[{"author":[{"orcid":"0000-0002-6246-1465","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Goran","full_name":"Arnqvist, Goran","last_name":"Arnqvist"}],"day":"23","article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"OA_type":"green","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2025.04.09.647826","open_access":"1"}],"citation":{"chicago":"Khudiakova, Kseniia, Nicholas H Barton, and Goran Arnqvist. “Sign Epistasis Extends the Effects of Balancing Selection on Genetic Diversity.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.04.09.647826\">https://doi.org/10.1101/2025.04.09.647826</a>.","ama":"Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of balancing selection on genetic diversity. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.04.09.647826\">10.1101/2025.04.09.647826</a>","ieee":"K. Khudiakova, N. H. Barton, and G. Arnqvist, “Sign epistasis extends the effects of balancing selection on genetic diversity,” <i>bioRxiv</i>. .","mla":"Khudiakova, Kseniia, et al. “Sign Epistasis Extends the Effects of Balancing Selection on Genetic Diversity.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.04.09.647826\">10.1101/2025.04.09.647826</a>.","apa":"Khudiakova, K., Barton, N. H., &#38; Arnqvist, G. (n.d.). Sign epistasis extends the effects of balancing selection on genetic diversity. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.04.09.647826\">https://doi.org/10.1101/2025.04.09.647826</a>","short":"K. Khudiakova, N.H. Barton, G. Arnqvist, BioRxiv (n.d.).","ista":"Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of balancing selection on genetic diversity. bioRxiv, <a href=\"https://doi.org/10.1101/2025.04.09.647826\">10.1101/2025.04.09.647826</a>."},"abstract":[{"text":"Balancing selection, a form of selection that maintains genetic diversity, is difficult to detect, and the importance of balancing selection for the maintenance of genetic variation may be larger than often assumed. We model the possibility that the diversity-promoting effects of balancing selection extend to other loci that show sign epistasis with a locus under balancing selection. Rather than focusing on overdominance, as was done in previous efforts, we explore the effects of negative frequency dependence and show that this has important effects on the conditions under which the diversity-promoting effect of epistasis can occur in diploids. Our results show that not only recombination rate but also the dominance of sign epistasis are key parameters that determine the maintenance of polymorphism beyond the locus under direct balancing selection. We suggest that the effect we explore may play a significant role, especially when balancing selection acts on major effect loci.","lang":"eng"}],"OA_place":"repository","month":"04","publication":"bioRxiv","date_published":"2026-04-23T00:00:00Z","date_updated":"2026-06-12T12:43:34Z","acknowledgement":"This work was funded by grants from the Swedish Research Council (2023-03730 to G.A.) and the DOC fellowship from the Austrian Academy of Science (26293 to K.K.).","doi":"10.1101/2025.04.09.647826","year":"2026","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-06-09T12:26:11Z","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"21918"}]},"project":[{"name":"The impact of deleterious mutations on small populations","grant_number":"26293","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8"}],"title":"Sign epistasis extends the effects of balancing selection on genetic 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Rust library for analyzing dendritic structures using quadric matrices. This project provides efficient tools for representing dendritic trees, computing quadric error metrics, and visualizing eigenvalue distributions on hexagonal plots.\r\n\r\nThis library implements quadric-based geometric analysis of dendritic structures, commonly found in neuroscience applications. Key features include:\r\n\r\nTree data structures: Hierarchical vertex and edge representations for dendritic trees\r\nQuadric matrices: Computation of quadric error metrics for edges and vertices\r\nVisualisation: Hexagonal plot generation using NormPolar transformations\r\nInteractive tools: Desktop application with plotting capabilities","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","citation":{"mla":"Bokor Bleile, Yossi, and Emanuele Cortinovis. <i>Quadrix</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21971\">10.15479/AT-ISTA-21971</a>.","apa":"Bokor Bleile, Y., &#38; Cortinovis, E. (2026). Quadrix. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21971\">https://doi.org/10.15479/AT-ISTA-21971</a>","ista":"Bokor Bleile Y, Cortinovis E. 2026. Quadrix, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21971\">10.15479/AT-ISTA-21971</a>.","short":"Y. Bokor Bleile, E. Cortinovis, (2026).","chicago":"Bokor Bleile, Yossi, and Emanuele Cortinovis. “Quadrix.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21971\">https://doi.org/10.15479/AT-ISTA-21971</a>.","ama":"Bokor Bleile Y, Cortinovis E. Quadrix. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21971\">10.15479/AT-ISTA-21971</a>","ieee":"Y. Bokor Bleile and E. Cortinovis, “Quadrix.” Institute of Science and Technology Austria, 2026."},"day":"15","tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"author":[{"orcid":"0000-0002-4861-9174","id":"920a7385-7995-11ef-9bfd-8c434cd8f3c2","first_name":"Yossi","last_name":"Bleile","full_name":"Bleile, Yossi"},{"first_name":"Emanuele","full_name":"Cortinovis, Emanuele","last_name":"Cortinovis"}]},{"scopus_import":"1","file_date_updated":"2026-06-16T09:11:35Z","department":[{"_id":"LaVe"},{"_id":"GradSch"}],"ddc":["540"],"status":"public","_id":"21980","corr_author":"1","date_updated":"2026-06-16T09:13:30Z","oa":1,"intvolume":"        26","publisher":"American Chemical Society","month":"06","OA_place":"publisher","page":"7429–7434","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","volume":26,"quality_controlled":"1","citation":{"chicago":"Gulyaev, Artem, Jyotisman Hazarika, Zhen-Fei Liu, and Latha Venkataraman. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” <i>Nano Letters</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">https://doi.org/10.1021/acs.nanolett.6c01462</a>.","ama":"Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. <i>Nano Letters</i>. 2026;26(22):7429–7434. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">10.1021/acs.nanolett.6c01462</a>","ieee":"A. Gulyaev, J. Hazarika, Z.-F. Liu, and L. Venkataraman, “A computationally efficient and accurate method for predicting conductance of single-molecule junctions,” <i>Nano Letters</i>, vol. 26, no. 22. American Chemical Society, pp. 7429–7434, 2026.","apa":"Gulyaev, A., Hazarika, J., Liu, Z.-F., &#38; Venkataraman, L. (2026). A computationally efficient and accurate method for predicting conductance of single-molecule junctions. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">https://doi.org/10.1021/acs.nanolett.6c01462</a>","mla":"Gulyaev, Artem, et al. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” <i>Nano Letters</i>, vol. 26, no. 22, American Chemical Society, 2026, pp. 7429–7434, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">10.1021/acs.nanolett.6c01462</a>.","short":"A. Gulyaev, J. Hazarika, Z.-F. Liu, L. Venkataraman, Nano Letters 26 (2026) 7429–7434.","ista":"Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. 2026. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 26(22), 7429–7434."},"has_accepted_license":"1","title":"A computationally efficient and accurate method for predicting conductance of single-molecule junctions","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","article_type":"letter_note","acknowledgement":"This work was supported primarily by the Institute of Science and Technology Austria. L.V. was supported in part by the National Science Foundation (No. NSF-DMR 2241180). Z.-F.L. was supported by an NSF CAREER Award, No. DMR-2044552 and an Alfred P. Sloan Research Fellowship, No. FG-2024-21750.","doi":"10.1021/acs.nanolett.6c01462","year":"2026","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-06-10T07:27:19Z","abstract":[{"lang":"eng","text":"Despite significant progress in the field of molecular electronics over the last two decades, the quantitative prediction of metal-molecule-metal junction conductance remains a challenge. The standard computational framework combines density functional theory (DFT) with nonequilibrium Green’s functions (NEGF) using low-rung exchange-correlation functionals such as PBE, which overestimate the conductances. More advanced correction methods exist but require complex workflows and high computational cost, limiting their accessibility. Here, we introduce a physically motivated approach that approximates results obtained with high-rung functionals. Our method fits the PBE-calculated transmission to a Breit-Wigner form and subsequently refines the fit parameters using molecular orbital energies and metal densities of states computed for the isolated subsystems with high-rung functionals. This approach is applicable to a broad range of molecular junctions yielding conductance values in quantitative agreement with experiments. Our approach is simple, low-cost, and accurate, making it well-suited for routine and large-scale prediction of single-molecule junction conductance."