictions using single-cell sequencing data. Our results show that DNA methylation turnover exhibits surprisingly rich spatiotemporal patterns that may be used by cells to control cell differentiation."}]},{"file_date_updated":"2026-02-24T06:57:44Z","publication":"PRX Life","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","article_number":"017001","date_published":"2026-01-23T00:00:00Z","OA_type":"gold","title":"Marr's three levels for embryonic development: Information, dynamical systems, gene networks","author":[{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"date_created":"2026-02-17T08:29:10Z","external_id":{"arxiv":["2510.24536"]},"project":[{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"abstract":[{"lang":"eng","text":"Developmental patterning comprises processes that range from purely instructed, where external signals specify cell fates, to fully self-organized, where spatial patterns emerge autonomously through cellular interactions. We propose that both extremes—as well as the continuum of intermediate cases—can be conceptualized as information-processing systems, whose operation can be described using “Marr's three levels of analysis”: the computational problem being solved, the algorithms employed, and their molecular implementation. At the first level, we argue that normative theories, such as information-theoretic optimization principles, provide a formalization of the computational problem. At the second level, we show how simplified information-processing architectures provide a framework for developmental algorithms, which are formalized mathematically using dynamical systems theory. At the third level, the implementation of developmental algorithms is described by mechanistic biophysical and gene regulatory network models."}],"date_updated":"2026-02-24T07:00:16Z","department":[{"_id":"GaTk"}],"intvolume":"         4","article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes","_id":"21282","day":"23","ddc":["570"],"quality_controlled":"1","citation":{"apa":"Brückner, D., &#38; Tkačik, G. (2026). Marr’s three levels for embryonic development: Information, dynamical systems, gene networks. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/fdcf-dkws\">https://doi.org/10.1103/fdcf-dkws</a>","ama":"Brückner D, Tkačik G. Marr’s three levels for embryonic development: Information, dynamical systems, gene networks. <i>PRX Life</i>. 2026;4. doi:<a href=\"https://doi.org/10.1103/fdcf-dkws\">10.1103/fdcf-dkws</a>","chicago":"Brückner, David, and Gašper Tkačik. “Marr’s Three Levels for Embryonic Development: Information, Dynamical Systems, Gene Networks.” <i>PRX Life</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/fdcf-dkws\">https://doi.org/10.1103/fdcf-dkws</a>.","ista":"Brückner D, Tkačik G. 2026. Marr’s three levels for embryonic development: Information, dynamical systems, gene networks. PRX Life. 4, 017001.","short":"D. Brückner, G. Tkačik, PRX Life 4 (2026).","mla":"Brückner, David, and Gašper Tkačik. “Marr’s Three Levels for Embryonic Development: Information, Dynamical Systems, Gene Networks.” <i>PRX Life</i>, vol. 4, 017001, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/fdcf-dkws\">10.1103/fdcf-dkws</a>.","ieee":"D. Brückner and G. Tkačik, “Marr’s three levels for embryonic development: Information, dynamical systems, gene networks,” <i>PRX Life</i>, vol. 4. American Physical Society, 2026."},"publisher":"American Physical Society","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2026-02-24T06:57:44Z","relation":"main_file","date_updated":"2026-02-24T06:57:44Z","file_name":"2026_PRXLife_Brueckner.pdf","file_size":1147994,"content_type":"application/pdf","checksum":"99ef02dd741c4536eeefd12d409d5269","file_id":"21352","access_level":"open_access","creator":"dernst","success":1}],"language":[{"iso":"eng"}],"oa":1,"year":"2026","has_accepted_license":"1","PlanS_conform":"1","doi":"10.1103/fdcf-dkws","month":"01","DOAJ_listed":"1","arxiv":1,"acknowledgement":"We thank Edouard Hannezo, Anna Kicheva, Fridtjof Brauns, and all members of the Brückner and Tkačik groups for feedback and inspiring discussions. This work was supported in part by European Research Council ERC-2023-SyG “Dynatrans” Grant No. 101118866 (G.T.). This work was conducted while visiting the Okinawa Institute of Science and Technology (OIST) through the Theoretical Sciences Visiting Program (TSVP); at the Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02; and at Lucullus, Vienna.","type":"journal_article","OA_place":"publisher","volume":4,"status":"public","publication_identifier":{"eissn":["2835-8279"]}},{"publication":"bioRxiv","language":[{"iso":"eng"}],"oa":1,"publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","doi":"10.64898/2026.02.11.705284","date_published":"2026-02-11T00:00:00Z","OA_type":"green","author":[{"last_name":"Polat Haas","first_name":"Feyza","full_name":"Polat Haas, Feyza"},{"full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","first_name":"Ana","last_name":"Villalba Requena"},{"last_name":"Rusina","first_name":"Polina","full_name":"Rusina, Polina"},{"full_name":"Gopalan, Anusha","first_name":"Anusha","last_name":"Gopalan"},{"last_name":"Fritz","first_name":"Hector","full_name":"Fritz, Hector"},{"last_name":"Akhmetkaliyev","first_name":"Azamat","full_name":"Akhmetkaliyev, Azamat"},{"full_name":"Ruehle, Frank","first_name":"Frank","last_name":"Ruehle"},{"full_name":"Einsiedel, Anna","last_name":"Einsiedel","first_name":"Anna"},{"first_name":"Anna","last_name":"Szczepinska","full_name":"Szczepinska, Anna"},{"full_name":"Kielisch, Fridolin","first_name":"Fridolin","last_name":"Kielisch"},{"first_name":"Jia-Xuan","last_name":"Chen","full_name":"Chen, Jia-Xuan"},{"first_name":"Susanne","last_name":"Nguyen","full_name":"Nguyen, Susanne"},{"full_name":"Schmidlin, Thierry","first_name":"Thierry","last_name":"Schmidlin"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"last_name":"Bailicata","first_name":"M. Felicia","full_name":"Bailicata, M. Felicia"},{"last_name":"Keller Valsecchi","first_name":"Claudia Isabelle","full_name":"Keller Valsecchi, Claudia Isabelle"}],"title":"The splicing paralogues SNRPB and SNRPN control differential metabolic states.","date_created":"2026-02-17T11:35:59Z","month":"02","abstract":[{"text":"Gene duplication underlies evolutionary innovation, yet many paralogues remain highly similar, raising questions about their functional divergence and physiological relevance. The spliceosomal Sm core protein SNRPB and its mammalian-specific paralogue SNRPN share over 90% sequence identity, but their distinct expression patterns - SNRPB being ubiquitous and SNRPN confined to the brain - suggest specialized functions. Why mammals have two different spliceosomes has remained obscure. Here, we generated isogenic human cell lines expressing ectopically either SNRPB or SNRPN exclusively and found that SNRPN stabilizes transcripts involved in energy metabolism and mitochondrial function, leading to increased mitochondrial abundance and oxygen consumption. Despite similar spliceosomal interactomes, SNRPN more strongly associates with the PRMT5 methylosome complex and exhibits dynamic arginine methylation in its C-terminal region that is sensitive to translation inhibition and amino acid availability. The SNRPN-dependent transcriptome responds to translation inhibition by stabilizing long, intron-rich genes involved in amino acid and energy metabolism. Our findings reveal a nutrient-sensitive, methylation-dependent mechanism that differentiates the two paralogues. This suggests that SNRPN functions as a metabolic-specialized spliceosomal subunit thereby providing tissue-specific adaptation of RNA processing in mammals.