}],"publication":"Nano Letters","external_id":{"pmid":["42223342"]},"file":[{"file_name":"2026_NanoLetters_Gulyaev.pdf","file_id":"22013","access_level":"open_access","relation":"main_file","checksum":"897551374cac28e0db26dcb0b676b8e7","success":1,"date_created":"2026-06-16T09:11:35Z","content_type":"application/pdf","file_size":3362800,"creator":"dernst","date_updated":"2026-06-16T09:11:35Z"}],"date_published":"2026-06-01T00:00:00Z","author":[{"last_name":"Gulyaev","full_name":"Gulyaev, Artem","id":"83ed7901-7380-11f0-bf20-a0788d5e654d","first_name":"Artem"},{"last_name":"Hazarika","full_name":"Hazarika, Jyotisman","id":"d87714c4-663d-11f0-bd06-caece19833e5","first_name":"Jyotisman","orcid":"0009-0007-2542-7878"},{"first_name":"Zhen-Fei","full_name":"Liu, Zhen-Fei","last_name":"Liu"},{"orcid":"0000-0002-6957-6089","last_name":"Venkataraman","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha"}],"day":"01","PlanS_conform":"1","pmid":1,"oa_version":"Published Version","issue":"22"},{"year":"2026","article_number":"105878","publication_identifier":{"issn":["0393-0440"],"eissn":["1879-1662"]},"doi":"10.1016/j.geomphys.2026.105878","date_created":"2026-06-10T07:29:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"title":"An easier way to compute 2-cocycles coming from a reduction for semidirect products","type":"journal_article","article_type":"original","publication_status":"epub_ahead","day":"21","PlanS_conform":"1","author":[{"full_name":"Goncharov, Viacheslav","last_name":"Goncharov","first_name":"Viacheslav","id":"8a0e2993-7114-11f0-b60e-f50e633649d8"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.geomphys.2026.105878","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"For Hamiltonian actions of semidirect products G = FxH, we study 2-cocycles arising from residual Hamiltonian actions of F on Hamiltonian reductions for H. The motivation comes from the study of Teichmüller spaces for surfaces with boundary, which carry Hamiltonian actions of the Virasoro algebra. In this paper, we give a general setup for the problem, and we suggest an easier way to obtain the Gelfand-Fuchs 2-cocycles for Hamiltonian actions on Teichmüller spaces.","lang":"eng"}],"external_id":{"arxiv":["2509.16169"]},"date_published":"2026-05-21T00:00:00Z","publication":"Journal of Geometry and Physics","date_updated":"2026-06-16T09:23:39Z","oa":1,"ddc":["000"],"department":[{"_id":"GradSch"}],"scopus_import":"1","arxiv":1,"_id":"21981","corr_author":"1","status":"public","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","citation":{"mla":"Goncharov, Viacheslav. “An Easier Way to Compute 2-Cocycles Coming from a Reduction for Semidirect Products.” <i>Journal of Geometry and Physics</i>, vol. 227, 105878, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.geomphys.2026.105878\">10.1016/j.geomphys.2026.105878</a>.","apa":"Goncharov, V. (2026). An easier way to compute 2-cocycles coming from a reduction for semidirect products. <i>Journal of Geometry and Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.geomphys.2026.105878\">https://doi.org/10.1016/j.geomphys.2026.105878</a>","short":"V. Goncharov, Journal of Geometry and Physics 227 (2026).","ista":"Goncharov V. 2026. An easier way to compute 2-cocycles coming from a reduction for semidirect products. Journal of Geometry and Physics. 227, 105878.","chicago":"Goncharov, Viacheslav. “An Easier Way to Compute 2-Cocycles Coming from a Reduction for Semidirect Products.” <i>Journal of Geometry and Physics</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.geomphys.2026.105878\">https://doi.org/10.1016/j.geomphys.2026.105878</a>.","ama":"Goncharov V. An easier way to compute 2-cocycles coming from a reduction for semidirect products. <i>Journal of Geometry and Physics</i>. 2026;227. doi:<a href=\"https://doi.org/10.1016/j.geomphys.2026.105878\">10.1016/j.geomphys.2026.105878</a>","ieee":"V. Goncharov, “An easier way to compute 2-cocycles coming from a reduction for semidirect products,” <i>Journal of Geometry and Physics</i>, vol. 227. Elsevier, 2026."},"volume":227,"quality_controlled":"1","OA_type":"hybrid","publisher":"Elsevier","intvolume":"       227","OA_place":"publisher","month":"05"},{"intvolume":"       113","publisher":"American Physical Society","OA_place":"publisher","month":"05","article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":113,"OA_type":"hybrid","quality_controlled":"1","has_accepted_license":"1","citation":{"apa":"Diaz Melian, V. L., Lenton, I. C., Binysh, J., Souslov, A., &#38; Waitukaitis, S. R. (2026). Geometry of the vapor layer under a Leidenfrost hydrogel sphere. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/m7gr-2t6j\">https://doi.org/10.1103/m7gr-2t6j</a>","mla":"Diaz Melian, Vicente L., et al. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” <i>Physical Review E</i>, vol. 113, no. 5, L053502, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/m7gr-2t6j\">10.1103/m7gr-2t6j</a>.","short":"V.L. Diaz Melian, I.C. Lenton, J. Binysh, A. Souslov, S.R. Waitukaitis, Physical Review E 113 (2026).","ista":"Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. 2026. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 113(5), L053502.","ama":"Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. <i>Physical Review E</i>. 2026;113(5). doi:<a href=\"https://doi.org/10.1103/m7gr-2t6j\">10.1103/m7gr-2t6j</a>","chicago":"Diaz Melian, Vicente L, Isaac C Lenton, Jack Binysh, Anton Souslov, and Scott R Waitukaitis. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” <i>Physical Review E</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/m7gr-2t6j\">https://doi.org/10.1103/m7gr-2t6j</a>.","ieee":"V. L. Diaz Melian, I. C. Lenton, J. Binysh, A. Souslov, and S. R. Waitukaitis, “Geometry of the vapor layer under a Leidenfrost hydrogel sphere,” <i>Physical Review E</i>, vol. 113, no. 5. American Physical Society, 2026."},"scopus_import":"1","arxiv":1,"ddc":["530"],"department":[{"_id":"ScWa"},{"_id":"GradSch"}],"file_date_updated":"2026-06-16T11:21:53Z","status":"public","_id":"21982","corr_author":"1","date_updated":"2026-06-16T11:24:18Z","oa":1,"abstract":[{"lang":"eng","text":"A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces."}],"publication":"Physical Review E","external_id":{"arxiv":["2507.04982"]},"file":[{"access_level":"open_access","relation":"main_file","file_name":"2026_PhysicalReviewE_DiazMelian.pdf","file_id":"22014","checksum":"902cc8d177c8d3ae9cfe07c30375c9a9","file_size":3173197,"success":1,"content_type":"application/pdf","date_created":"2026-06-16T11:21:53Z","date_updated":"2026-06-16T11:21:53Z","creator":"dernst"}],"date_published":"2026-05-14T00:00:00Z","author":[{"id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L","last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L"},{"full_name":"Lenton, Isaac C","last_name":"Lenton","first_name":"Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb","orcid":"0000-0002-5010-6984"},{"first_name":"Jack","full_name":"Binysh, Jack","last_name":"Binysh"},{"last_name":"Souslov","full_name":"Souslov, Anton","first_name":"Anton"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"day":"14","PlanS_conform":"1","oa_version":"Published Version","issue":"5","type":"journal_article","title":"Geometry of the vapor layer under a Leidenfrost hydrogel sphere","language":[{"iso":"eng"}],"publication_status":"published","article_type":"letter_note","doi":"10.1103/m7gr-2t6j","acknowledgement":"This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop and the Scientific Computing Facility. J.B. acknowledges funding from the European Union's Horizon research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101106500.","year":"2026","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"article_number":"L053502","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-06-10T07:36:41Z"},{"date_updated":"2026-06-16T12:37:02Z","oa":1,"arxiv":1,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"CaGu"},{"_id":"GaTk"}],"ddc":["570"],"status":"public","_id":"21983","corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","volume":99,"OA_type":"hybrid","quality_controlled":"1","citation":{"mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99, 102483, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>.","apa":"Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>","short":"E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics &#38; Development 99 (2026).","ista":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics &#38; Development. 99, 102483.","ama":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. 2026;99. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>","chicago":"Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>.","ieee":"E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026."},"has_accepted_license":"1","intvolume":"        99","publisher":"Elsevier","month":"05","OA_place":"publisher","doi":"10.1016/j.gde.2026.102483","acknowledgement":"We thank Nick Barton and Noa Ottilie Borst for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.).","article_number":"102483","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-06-10T07:37:12Z","type":"journal_article","title":"Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps","language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","author":[{"orcid":"0000-0003-2977-7844","full_name":"Mascolo, Elia","last_name":"Mascolo","first_name":"Elia","id":"776a6ed0-a053-11f0-8635-80b95e0e0d53"},{"full_name":"Körei, Reka E","last_name":"Körei","first_name":"Reka E","id":"50FDE43E-AA30-11E9-A72B-8A12E6697425"},{"full_name":"Herrera-Álvarez, Santiago","last_name":"Herrera-Álvarez","first_name":"Santiago"},{"last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Justin","full_name":"Crocker, Justin","last_name":"Crocker"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"PlanS_conform":"1","day":"09","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.gde.2026.102483","open_access":"1"}],"abstract":[{"text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology.","lang":"eng"}],"publication":"Current Opinion in Genetics & Development","external_id":{"arxiv":["2601.19681"]},"date_published":"2026-05-09T00:00:00Z"},{"oa_version":"Published Version","pmid":1,"issue":"6","author":[{"last_name":"Wu","full_name":"Wu, Bryan","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","first_name":"Bryan"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"day":"01","PlanS_conform":"1","publication":"Evolution","date_published":"2026-06-01T00:00:00Z","external_id":{"pmid":["41968110"]},"file":[{"file_id":"22015","file_name":"2026_Evolution_Wu.pdf","relation":"main_file","access_level":"open_access","checksum":"6d0f48566a7a36cb0c469e1968c9cb1c","content_type":"application/pdf","date_created":"2026-06-16T12:45:09Z","success":1,"file_size":2077781,"creator":"dernst","date_updated":"2026-06-16T12:45:09Z"}],"abstract":[{"lang":"eng","text":"Upon infecting a bacterial cell, temperate phages make a decision between lysis and lysogeny. While research has previously explored how phages sense environmental information to make this choice, most studies have focused on modelling known mechanisms that impact the decision. These mechanisms tell us what environmental information the phage does respond to, but not what it should respond to, as the signals sensed by the phage may serve as proxies for other sources of information. Here, using a mechanism-agnostic population dynamics model, we find that irreversible phage binding to lysogens protects sensitive host cells from infection. This results in lysogens being an additional environmental factor that the phage should sense while making its decision to undergo lysis or lysogeny. Using this model, we derive a responsive lysogeny probability for phages that respond to both cell and lysogen densities optimized towards invading phage-occupied systems, and show that it is more capable of invading and resisting invasion than phage with fixed lysogeny probabilities across different environmental conditions."