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.64898/2026.02.11.705284","open_access":"1"}],"date_updated":"2026-02-23T11:03:33Z","acknowledgement":"We thank Oliver Mühlemann and Alex Hofer (University of Bern) for sharing SMG inhibitors\r\nand for their expertise in nonsense-mediated mRNA decay and Maria Hondele for critical\r\nreading of the manuscript draft. We also thank the IMB Genomics Core Facility for assistance\r\nwith library preparation and sequencing, Martin Möckel and the IMB Protein Production Core\r\nFacility for providing enzymes used in this work, Marton Gelleri together with the IMB\r\nMicroscopy Core Facility for support with microscopy and FRAP experiments, Jasmin Cartano\r\nfor proteomics sample processing and the IMB Flow Cytometry Core Facility for support. In\r\naddition, we thank the Imaging Core Facility (IMCF) and the FACS Core Facility at the\r\nBiozentrum, University of Basel, for technical assistance. CIKV acknowledges funding by the\r\nDeutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Individual Grant\r\nProject no. 513744403, Scientific Network Grant Project no. 531902894, GRK2526 “Genevo”\r\n- Project no. 407023052”, GRK2859 (“4R”) - Project no. 491145305, Forschungsinitiative\r\nRheinland-Pfalz (ReALity), the EMBO Young Investigator Program (5795), institutional\r\nfunding from the Institute of Molecular Biology and funds from the Kanton Basel-Stadt and\r\nBasel-Land provided to the Biozentrum of the University Basel. J.H.G.F.G. was part of the\r\n‘Science of Healthy Ageing Research Programme’ (SHARP) initiative funded by RhinelandPalatinate’s Ministry of Science, Education and Culture. PR is funded by the Biozentrum PhD\r\nFellowships Program. MFB received financial support from the intramural High Potentials\r\nGrant program of the University Medical Center Mainz, Forschungsinitiative Rheinland-Pfalz\r\n(ReALity) and Stiftungen zugunsten der Medizinischen Fakultät der LMU Klinikum (26069).\r\nInstruments in the IMB core facilities were supported by funds from the DFG: Laser Scanning\r\nConfocal (Leica Stellaris 8 Falcon, funded by the DFG - Project #497669232), Orbitrap Astral system (funded by the DFG - Project #524805621) and BD LSRFortessa SOPR is funded by\r\nthe DFG - Project #210253511.\r\n","department":[{"_id":"SiHi"}],"oa_version":"Preprint","article_processing_charge":"No","_id":"21290","type":"preprint","day":"11","OA_place":"repository","citation":{"ama":"Polat Haas F, Villalba Requena A, Rusina P, et al. The splicing paralogues SNRPB and SNRPN control differential metabolic states. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.64898/2026.02.11.705284\">10.64898/2026.02.11.705284</a>","apa":"Polat Haas, F., Villalba Requena, A., Rusina, P., Gopalan, A., Fritz, H., Akhmetkaliyev, A., … Keller Valsecchi, C. I. (n.d.). The splicing paralogues SNRPB and SNRPN control differential metabolic states. <i>bioRxiv</i>. <a href=\"https://doi.org/10.64898/2026.02.11.705284\">https://doi.org/10.64898/2026.02.11.705284</a>","chicago":"Polat Haas, Feyza, Ana Villalba Requena, Polina Rusina, Anusha Gopalan, Hector Fritz, Azamat Akhmetkaliyev, Frank Ruehle, et al. “The Splicing Paralogues SNRPB and SNRPN Control Differential Metabolic States.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.64898/2026.02.11.705284\">https://doi.org/10.64898/2026.02.11.705284</a>.","ista":"Polat Haas F, Villalba Requena A, Rusina P, Gopalan A, Fritz H, Akhmetkaliyev A, Ruehle F, Einsiedel A, Szczepinska A, Kielisch F, Chen J-X, Nguyen S, Schmidlin T, Hippenmeyer S, Bailicata MF, Keller Valsecchi CI. The splicing paralogues SNRPB and SNRPN control differential metabolic states. bioRxiv, <a href=\"https://doi.org/10.64898/2026.02.11.705284\">10.64898/2026.02.11.705284</a>.","ieee":"F. Polat Haas <i>et al.</i>, “The splicing paralogues SNRPB and SNRPN control differential metabolic states.,” <i>bioRxiv</i>. .","short":"F. Polat Haas, A. Villalba Requena, P. Rusina, A. Gopalan, H. Fritz, A. Akhmetkaliyev, F. Ruehle, A. Einsiedel, A. Szczepinska, F. Kielisch, J.-X. Chen, S. Nguyen, T. Schmidlin, S. Hippenmeyer, M.F. Bailicata, C.I. Keller Valsecchi, BioRxiv (n.d.).","mla":"Polat Haas, Feyza, et al. “The Splicing Paralogues SNRPB and SNRPN Control Differential Metabolic States.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.64898/2026.02.11.705284\">10.64898/2026.02.11.705284</a>."