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-06-10T07:38:12Z","doi":"10.1093/evolut/qpag061","acknowledgement":"We thank Fyodor Kondrashov and Gašper Tkačik for valuable input and guidance in building the model, and Stephen Abedon as well as the two anonymous reviewers for the comments provided on the manuscript.","year":"2026","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","article_type":"original","title":"Responsive lysogeny under nonproductive phage binding","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","volume":80,"OA_type":"hybrid","citation":{"ista":"Wu B, Guet CC. 2026. Responsive lysogeny under nonproductive phage binding. Evolution. 80(6), 1365–1373.","short":"B. Wu, C.C. Guet, Evolution 80 (2026) 1365–1373.","apa":"Wu, B., &#38; Guet, C. C. (2026). Responsive lysogeny under nonproductive phage binding. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpag061\">https://doi.org/10.1093/evolut/qpag061</a>","mla":"Wu, Bryan, and Calin C. Guet. “Responsive Lysogeny under Nonproductive Phage Binding.” <i>Evolution</i>, vol. 80, no. 6, Oxford University Press, 2026, pp. 1365–73, doi:<a href=\"https://doi.org/10.1093/evolut/qpag061\">10.1093/evolut/qpag061</a>.","ieee":"B. Wu and C. C. Guet, “Responsive lysogeny under nonproductive phage binding,” <i>Evolution</i>, vol. 80, no. 6. Oxford University Press, pp. 1365–1373, 2026.","chicago":"Wu, Bryan, and Calin C Guet. “Responsive Lysogeny under Nonproductive Phage Binding.” <i>Evolution</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/evolut/qpag061\">https://doi.org/10.1093/evolut/qpag061</a>.","ama":"Wu B, Guet CC. Responsive lysogeny under nonproductive phage binding. <i>Evolution</i>. 2026;80(6):1365-1373. doi:<a href=\"https://doi.org/10.1093/evolut/qpag061\">10.1093/evolut/qpag061</a>"},"has_accepted_license":"1","page":"1365-1373","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","month":"06","OA_place":"publisher","intvolume":"        80","publisher":"Oxford University Press","related_material":{"link":[{"url":"https://github.com/theguetlab/responsive-lysogeny","relation":"software"}]},"oa":1,"date_updated":"2026-06-16T12:46:02Z","status":"public","corr_author":"1","_id":"21985","scopus_import":"1","file_date_updated":"2026-06-16T12:45:09Z","department":[{"_id":"CaGu"}],"ddc":["570"]},{"OA_place":"publisher","month":"05","publisher":"American Chemical Society","intvolume":"         6","has_accepted_license":"1","citation":{"chicago":"York, Emma, and Latha Venkataraman. “Scanning Tunneling Microscope-Based Break-Junction Technique - A Tutorial.” <i>ACS Physical Chemistry Au</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acsphyschemau.6c00026\">https://doi.org/10.1021/acsphyschemau.6c00026</a>.","ama":"York E, Venkataraman L. Scanning tunneling microscope-based break-junction technique - A tutorial. <i>ACS Physical Chemistry Au</i>. 2026;6(3):408-424. doi:<a href=\"https://doi.org/10.1021/acsphyschemau.6c00026\">10.1021/acsphyschemau.6c00026</a>","ieee":"E. York and L. Venkataraman, “Scanning tunneling microscope-based break-junction technique - A tutorial,” <i>ACS Physical Chemistry Au</i>, vol. 6, no. 3. American Chemical Society, pp. 408–424, 2026.","apa":"York, E., &#38; Venkataraman, L. (2026). Scanning tunneling microscope-based break-junction technique - A tutorial. <i>ACS Physical Chemistry Au</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphyschemau.6c00026\">https://doi.org/10.1021/acsphyschemau.6c00026</a>","mla":"York, Emma, and Latha Venkataraman. “Scanning Tunneling Microscope-Based Break-Junction Technique - A Tutorial.” <i>ACS Physical Chemistry Au</i>, vol. 6, no. 3, American Chemical Society, 2026, pp. 408–24, doi:<a href=\"https://doi.org/10.1021/acsphyschemau.6c00026\">10.1021/acsphyschemau.6c00026</a>.","ista":"York E, Venkataraman L. 2026. Scanning tunneling microscope-based break-junction technique - A tutorial. ACS Physical Chemistry Au. 6(3), 408–424.","short":"E. York, L. Venkataraman, ACS Physical Chemistry Au 6 (2026) 408–424."},"volume":6,"OA_type":"gold","quality_controlled":"1","article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"408-424","corr_author":"1","_id":"21986","status":"public","ddc":["540"],"file_date_updated":"2026-06-19T06:31:16Z","department":[{"_id":"LaVe"}],"scopus_import":"1","oa":1,"date_updated":"2026-06-22T06:19:21Z","date_published":"2026-05-04T00:00:00Z","file":[{"creator":"dernst","date_updated":"2026-06-19T06:31:16Z","success":1,"content_type":"application/pdf","date_created":"2026-06-19T06:31:16Z","file_size":11251172,"checksum":"1dc16bdfb1c1cd3acde802f4350cb42a","file_name":"2026_ACSPhysChem_York.pdf","file_id":"22020","access_level":"open_access","relation":"main_file"}],"external_id":{"chemrxivid":["10.26434/chemrxiv.15000474/v1"],"pmid":["42221941"]},"publication":"ACS Physical Chemistry Au","abstract":[{"text":"Over the past two decades, molecular electronics has made significant progress toward discovering nanoscale analogues of conventional electronic components, largely enabled by the development of the scanning tunneling microscope-based break-junction (STM-BJ) technique. The STM-BJ technique enables precise and highly reproducible measurement of a molecule’s electronic transport properties, making it a powerful technique to explore physiochemical and electrochemical phenomena that are otherwise difficult to access. It has gained substantial popularity in the past 20 years, with experiments becoming increasingly diverse and sophisticated. Despite the wealth of literature, an accessible, practical guide to performing STM-BJ experiments and interpreting the data is largely absent. This tutorial includes a brief background into the development of STM-BJ measurements, followed by detailed explanations of instrumentation, data collection, statistical analysis, variations on standard experiments, and some troubleshooting methods. It is aimed at researchers looking to begin or improve STM-BJ studies in their laboratories, graduate students and postdoctoral researchers learning the technique, and readers seeking to critically evaluate the growing body of STM-BJ literature.","lang":"eng"}],"das_tickbox":"1","issue":"3","pmid":1,"oa_version":"Published Version","PlanS_conform":"1","day":"04","author":[{"first_name":"Emma","id":"08dde91e-8e0a-11f0-9d7d-9e8d80864f16","full_name":"York, Emma","last_name":"York"},{"orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","last_name":"Venkataraman","full_name":"Venkataraman, Latha"}],"article_type":"original","DOAJ_listed":"1","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","title":"Scanning tunneling microscope-based break-junction technique - A tutorial","date_created":"2026-06-10T07:38:41Z","chemrxivid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2694-2445"]},"year":"2026","acknowledgement":"We thank Michael Inkpen, Timothy Su, Masha Kamenetska, and Wanzhuo Shi for comments and Jyotisman Hazarika for data collection. This work was supported in part by the National Science Foundation (NSF-DMR 2241180) and by the Institute of Science and Technology Austria.","doi":"10.1021/acsphyschemau.6c00026"},{"article_number":"101277","year":"2026","publication_identifier":{"eissn":["2666-979X"]},"doi":"10.1016/j.xgen.2026.101277","acknowledgement":"We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","date_created":"2026-06-10T07:39:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"type":"journal_article","title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population","article_type":"original","DOAJ_listed":"1","publication_status":"inpress","day":"09","author":[{"first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","full_name":"Krätschmer, Ilse","last_name":"Krätschmer","orcid":"0000-0002-5636-9259"},{"last_name":"Hegemann","full_name":"Hegemann, Laura","first_name":"Laura"},{"first_name":"Robin J.","full_name":"Hofmeister, Robin J.","last_name":"Hofmeister"},{"full_name":"Corfield, Elizabeth C.","last_name":"Corfield","first_name":"Elizabeth C."},{"first_name":"Mahdi","full_name":"Mahmoudi, Mahdi","last_name":"Mahmoudi"},{"full_name":"Delaneau, Olivier","last_name":"Delaneau","first_name":"Olivier"},{"first_name":"Ole A.","full_name":"Andreassen, Ole A.","last_name":"Andreassen"},{"last_name":"Campbell","full_name":"Campbell, Archie","first_name":"Archie"},{"first_name":"Caroline","full_name":"Hayward, Caroline","last_name":"Hayward"},{"first_name":"Riccardo E.","full_name":"Marioni, Riccardo E.","last_name":"Marioni"},{"full_name":"Ystrom, Eivind","last_name":"Ystrom","first_name":"Eivind"},{"first_name":"Alexandra","full_name":"Havdahl, Alexandra","last_name":"Havdahl"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.xgen.2026.101277","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide."}],"external_id":{"pmid":["40909755"]},"date_published":"2026-06-09T00:00:00Z","publication":"Cell Genomics","date_updated":"2026-06-19T07:00:47Z","oa":1,"department":[{"_id":"MaRo"}],"scopus_import":"1","corr_author":"1","_id":"21987","status":"public","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>, 101277, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>.","apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (n.d.). Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>","short":"I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics (n.d.).","ista":"Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics., 101277.","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>.","ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>","ieee":"I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” <i>Cell Genomics</i>. Elsevier."},"quality_controlled":"1","OA_type":"gold","publisher":"Elsevier","OA_place":"publisher","month":"06"},{"author":[{"orcid":"0000-0001-9381-3577","full_name":"Ge, Zengxiang","last_name":"Ge","first_name":"Zengxiang","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8"},{"last_name":"Koczka","full_name":"Koczka, Lilla","first_name":"Lilla"},{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vladimirtsev, Dmitrii","last_name":"Vladimirtsev","first_name":"Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d"},{"full_name":"Kassem, Nada","last_name":"Kassem","first_name":"Nada"},{"full_name":"Ait Ikene, Sara","last_name":"Ait Ikene","first_name":"Sara","id":"6a0bb896-6bad-11f1-9bef-906e9eb76034"},{"full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"day":"30","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2025.10.07.680881","open_access":"1"}],"abstract":[{"text":"Adaptive plant development is orchestrated, among others, by directional, intercellular transport of the phytohormone auxin. Self-organizing development, such as flexible vasculature formation, depends on so-called auxin canalization, manifested by the gradual formation of auxin transport channels through feedback between auxin signalling and transport. Herein, we identify MAKR6 as an important, novel component in this feedback. MAKR6 expression accumulates strongly in vascular cells and is tightly regulated by auxin via the Aux/IAA-ARF-WRKY23 transcriptional network. MAKR6 is required for auxin canalization-dependent processes, including leaf venation, vasculature regeneration, and de novo auxin channel formation from local auxin sources. Mechanistically, MAKR6 interacts with the PIN1 auxin transporter, modulating its trafficking and polarization. MAKR6 also associates with and integrates two key receptor-like kinase complexes involved in canalization, TMK1/4 and the CAMEL-CANAR. Together, our study establishes MAKR6 as a multifaceted regulator that couples transcriptional auxin signalling to PIN1 repolarization and coordinates multiple RLK-mediated signalling pathways during canalization. This provides mechanistic insights into auxin canalization and exemplifies a framework for exploring similar regulatory nodes in other developmental contexts.","lang":"eng"}],"publication":"bioRxiv","date_published":"2026-05-30T00:00:00Z","acknowledgement":"We would like to thank Dr. Yvon Jaillais (ENS, Lyon) for sharing MAKR2 materials. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF) and the Lab Support Facility (LSF). The research in the Friml group leading to these results was funded by the European Research Council (ERC): 101142681 CYNIPS; and the Austrian Science Fund (FWF): I 6123-B and P 37051-B. Ewa Mazur was supported by the National Science Centre (NCN), Poland, under the OPUS call in the WEAVE programme: 2021/43/I/NZ1/01835.","doi":"10.1101/2025.10.07.680881","year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-06-13T16:57:07Z","title":"MAKR6 integrates TMK and CAMEL/CANAR signalling for auxin canalization in Arabidopsis","type":"preprint","project":[{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"language":[{"iso":"eng"}],"publication_status":"submitted","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","OA_type":"green","citation":{"chicago":"Ge, Zengxiang, Lilla Koczka, Ewa Mazur, Gergely Molnar, Dmitrii Vladimirtsev, Nada Kassem, Sara Ait Ikene, Lukas Fiedler, and Jiří Friml. “MAKR6 Integrates TMK and CAMEL/CANAR Signalling for Auxin Canalization in Arabidopsis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.10.07.680881\">https://doi.org/10.1101/2025.10.07.680881</a>.","ama":"Ge Z, Koczka L, Mazur E, et al. MAKR6 integrates TMK and CAMEL/CANAR signalling for auxin canalization in Arabidopsis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.10.07.680881\">10.1101/2025.10.07.680881</a>","ieee":"Z. Ge <i>et al.</i>, “MAKR6 integrates TMK and CAMEL/CANAR signalling for auxin canalization in Arabidopsis,” <i>bioRxiv</i>. .","apa":"Ge, Z., Koczka, L., Mazur, E., Molnar, G., Vladimirtsev, D., Kassem, N., … Friml, J. (n.d.). MAKR6 integrates TMK and CAMEL/CANAR signalling for auxin canalization in Arabidopsis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.10.07.680881\">https://doi.org/10.1101/2025.10.07.680881</a>","mla":"Ge, Zengxiang, et al. “MAKR6 Integrates TMK and CAMEL/CANAR Signalling for Auxin Canalization in Arabidopsis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.10.07.680881\">10.1101/2025.10.07.680881</a>.","ista":"Ge Z, Koczka L, Mazur E, Molnar G, Vladimirtsev D, Kassem N, Ait Ikene S, Fiedler L, Friml J. MAKR6 integrates TMK and CAMEL/CANAR signalling for auxin canalization in Arabidopsis. bioRxiv, <a href=\"https://doi.org/10.1101/2025.10.07.680881\">10.1101/2025.10.07.680881</a>.","short":"Z. Ge, L. Koczka, E. Mazur, G. Molnar, D. Vladimirtsev, N. Kassem, S. Ait Ikene, L. Fiedler, J. Friml, BioRxiv (n.d.)."},"has_accepted_license":"1","month":"05","OA_place":"repository","date_updated":"2026-06-19T07:14:01Z","oa":1,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"ddc":["580"],"status":"public","corr_author":"1","_id":"21994"},{"oa":1,"date_updated":"2026-06-19T09:58:52Z","_id":"21997","status":"public","ddc":["520"],"department":[{"_id":"YlGo"}],"file_date_updated":"2026-06-19T09:56:29Z","arxiv":1,"scopus_import":"1","has_accepted_license":"1","citation":{"chicago":"Li, Zhenwei, Dandan Wei, Shi Jia, Hailiang Chen, Hongwei Ge, Zhuo Chen, Yangyang Zhang, Xuefei Chen, and Zhanwen Han. “A Path to Constraints on Common Envelope Ejection in Massive Binaries: Full Evolutionary Reconstruction of Three Black Hole X-Ray Binaries.” <i>The Astrophysical Journal</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/1538-4357/ae66fd\">https://doi.org/10.3847/1538-4357/ae66fd</a>.","ama":"Li Z, Wei D, Jia S, et al. A path to constraints on common envelope ejection in massive binaries: Full evolutionary reconstruction of three Black Hole X-ray binaries. <i>The Astrophysical Journal</i>. 2026;1004(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae66fd\">10.3847/1538-4357/ae66fd</a>","ieee":"Z. Li <i>et al.</i>, “A path to constraints on common envelope ejection in massive binaries: Full evolutionary reconstruction of three Black Hole X-ray binaries,” <i>The Astrophysical Journal</i>, vol. 1004, no. 1. IOP Publishing, 2026.","apa":"Li, Z., Wei, D., Jia, S., Chen, H., Ge, H., Chen, Z., … Han, Z. (2026). A path to constraints on common envelope ejection in massive binaries: Full evolutionary reconstruction of three Black Hole X-ray binaries. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae66fd\">https://doi.org/10.3847/1538-4357/ae66fd</a>","mla":"Li, Zhenwei, et al. “A Path to Constraints on Common Envelope Ejection in Massive Binaries: Full Evolutionary Reconstruction of Three Black Hole X-Ray Binaries.” <i>The Astrophysical Journal</i>, vol. 1004, no. 1, 31, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae66fd\">10.3847/1538-4357/ae66fd</a>.","ista":"Li Z, Wei D, Jia S, Chen H, Ge H, Chen Z, Zhang Y, Chen X, Han Z. 2026. A path to constraints on common envelope ejection in massive binaries: Full evolutionary reconstruction of three Black Hole X-ray binaries. The Astrophysical Journal. 1004(1), 31.","short":"Z. Li, D. Wei, S. Jia, H. Chen, H. Ge, Z. Chen, Y. Zhang, X. Chen, Z. Han, The Astrophysical Journal 1004 (2026)."},"quality_controlled":"1","volume":1004,"OA_type":"gold","article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_place":"publisher","month":"06","publisher":"IOP Publishing","intvolume":"      1004","date_created":"2026-06-14T22:01:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"year":"2026","article_number":"31","doi":"10.3847/1538-4357/ae66fd","acknowledgement":"We deeply thank the referee for a very careful reading and constructive comments that have led to the improvement of the manuscript. The authors are grateful to Poshak Gandhi for his valuable suggestions and feedback on this work. This work is supported by the Natural Science Foundation of China (grant Nos. 12125303, 12525304, 12288102, 12473034, 12103028, 12333008, 12422305, 12090040/3, 12273105, 11703081, 11422324, 12073070, and 12173081), the CAS Project for Young Scientists in Basic Research (YSBR-148), the Strategic Priority Research Program of the Chinese Academy of Sciences (grant Nos. XDB1160303, XDB1160201, and XDB1160000), the National Key R&D Program of China (grant Nos. 2021YFA1600403 and 2021YFA1600400), the Key Research Program of Frontier Sciences of CAS (No. ZDBS-LY-7005), the “CAS Light of West China”, the Yunnan Revitalization Talent Support Program-Science & Technology Champion Project (No. 202305AB350003) and Young Talent Project, the International Centre of Supernovae (ICESUN), Yunnan Key Laboratory of Supernova Research (Nos. 202302AN360001 and 202201BC070003), Yunnan Fundamental Research Projects (No. 202401AT070139), and the Natural Science Foundation of Henan Province (No. 242300420944). X.C. acknowledges the New Cornerstone Science Foundation through the XPLORER PRIZE. The authors gratefully acknowledge the “PHOENIX Supercomputing Platform” jointly operated by the Binary Population Synthesis Group and the Stellar Astrophysics Group at Yunnan Observatories, Chinese Academy of Sciences.","article_type":"original","DOAJ_listed":"1","publication_status":"published","language":[{"iso":"eng"}],"title":"A path to constraints on common envelope ejection in massive binaries: Full evolutionary reconstruction of three Black Hole X-ray binaries","type":"journal_article","issue":"1","oa_version":"Published Version","PlanS_conform":"1","day":"10","author":[{"full_name":"Li, Zhenwei","last_name":"Li","first_name":"Zhenwei"},{"id":"5dd129bd-0601-11ef-b325-833284687b76","first_name":"Dandan","last_name":"Wei","full_name":"Wei, Dandan"},{"last_name":"Jia","full_name":"Jia, Shi","first_name":"Shi"},{"first_name":"Hailiang","last_name":"Chen","full_name":"Chen, Hailiang"},{"last_name":"Ge","full_name":"Ge, Hongwei","first_name":"Hongwei"},{"full_name":"Chen, Zhuo","last_name":"Chen","first_name":"Zhuo"},{"last_name":"Zhang","full_name":"Zhang, Yangyang","first_name":"Yangyang"},{"last_name":"Chen","full_name":"Chen, Xuefei","first_name":"Xuefei"},{"full_name":"Han, Zhanwen","last_name":"Han","first_name":"Zhanwen"}],"file":[{"file_id":"22099","file_name":"2026_AstrophysicalJour_Li.pdf","relation":"main_file","access_level":"open_access","checksum":"bb76fbb51f8d2834cb79f19e7932e3bd","date_created":"2026-06-19T09:56:29Z","content_type":"application/pdf","success":1,"file_size":3386217,"creator":"dernst","date_updated":"2026-06-19T09:56:29Z"}],"date_published":"2026-06-10T00:00:00Z","external_id":{"arxiv":["2604.10440"]},"publication":"The Astrophysical Journal","abstract":[{"lang":"eng","text":"The massive binary common envelope (CE) phase plays a pivotal role in the formation of close black hole (BH)/neutron star binaries, yet significant uncertainties remain in our understanding of this process. In this study, we aim to constrain the massive binary CE phase by systematically reconstructing three observed BH X-ray binaries (BHXBs): GRO J1655-40, SAX J1819.3-2525, and 4U 1543-47. Through comprehensive binary evolution simulations and parametric supernova modeling, we establish lower limits for the CE efficiency parameters under different energy considerations within the standard energy formalism. Specifically, we derive minimum values for three cases: α0.5U and αU, representing CE efficiencies with half and all of the internal energy contributing to the envelope ejection, respectively, and αH, accounting for the envelope’s enthalpy. Our analysis reveals that the self-consistent formation of these three BHXBs requires CE efficiency parameters satisfying α0.5U ≳ 6.7, αU ≳ 4.2, and αH ≳ 1.7. Notably, we find no viable solutions with CE efficiency values below unity, even when considering the most extreme scenarios, in which the envelope binding energy is significantly reduced through enthalpy inclusion. Our results strongly imply that either additional energy sources are required or the formalism itself must be revised. Furthermore, we quantitatively assess the impact of BH natal kicks on our results. A key finding is that 4U 1543-47’s formation requires substantial natal kicks (≳50 km s−1), as lower kick velocities are incompatible with isolated binary evolution."