},"status":"public"},{"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2026","doi":"10.1038/s41567-025-03166-3","has_accepted_license":"1","PlanS_conform":"1","month":"02","arxiv":1,"acknowledgement":"The work was supported by the Simons Foundation (grant number 662960, to B.H.). Open access funding provided by Institute of Science and Technology (IST Austria).","type":"journal_article","OA_place":"publisher","status":"public","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication":"Nature Physics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"epub_ahead","corr_author":"1","OA_type":"hybrid","date_published":"2026-02-17T00:00:00Z","date_created":"2026-02-17T11:38:41Z","external_id":{"arxiv":["2311.11474"]},"title":"Discontinuous transition to shear flow turbulence","author":[{"orcid":"0000-0002-4843-6853","last_name":"Yang","first_name":"Bowen","full_name":"Yang, Bowen","id":"71b6ff4b-15b2-11ec-abd3-aef6b028cf7e"},{"last_name":"Zhuang","first_name":"Yi","full_name":"Zhuang, Yi","id":"3677B57C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gökhan","last_name":"Yalniz","orcid":"0000-0002-8490-9312","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan"},{"last_name":"Vasudevan","first_name":"Mukund","full_name":"Vasudevan, Mukund","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7173-4923","first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"abstract":[{"lang":"eng","text":"Depending on the type of flow, the transition to turbulence can take one of two forms: either turbulence arises from a sequence of instabilities or from the spatial proliferation of transiently chaotic domains, a process analogous to directed percolation. The former scenario is commonly referred to as a supercritical transition and frequently encountered in flows destabilized by body forces, whereas the latter subcritical transition is common in shear flows. Both cases are inherently continuous in a sense that the transformation from ordered laminar to fully turbulent fluid motion is only accomplished gradually with flow speed. Here we show that these established transition types do not account for the more general setting of shear flows subject to body forces. The combination of the two continuous scenarios leads to the attenuation of spatial coupling; with increasing forcing amplitude, the transition becomes increasingly sharp and eventually discontinuous. We argue that the suppression of laminar–turbulent coexistence and the approach towards a discontinuous phase transition potentially apply to a broad range of situations including flows subject to, for example, buoyancy, centrifugal or electromagnetic forces."}],"date_updated":"2026-02-23T11:36:46Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"article_type":"original","scopus_import":"1","_id":"21295","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","day":"17","ddc":["532"],"citation":{"short":"B. Yang, Y. Zhuang, G. Yalniz, M. Vasudevan, E. Marensi, B. Hof, Nature Physics (2026).","mla":"Yang, Bowen, et al. “Discontinuous Transition to Shear Flow Turbulence.” <i>Nature Physics</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41567-025-03166-3\">10.1038/s41567-025-03166-3</a>.","ieee":"B. Yang, Y. Zhuang, G. Yalniz, M. Vasudevan, E. Marensi, and B. Hof, “Discontinuous transition to shear flow turbulence,” <i>Nature Physics</i>. Springer Nature, 2026.","ista":"Yang B, Zhuang Y, Yalniz G, Vasudevan M, Marensi E, Hof B. 2026. Discontinuous transition to shear flow turbulence. Nature Physics.","chicago":"Yang, Bowen, Yi Zhuang, Gökhan Yalniz, Mukund Vasudevan, Elena Marensi, and Björn Hof. “Discontinuous Transition to Shear Flow Turbulence.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-025-03166-3\">https://doi.org/10.1038/s41567-025-03166-3</a>.","apa":"Yang, B., Zhuang, Y., Yalniz, G., Vasudevan, M., Marensi, E., &#38; Hof, B. (2026). Discontinuous transition to shear flow turbulence. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03166-3\">https://doi.org/10.1038/s41567-025-03166-3</a>","ama":"Yang B, Zhuang Y, Yalniz G, Vasudevan M, Marensi E, Hof B. Discontinuous transition to shear flow turbulence. <i>Nature Physics</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41567-025-03166-3\">10.1038/s41567-025-03166-3</a>"},"quality_controlled":"1","publisher":"Springer Nature"}]