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-06-14T22:01:42Z","acknowledgement":"We thank the referees for detailed and highly constructive reports that significantly improved the scope and breadth of the manuscript. J.C. thanks Hollis Akins, Volker Bromm, Rui Chaves-Marques, Steve Finkelstein, Karl Gebhardt, Keith Hawkins, Harley Katz, Stellar Offner, Daniel Schaerer, Grace Telford, and Jorick Vink for conversations that improved the Letter. A.d.G. acknowledges support from a Clay Fellowship awarded by the Smithsonian Astrophysical Observatory. M.B.K. acknowledges support from NSF grants AST-2108962 and AST-2408247; NASA grant 80NSSC22K0827; HST-GO-16686, HST-AR-17028, JWST-GO-03788, and JWST-AR-06278 from the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS5-26555; and from the Samuel T. and Fern Yanagisawa Regents Professorship in Astronomy at UT Austin. A.A.C.S. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) in the form of an Emmy Noether Research Group—Project-ID 445674056 (SA4064/1-1, PI Sander). A.A.C.S. further acknowledges support from the Deutsches Zentrum für Luft und Raumfahrt (DLR) grant grants 50 OR 2509 (PI: A.A.C. Sander) and 50 OR 2306 (PI: V. Ramachandran/A.A.C. Sander) as well as from the Federal Ministry of Research, Technology, and Space (BMFTR) and the Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments. This project was cofunded by the European Union (Project 101183150—OCEANS).\r\n\r\nThis work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs 1180, 1181, 1208, 1212, 1213, 1215, 1286, 1345, 1433, 2198, 2561, 2750, 2767, 4106, 4233, 5105, 5224, 6368, and 6585.","doi":"10.3847/2041-8213/ae6dae","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"year":"2026","article_number":"L4","publication_status":"published","DOAJ_listed":"1","article_type":"original","title":"Little Red Dots as globular clusters in formation","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","issue":"1","author":[{"last_name":"Chisholm","full_name":"Chisholm, John","first_name":"John"},{"full_name":"Berg, Danielle A.","last_name":"Berg","first_name":"Danielle A."},{"first_name":"Michael","full_name":"Boylan-Kolchin, Michael","last_name":"Boylan-Kolchin"},{"full_name":"De Graaff, Anna","last_name":"De Graaff","first_name":"Anna"},{"first_name":"Lukas J.","last_name":"Furtak","full_name":"Furtak, Lukas J."},{"first_name":"Vasily","last_name":"Kokorev","full_name":"Kokorev, Vasily"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"first_name":"Julian B.","last_name":"Muñoz","full_name":"Muñoz, Julian B."},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"last_name":"Sander","full_name":"Sander, Andreas A.C.","first_name":"Andreas A.C."}],"day":"10","PlanS_conform":"1","publication":"The Astrophysical Journal Letters","file":[{"file_id":"22098","file_name":"2026_AstrophysicalJourLetters_Chisholm.pdf","relation":"main_file","access_level":"open_access","checksum":"66949af6e620c8ef37de42688829a3e3","content_type":"application/pdf","date_created":"2026-06-19T09:45:21Z","success":1,"file_size":919919,"creator":"dernst","date_updated":"2026-06-19T09:45:21Z"}],"external_id":{"arxiv":["2602.15935"]},"date_published":"2026-06-10T00:00:00Z","abstract":[{"text":"Little Red Dots (LRDs), among the most enigmatic high-redshift discoveries by JWST, are commonly believed to be powered by accreting supermassive black holes. Here, we explore the possibility that these sources are globular clusters in formation, with rest-frame UV arising from a very young stellar population and rest-frame optical from a short-lived supermassive (>104 M⊙) star. The spectral profiles of LRDs are broadly consistent with this scenario, though the observed temperatures and bolometric luminosities favor emission reprocessed by optically thick continuum-driven winds not fully captured by current models. The LRD z ∼ 5−7 UV luminosity function naturally evolves, under standard evolutionary and mass-loss prescriptions, into a present-day mass function with a turnover at log10(M*/M⊙) = 5.3 and an exponential cutoff at high masses, consistent with local globular cluster populations. We estimate the total present-day number density of LRDs formed across all redshifts to be ≈0.3 Mpc−3, similar within uncertainties to local globular clusters. The observed LRD redshift range matches the age distribution of metal-poor globular clusters, without current LRD counterparts to the metal-rich population. If LRDs are globular clusters in formation, we predict chemical abundance patterns characteristic of multiple stellar populations, including enhanced He and N, and potential Na–O and Al–Mg anticorrelations. These results offer a local perspective to explore this surprisingly abundant population of distant sources, and a potential new window into extreme stellar astrophysics in the early Universe.","lang":"eng"}],"oa":1,"date_updated":"2026-06-19T09:50:33Z","status":"public","_id":"21998","scopus_import":"1","arxiv":1,"file_date_updated":"2026-06-19T09:45:21Z","department":[{"_id":"JoMa"}],"ddc":["520"],"OA_type":"gold","volume":1004,"quality_controlled":"1","citation":{"ieee":"J. Chisholm <i>et al.</i>, “Little Red Dots as globular clusters in formation,” <i>The Astrophysical Journal Letters</i>, vol. 1004, no. 1. IOP Publishing, 2026.","ama":"Chisholm J, Berg DA, Boylan-Kolchin M, et al. Little Red Dots as globular clusters in formation. <i>The Astrophysical Journal Letters</i>. 2026;1004(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ae6dae\">10.3847/2041-8213/ae6dae</a>","chicago":"Chisholm, John, Danielle A. Berg, Michael Boylan-Kolchin, Anna De Graaff, Lukas J. Furtak, Vasily Kokorev, Jorryt J Matthee, Julian B. Muñoz, Rohan P. Naidu, and Andreas A.C. Sander. “Little Red Dots as Globular Clusters in Formation.” <i>The Astrophysical Journal Letters</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/2041-8213/ae6dae\">https://doi.org/10.3847/2041-8213/ae6dae</a>.","short":"J. Chisholm, D.A. Berg, M. Boylan-Kolchin, A. De Graaff, L.J. Furtak, V. Kokorev, J.J. Matthee, J.B. Muñoz, R.P. Naidu, A.A.C. Sander, The Astrophysical Journal Letters 1004 (2026).","ista":"Chisholm J, Berg DA, Boylan-Kolchin M, De Graaff A, Furtak LJ, Kokorev V, Matthee JJ, Muñoz JB, Naidu RP, Sander AAC. 2026. Little Red Dots as globular clusters in formation. The Astrophysical Journal Letters. 1004(1), L4.","apa":"Chisholm, J., Berg, D. A., Boylan-Kolchin, M., De Graaff, A., Furtak, L. J., Kokorev, V., … Sander, A. A. C. (2026). Little Red Dots as globular clusters in formation. <i>The Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ae6dae\">https://doi.org/10.3847/2041-8213/ae6dae</a>","mla":"Chisholm, John, et al. “Little Red Dots as Globular Clusters in Formation.” <i>The Astrophysical Journal Letters</i>, vol. 1004, no. 1, L4, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/2041-8213/ae6dae\">10.3847/2041-8213/ae6dae</a>."},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes","month":"06","OA_place":"publisher","intvolume":"      1004","publisher":"IOP Publishing"},{"OA_place":"publisher","month":"01","publisher":"Elsevier","intvolume":"       290","has_accepted_license":"1","citation":{"ieee":"G. Cipolloni, L. Erdös, and Y. Xu, “Optimal decay of eigenvector overlap for non-Hermitian random matrices,” <i>Journal of Functional Analysis</i>, vol. 290, no. 1. Elsevier, 2026.","ama":"Cipolloni G, Erdös L, Xu Y. Optimal decay of eigenvector overlap for non-Hermitian random matrices. <i>Journal of Functional Analysis</i>. 2026;290(1). doi:<a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">10.1016/j.jfa.2025.111180</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Yuanyuan Xu. “Optimal Decay of Eigenvector Overlap for Non-Hermitian Random Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">https://doi.org/10.1016/j.jfa.2025.111180</a>.","short":"G. Cipolloni, L. Erdös, Y. Xu, Journal of Functional Analysis 290 (2026).","ista":"Cipolloni G, Erdös L, Xu Y. 2026. Optimal decay of eigenvector overlap for non-Hermitian random matrices. Journal of Functional Analysis. 290(1), 111180.","apa":"Cipolloni, G., Erdös, L., &#38; Xu, Y. (2026). Optimal decay of eigenvector overlap for non-Hermitian random matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">https://doi.org/10.1016/j.jfa.2025.111180</a>","mla":"Cipolloni, Giorgio, et al. “Optimal Decay of Eigenvector Overlap for Non-Hermitian Random Matrices.” <i>Journal of Functional Analysis</i>, vol. 290, no. 1, 111180, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">10.1016/j.jfa.2025.111180</a>."},"quality_controlled":"1","OA_type":"hybrid","volume":290,"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","_id":"20328","status":"public","ddc":["510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2026-01-05T13:05:47Z","scopus_import":"1","arxiv":1,"oa":1,"date_updated":"2026-06-03T13:12:14Z","external_id":{"isi":["001583178200001"],"oaworkid":["w4413883397"],"arxiv":["2411.16572"]},"date_published":"2026-01-01T00:00:00Z","file":[{"file_name":"2026_JourFuncAnalysis_Cipolloni.pdf","file_id":"20947","relation":"main_file","access_level":"open_access","checksum":"ee53d5e695f0df11e017c8c9242a2b04","success":1,"content_type":"application/pdf","date_created":"2026-01-05T13:05:47Z","file_size":2503887,"creator":"dernst","date_updated":"2026-01-05T13:05:47Z"}],"publication":"Journal of Functional Analysis","abstract":[{"text":"We consider the standard overlap (math formular) of any bi-orthogonal family of left and right eigenvectors of a large random matrix X with centred i.i.d. entries and we prove that it decays as an inverse second power of the distance between the corresponding eigenvalues. This extends similar results for the complex Gaussian ensemble from Bourgade and Dubach [15], as well as Benaych-Georges and Zeitouni [13], to any i.i.d. matrix ensemble in both symmetry classes. As a main tool, we prove a two-resolvent local law for the Hermitisation of X uniformly in the spectrum with optimal decay rate and optimal dependence on the density near the spectral edge.","lang":"eng"}],"issue":"1","oa_version":"Published Version","PlanS_conform":"1","day":"01","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0003-1559-1205","last_name":"Xu","full_name":"Xu, Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","first_name":"Yuanyuan"}],"article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"title":"Optimal decay of eigenvector overlap for non-Hermitian random matrices","type":"journal_article","date_created":"2025-09-10T05:46:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","publication_identifier":{"issn":["0022-1236"]},"article_number":"111180","oaworkid":1,"doi":"10.1016/j.jfa.2025.111180","acknowledgement":"Partially supported by ERC Advanced Grant “RMTBeyond” No. 101020331. Partially supported by National Key R&D Program of China No. 2024YFA1013503."},{"month":"01","OA_place":"publisher","publisher":"Elsevier","intvolume":"       176","citation":{"ama":"Christoph M, Nenadov R, Petrova KH. The Hamilton space of pseudorandom graphs. <i>Journal of Combinatorial Theory Series B</i>. 2026;176:254-267. doi:<a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">10.1016/j.jctb.2025.09.002</a>","chicago":"Christoph, Micha, Rajko Nenadov, and Kalina H Petrova. “The Hamilton Space of Pseudorandom Graphs.” <i>Journal of Combinatorial Theory Series B</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">https://doi.org/10.1016/j.jctb.2025.09.002</a>.","ieee":"M. Christoph, R. Nenadov, and K. H. Petrova, “The Hamilton space of pseudorandom graphs,” <i>Journal of Combinatorial Theory Series B</i>, vol. 176. Elsevier, pp. 254–267, 2026.","apa":"Christoph, M., Nenadov, R., &#38; Petrova, K. H. (2026). The Hamilton space of pseudorandom graphs. <i>Journal of Combinatorial Theory Series B</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">https://doi.org/10.1016/j.jctb.2025.09.002</a>","mla":"Christoph, Micha, et al. “The Hamilton Space of Pseudorandom Graphs.” <i>Journal of Combinatorial Theory Series B</i>, vol. 176, Elsevier, 2026, pp. 254–67, doi:<a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">10.1016/j.jctb.2025.09.002</a>.","ista":"Christoph M, Nenadov R, Petrova KH. 2026. The Hamilton space of pseudorandom graphs. Journal of Combinatorial Theory Series B. 176, 254–267.","short":"M. Christoph, R. Nenadov, K.H. Petrova, Journal of Combinatorial Theory Series B 176 (2026) 254–267."},"has_accepted_license":"1","OA_type":"hybrid","quality_controlled":"1","volume":176,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"Yes (via OA deal)","page":"254-267","corr_author":"1","_id":"20422","status":"public","file_date_updated":"2026-01-05T13:29:34Z","department":[{"_id":"MaKw"}],"ddc":["510"],"scopus_import":"1","arxiv":1,"oa":1,"date_updated":"2026-01-05T13:29:52Z","file":[{"access_level":"open_access","relation":"main_file","file_id":"20953","file_name":"2026_JourCombTheoryB_Christoph.pdf","checksum":"60676af4af4b3243ba187e7d65440d99","file_size":688924,"date_created":"2026-01-05T13:29:34Z","content_type":"application/pdf","success":1,"date_updated":"2026-01-05T13:29:34Z","creator":"dernst"}],"date_published":"2026-01-01T00:00:00Z","external_id":{"isi":["001585783400001"],"arxiv":["2402.01447"]},"publication":"Journal of Combinatorial Theory Series B","abstract":[{"lang":"eng","text":"We show that if n is odd and p>=Clog n/n, then with high probability Hamilton cycles in G(n,p) span its cycle space. More generally, we show this holds for a class of graphs satisfying certain natural pseudorandom properties. The proof is based on a novel idea of parity-switchers, which can be thought of as analogues of absorbers in the context of cycle spaces. As another application of our method, we show that Hamilton cycles in a near-Dirac graph G, that is, a graph G with odd n vertices and minimum degree n/2+C for sufficiently large constant C, span its cycle space.\r\n"}],"oa_version":"Published Version","day":"01","PlanS_conform":"1","author":[{"first_name":"Micha","last_name":"Christoph","full_name":"Christoph, Micha"},{"full_name":"Nenadov, Rajko","last_name":"Nenadov","first_name":"Rajko"},{"full_name":"Petrova, Kalina H","last_name":"Petrova","first_name":"Kalina H","id":"554ff4e4-f325-11ee-b0c4-a10dbd523381"}],"article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"title":"The Hamilton space of pseudorandom graphs","type":"journal_article","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"date_created":"2025-10-05T22:01:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","publication_identifier":{"issn":["0095-8956"],"eissn":["1096-0902"]},"acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. Image 1 Part of this research was conducted while the author was at Department of Computer Science, ETH Zürich, Switzerland. This author was supported by grant no. CRSII5 173721 of the Swiss National Science Foundation.","doi":"10.1016/j.jctb.2025.09.002"},{"day":"01","PlanS_conform":"1","author":[{"full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890"},{"orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano"},{"orcid":"0000-0003-0464-3823","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","first_name":"Ondrej","last_name":"Draganov","full_name":"Draganov, Ondrej"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"oa_version":"Published Version","abstract":[{"text":"Given a locally finite set A⊆Rd and a coloring χ:A→{0,1,…,s}, we introduce the chromatic Delaunay mosaic of χ, which is a Delaunay mosaic in Rs+d that represents how points of different colors mingle. Our main results are bounds on the size of the chromatic Delaunay mosaic, in which we assume that d and s are constants. For example, if A is finite with n=#A, and the coloring is random, then the chromatic Delaunay mosaic has O(n⌈d/2⌉) cells in expectation. In contrast, for Delone sets and Poisson point processes in Rd, the expected number of cells within a closed ball is only a constant times the number of points in this ball. Furthermore, in R2 all colorings of a dense set of n points have chromatic Delaunay mosaics of size O(n). This encourages the use of chromatic Delaunay mosaics in applications.","lang":"eng"}],"date_published":"2026-01-01T00:00:00Z","external_id":{"arxiv":["2212.03121"],"isi":["001584166900001"]},"file":[{"access_level":"open_access","relation":"main_file","file_name":"2026_DiscreteCompGeom_Biswas.pdf","file_id":"20952","checksum":"0addb5c1b78142f9fb453bfa04695400","file_size":570922,"success":1,"date_created":"2026-01-05T13:21:20Z","content_type":"application/pdf","date_updated":"2026-01-05T13:21:20Z","creator":"dernst"}],"publication":"Discrete and Computational Geometry","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"year":"2026","doi":"10.1007/s00454-025-00778-7","acknowledgement":"The fourth author thanks Boris Aronov for insightful discussions on the size of the overlay of Voronoi tessellations. Open access funding provided by Institute of Science and Technology (IST Austria). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","date_created":"2025-10-12T22:01:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"isi":1,"title":"On the size of chromatic Delaunay mosaics","type":"journal_article","project":[{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"article_type":"original","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"Yes (via OA deal)","page":"24-47","citation":{"apa":"Biswas, R., Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (2026). On the size of chromatic Delaunay mosaics. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00778-7\">https://doi.org/10.1007/s00454-025-00778-7</a>","mla":"Biswas, Ranita, et al. “On the Size of Chromatic Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>, vol. 75, Springer Nature, 2026, pp. 24–47, doi:<a href=\"https://doi.org/10.1007/s00454-025-00778-7\">10.1007/s00454-025-00778-7</a>.","short":"R. Biswas, S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, Discrete and Computational Geometry 75 (2026) 24–47.","ista":"Biswas R, Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2026. On the size of chromatic Delaunay mosaics. Discrete and Computational Geometry. 75, 24–47.","ama":"Biswas R, Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. On the size of chromatic Delaunay mosaics. <i>Discrete and Computational Geometry</i>. 2026;75:24-47. doi:<a href=\"https://doi.org/10.1007/s00454-025-00778-7\">10.1007/s00454-025-00778-7</a>","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “On the Size of Chromatic Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00454-025-00778-7\">https://doi.org/10.1007/s00454-025-00778-7</a>.","ieee":"R. Biswas, S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “On the size of chromatic Delaunay mosaics,” <i>Discrete and Computational Geometry</i>, vol. 75. Springer Nature, pp. 24–47, 2026."},"has_accepted_license":"1","quality_controlled":"1","volume":75,"OA_type":"hybrid","publisher":"Springer Nature","intvolume":"        75","month":"01","OA_place":"publisher","date_updated":"2026-01-05T13:21:56Z","oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"15090"}]},"department":[{"_id":"HeEd"}],"file_date_updated":"2026-01-05T13:21:20Z","ddc":["510"],"arxiv":1,"scopus_import":"1","_id":"20456","corr_author":"1","status":"public"},{"article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"title":"Odd-Ramsey numbers of complete bipartite graphs","type":"journal_article","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"date_created":"2025-10-16T13:14:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"104235","year":"2026","publication_identifier":{"issn":["0195-6698"]},"acknowledgement":"The authors would like to thank Gilles Zémor for a helpful clarification on [3], Deepak Bal and Patrick Bennett for bringing [25] to their attention, and both referees for several helpful comments.\r\nS.B.: Most of this research was conducted while the author was at the School of Mathematics, University of Birmingham, Birmingham, United Kingdom. The research leading to these results was supported by EPSRC, United Kingdom, grant no. EP/V048287/1 and by ERC Advanced Grants “GeoScape”, no. 882971 and “ERMiD”, no. 101054936. There are no additional data beyond that contained within the main manuscript.\r\nS.D.: Research supported by Taiwan NSTC grants 111-2115-M-002-009-MY2 and 113-2628-M-002-008-MY4.\r\nK.P.: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. Parts of this research was conducted while K.P. was at the Department of Computer Science, ETH Zürich, Switzerland, supported by Swiss National Science Foundation, Switzerland , grant no. CRSII5 173721.","doi":"10.1016/j.ejc.2025.104235","date_published":"2026-01-01T00:00:00Z","file":[{"date_created":"2026-01-05T13:34:40Z","content_type":"application/pdf","success":1,"file_size":563029,"creator":"dernst","date_updated":"2026-01-05T13:34:40Z","file_id":"20954","file_name":"2026_EuropJourCombinatorics_Boyadzhiyska.pdf","access_level":"open_access","relation":"main_file","checksum":"52883daa217398396cbf9b8ad9ddae92"}],"external_id":{"arxiv":["2410.05887"],"isi":["001573380700001"]},"publication":"European Journal of Combinatorics","abstract":[{"lang":"eng","text":"In his study of graph codes, Alon introduced the concept of the odd-Ramsey number of a family of graphs H in Kn, defined as the minimum number of colours needed to colour the edges of K so that every copy of a graph H E H intersects some colour class in an odd number of edges. In this paper, we focus on complete bipartite graphs. First, we completely resolve the problem when H is the family of all spanning complete bipartite graphs on n vertices. We then focus on its subfamilies, that is, {Kt,n-t : t E T} for a fixed set of integers T c [[n/2]]. We prove that the odd-Ramsey problem is equivalent to determining the maximum dimension of a linear binary code avoiding codewords of given weights, and leverage known results from coding theory to deduce asymptotically tight bounds in our setting. We conclude with bounds for the odd-Ramsey numbers of fixed (that is, non-spanning) complete bipartite subgraphs."}],"oa_version":"Published Version","day":"01","PlanS_conform":"1","author":[{"first_name":"Simona","full_name":"Boyadzhiyska, Simona","last_name":"Boyadzhiyska"},{"full_name":"Das, Shagnik","last_name":"Das","first_name":"Shagnik"},{"first_name":"Thomas","full_name":"Lesgourgues, Thomas","last_name":"Lesgourgues"},{"id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","first_name":"Kalina H","last_name":"Petrova","full_name":"Petrova, Kalina H"}],"_id":"20482","corr_author":"1","status":"public","file_date_updated":"2026-01-05T13:34:40Z","department":[{"_id":"MaKw"}],"ddc":["500"],"scopus_import":"1","arxiv":1,"oa":1,"date_updated":"2026-01-05T13:34:48Z","month":"01","OA_place":"publisher","publisher":"Elsevier","intvolume":"       131","citation":{"ama":"Boyadzhiyska S, Das S, Lesgourgues T, Petrova KH. Odd-Ramsey numbers of complete bipartite graphs. <i>European Journal of Combinatorics</i>. 2026;131. doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">10.1016/j.ejc.2025.104235</a>","chicago":"Boyadzhiyska, Simona, Shagnik Das, Thomas Lesgourgues, and Kalina H Petrova. “Odd-Ramsey Numbers of Complete Bipartite Graphs.” <i>European Journal of Combinatorics</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">https://doi.org/10.1016/j.ejc.2025.104235</a>.","ieee":"S. Boyadzhiyska, S. Das, T. Lesgourgues, and K. H. Petrova, “Odd-Ramsey numbers of complete bipartite graphs,” <i>European Journal of Combinatorics</i>, vol. 131. Elsevier, 2026.","apa":"Boyadzhiyska, S., Das, S., Lesgourgues, T., &#38; Petrova, K. H. (2026). Odd-Ramsey numbers of complete bipartite graphs. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">https://doi.org/10.1016/j.ejc.2025.104235</a>","mla":"Boyadzhiyska, Simona, et al. “Odd-Ramsey Numbers of Complete Bipartite Graphs.” <i>European Journal of Combinatorics</i>, vol. 131, 104235, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">10.1016/j.ejc.2025.104235</a>.","short":"S. Boyadzhiyska, S. Das, T. Lesgourgues, K.H. Petrova, European Journal of Combinatorics 131 (2026).","ista":"Boyadzhiyska S, Das S, Lesgourgues T, Petrova KH. 2026. Odd-Ramsey numbers of complete bipartite graphs. European Journal of Combinatorics. 131, 104235."},"has_accepted_license":"1","volume":131,"quality_controlled":"1","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1},{"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"date_published":"2026-01-08T00:00:00Z","file":[{"file_size":1201,"content_type":"text/plain","date_created":"2025-12-17T10:09:25Z","success":1,"date_updated":"2025-12-17T10:09:25Z","creator":"llayanaf","access_level":"open_access","relation":"main_file","file_id":"20834","file_name":"README.txt","checksum":"0b79be6229f2ad9ac117ef00fc4f5c0e"},{"checksum":"daf1c03149dd170b14e5c8e109ee3c77","file_id":"20835","file_name":"Supplementary_Datasets.zip","access_level":"open_access","relation":"main_file","creator":"llayanaf","date_updated":"2025-12-17T10:10:11Z","content_type":"application/zip","date_created":"2025-12-17T10:10:11Z","success":1,"file_size":19052849},{"success":1,"date_created":"2025-12-17T10:12:05Z","content_type":"application/zip","file_size":4575,"creator":"llayanaf","date_updated":"2025-12-17T10:12:05Z","file_name":"Perl_scripts.zip","file_id":"20837","access_level":"open_access","relation":"main_file","checksum":"251e7aab01917c2ad2fbccf465492ea1"},{"checksum":"3cabf143b8cd286eae48c598da2b03bd","file_id":"20959","file_name":"Supplementary_Tables.zip","access_level":"open_access","relation":"main_file","creator":"llayanaf","date_updated":"2026-01-08T01:35:08Z","content_type":"application/zip","date_created":"2026-01-08T01:35:08Z","success":1,"file_size":572362}],"month":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"8","article_processing_charge":"No","author":[{"orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","full_name":"Layana Franco, Lorena Alexandra","last_name":"Layana Franco"},{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"citation":{"ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science and Technology Austria, 2026.","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20833\">https://doi.org/10.15479/AT-ISTA-20833</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20833\">10.15479/AT-ISTA-20833</a>","ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-20833\">10.15479/AT-ISTA-20833</a>.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2026). Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20833\">https://doi.org/10.15479/AT-ISTA-20833</a>","mla":"Layana Franco, Lorena Alexandra, et al. <i>Research Data for “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20833\">10.15479/AT-ISTA-20833</a>."},"has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2026-01-08T01:35:08Z","department":[{"_id":"BeVi"}],"title":"Research Data for 'Causes and consequences of sex-chromosome turnovers in Diptera'","type":"research_data","_id":"20833","corr_author":"1","status":"public","year":"2026","doi":"10.15479/AT-ISTA-20833","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"date_updated":"2026-06-10T09:21:49Z","oa":1,"date_created":"2025-12-17T10:10:57Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d"},{"article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","volume":9,"OA_type":"gold","has_accepted_license":"1","citation":{"ama":"Agafonova S, Rosello P, Mekonnen M, Hosten O. One-milligram torsional pendulum toward experiments at the quantum-gravity interface. <i>Communications Physics</i>. 2026;9. doi:<a href=\"https://doi.org/10.1038/s42005-026-02514-w\">10.1038/s42005-026-02514-w</a>","chicago":"Agafonova, Sofia, Pere Rosello, Manuel Mekonnen, and Onur Hosten. “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” <i>Communications Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s42005-026-02514-w\">https://doi.org/10.1038/s42005-026-02514-w</a>.","ieee":"S. Agafonova, P. Rosello, M. Mekonnen, and O. Hosten, “One-milligram torsional pendulum toward experiments at the quantum-gravity interface,” <i>Communications Physics</i>, vol. 9. Springer Nature, 2026.","apa":"Agafonova, S., Rosello, P., Mekonnen, M., &#38; Hosten, O. (2026). One-milligram torsional pendulum toward experiments at the quantum-gravity interface. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-026-02514-w\">https://doi.org/10.1038/s42005-026-02514-w</a>","mla":"Agafonova, Sofia, et al. “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” <i>Communications Physics</i>, vol. 9, 80, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s42005-026-02514-w\">10.1038/s42005-026-02514-w</a>.","short":"S. Agafonova, P. Rosello, M. Mekonnen, O. Hosten, Communications Physics 9 (2026).","ista":"Agafonova S, Rosello P, Mekonnen M, Hosten O. 2026. One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. 9, 80."},"intvolume":"         9","publisher":"Springer Nature","OA_place":"publisher","month":"03","date_updated":"2026-06-10T08:36:06Z","oa":1,"related_material":{"record":[{"id":"20842","relation":"research_data","status":"public"}]},"arxiv":1,"scopus_import":"1","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"OnHo"}],"file_date_updated":"2026-03-16T10:07:46Z","status":"public","_id":"20840","corr_author":"1","author":[{"orcid":"0000-0003-0582-2946","full_name":"Agafonova, Sofya","last_name":"Agafonova","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"first_name":"Pere","full_name":"Rosello, Pere","last_name":"Rosello"},{"first_name":"Manuel","last_name":"Mekonnen","full_name":"Mekonnen, Manuel"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X"}],"PlanS_conform":"1","day":"04","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Probing the possibility of entanglement generation through gravity offers a path to tackle the question of whether gravitational fields possess a quantum mechanical nature. A potential realization necessitates systems with low-frequency dynamics at an optimal mass scale, for which the microgram-to-milligram range is a strong contender. Here, after refining a figure-of-merit for the problem, we present a 1-milligram torsional pendulum operating at 18 Hz. We demonstrate laser cooling its motion from room temperature to 240 microkelvins, surpassing by over 20-fold the coldest motions attained for oscillators ranging from micrograms to kilograms. We quantify and contrast the utility of the current approach with other platforms. The achieved performance and large improvement potential highlight milligram-scale torsional pendulums as a powerful platform for precision measurements relevant to future studies at the quantum-gravity interface."}],"publication":"Communications Physics","date_published":"2026-03-04T00:00:00Z","external_id":{"arxiv":["2408.09445"]},"file":[{"access_level":"open_access","relation":"main_file","file_name":"2026_CommunicationsPhysics_Agafonova.pdf","file_id":"21457","checksum":"62e2175e7e3ad49260ae6a7b4e0860a2","file_size":1901772,"success":1,"content_type":"application/pdf","date_created":"2026-03-16T10:07:46Z","date_updated":"2026-03-16T10:07:46Z","creator":"dernst"}],"doi":"10.1038/s42005-026-02514-w","acknowledgement":"We thank Gerard Higgins, Andrei Militaru, Nikolai Kiesel, and Markus Aspelmeyer for useful discussions on the topic of the figure-of-merit. We thank Teodor Strömberg for helping with the additional characterizations of the optical lever noise. We thank Johannes Fink and Scott Waitukaitis for their helpful feedback on the manuscript. This work was supported by Institute of Science and Technology Austria and the European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","year":"2026","publication_identifier":{"eissn":["2399-3650"]},"article_number":"80","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-21T11:39:04Z","project":[{"grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}],"title":"One-milligram torsional pendulum toward experiments at the quantum-gravity interface","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","DOAJ_listed":"1"},{"issue":"1","oa_version":"Published Version","PlanS_conform":"1","day":"01","author":[{"full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi","first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","orcid":"0009-0000-9773-1931"}],"file":[{"file_size":958382,"date_created":"2026-01-05T12:36:39Z","content_type":"application/pdf","success":1,"date_updated":"2026-01-05T12:36:39Z","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"20945","file_name":"2026_CalculusVariations_Quattrocchi.pdf","checksum":"635370d64abaf444f50f5cca60bba1be"}],"external_id":{"arxiv":["2403.07803"]},"date_published":"2026-01-01T00:00:00Z","publication":"Calculus of Variations and Partial Differential Equations","abstract":[{"text":"We prove the convergence of a modified Jordan–Kinderlehrer–Otto scheme to a solution\r\nto the Fokker–Planck equation in Ω e R^d with general—strictly positive and temporally\r\nconstant—Dirichlet boundary conditions. We work under mild assumptions on the domain,\r\nthe drift, and the initial datum. In the special case where Ω is an interval in R1, we prove\r\nthat such a solution is a gradient flow—curve of maximal slope—within a suitable space of\r\nmeasures, endowed with a modified Wasserstein distance. Our discrete scheme and modified\r\ndistance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures\r\nAppl. 94, (2010), pp. 107–130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41–88]\r\non an optimal-transport approach to evolution equations with Dirichlet boundary conditions.\r\nSimilarly to these works, we allow the mass to flow from/to the boundary ∂Ω throughout\r\nthe evolution. However, our leading idea is to also keep track of the mass at the boundary\r\nby working with measures defined on the whole closure Ω . The driving functional is a\r\nmodification of the classical relative entropy that also makes use of the information at the\r\nboundary. As an intermediate result, when Ω is an interval in R1, we find a formula for the\r\ndescending slope of this geodesically nonconvex functional.","lang":"eng"}],"date_created":"2025-12-29T12:06:26Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"year":"2026","article_number":"23","acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful comments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, Oliver Tse for pointing out the reference [10], and the anonymous reviewer for carefully reading this manuscript and providing valuable suggestions. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s00526-025-03193-1","article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","type":"journal_article","has_accepted_license":"1","citation":{"ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 65, no. 1. Springer Nature, 2026.","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00526-025-03193-1\">https://doi.org/10.1007/s00526-025-03193-1</a>.","ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>Calculus of Variations and Partial Differential Equations</i>. 2026;65(1). doi:<a href=\"https://doi.org/10.1007/s00526-025-03193-1\">10.1007/s00526-025-03193-1</a>","short":"F. Quattrocchi, Calculus of Variations and Partial Differential Equations 65 (2026).","ista":"Quattrocchi F. 2026. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. Calculus of Variations and Partial Differential Equations. 65(1), 23.","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 65, no. 1, 23, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s00526-025-03193-1\">10.1007/s00526-025-03193-1</a>.","apa":"Quattrocchi, F. (2026). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-025-03193-1\">https://doi.org/10.1007/s00526-025-03193-1</a>"},"OA_type":"hybrid","volume":65,"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_place":"publisher","month":"01","publisher":"Springer Nature","intvolume":"        65","oa":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"20571"}]},"date_updated":"2026-04-07T08:37:46Z","_id":"20865","corr_author":"1","status":"public","ddc":["510"],"file_date_updated":"2026-01-05T12:36:39Z","department":[{"_id":"JaMa"}],"scopus_import":"1","arxiv":1},{"author":[{"full_name":"Dmytrenko, Oleg","last_name":"Dmytrenko","first_name":"Oleg"},{"last_name":"Yuan","full_name":"Yuan, Biao","first_name":"Biao"},{"last_name":"Crosby","full_name":"Crosby, Kadin T.","first_name":"Kadin T."},{"first_name":"Max","full_name":"Krebel, Max","last_name":"Krebel"},{"last_name":"Chen","full_name":"Chen, Xiye","first_name":"Xiye"},{"last_name":"Nowak","full_name":"Nowak, Jakub S.","first_name":"Jakub S."},{"full_name":"Chramiec-Głąbik, Andrzej","last_name":"Chramiec-Głąbik","first_name":"Andrzej"},{"first_name":"Bamidele","last_name":"Filani","full_name":"Filani, Bamidele"},{"first_name":"Anne-Sophie","last_name":"Gribling-Burrer","full_name":"Gribling-Burrer, Anne-Sophie"},{"first_name":"Wiep","full_name":"van der Toorn, Wiep","last_name":"van der Toorn"},{"last_name":"von Kleist","full_name":"von Kleist, Max","first_name":"Max"},{"full_name":"Achmedov, Tatjana","last_name":"Achmedov","first_name":"Tatjana"},{"first_name":"Redmond P.","full_name":"Smyth, Redmond P.","last_name":"Smyth"},{"first_name":"Sebastian","full_name":"Glatt, Sebastian","last_name":"Glatt"},{"full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753"},{"first_name":"Dirk W.","full_name":"Heinz, Dirk W.","last_name":"Heinz"},{"last_name":"Jackson","full_name":"Jackson, Ryan N.","first_name":"Ryan N."},{"first_name":"Chase L.","full_name":"Beisel, Chase L.","last_name":"Beisel"}],"day":"07","PlanS_conform":"1","pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1038/s41586-025-09852-9","open_access":"1"}],"abstract":[{"lang":"eng","text":"In all domains of life, tRNAs mediate the transfer of genetic information from mRNAs to proteins. As their depletion suppresses translation and, consequently, viral replication, tRNAs represent long-standing and increasingly recognized targets of innate immunity1,2,3,4,5. Here we report Cas12a3 effector nucleases from type V CRISPR–Cas adaptive immune systems in bacteria that preferentially cleave tRNAs after recognition of target RNA. Cas12a3 orthologues belong to one of two previously unreported nuclease clades that exhibit RNA-mediated cleavage of non-target RNA, and are distinct from all other known type V systems. Through cell-based and biochemical assays and direct RNA sequencing, we demonstrate that recognition of a complementary target RNA by the CRISPR RNA triggers Cas12a3 to cleave the conserved 5′-CCA-3′ tail of diverse tRNAs to drive growth arrest and anti-phage defence. Cryogenic electron microscopy structures further revealed a distinct tRNA-loading domain that positions the tRNA tail in the RuvC active site of the nuclease. By designing synthetic reporters that mimic the tRNA acceptor stem and tail, we expanded the capacity of current CRISPR-based diagnostics for multiplexed RNA detection. Overall, these findings reveal widespread tRNA inactivation as a previously unrecognized CRISPR-based immune strategy that broadens the application space of the existing CRISPR toolbox."}],"publication":"Nature","date_published":"2026-01-07T00:00:00Z","external_id":{"pmid":["41501459"]},"doi":"10.1038/s41586-025-09852-9","acknowledgement":"We thank Ł. Koziej for processing of the initial cryo-EM datasets, S. Schmelz for support in cryo-EM, A. Gatzemeier for assistance in the purification of dBa1Cas12a3, R. Rarose for support with the in vitro RNA experiments, M. Kaminski for providing purified PsmCas13b protein, L. Schönemann for protein purification, and C. Krempl and S. Backesfor providing the RSV and influenza A transcript-encoding plasmids. This work was supported through funding by the European Research Council (101001394 to S.G.; 865973 and 101158249 to C.L.B.), the R. Gaurth Hansen Family (to R.N.J.), the National Institutes of Health (R35GM138080 to R.N.J.), the PostDoc Plus Program from the Graduate School of Life Sciences at Julius-Maximilians-Universität Würzburg (to O.D.), and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy–The Berlin Mathematics Research Center MATH+ (EXC−2046/1, project ID: 390685689 to M.v.K.). Open access funding provided by Helmholtz-Zentrum für Infektionsforschung GmbH (HZI).","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-01-08T07:57:17Z","type":"journal_article","title":"RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity","language":[{"iso":"eng"}],"publication_status":"epub_ahead","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","quality_controlled":"1","citation":{"mla":"Dmytrenko, Oleg, et al. “RNA-Triggered Cas12a3 Cleaves TRNA Tails to Execute Bacterial Immunity.” <i>Nature</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41586-025-09852-9\">10.1038/s41586-025-09852-9</a>.","apa":"Dmytrenko, O., Yuan, B., Crosby, K. T., Krebel, M., Chen, X., Nowak, J. S., … Beisel, C. L. (2026). RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09852-9\">https://doi.org/10.1038/s41586-025-09852-9</a>","short":"O. Dmytrenko, B. Yuan, K.T. Crosby, M. Krebel, X. Chen, J.S. Nowak, A. Chramiec-Głąbik, B. Filani, A.-S. Gribling-Burrer, W. van der Toorn, M. von Kleist, T. Achmedov, R.P. Smyth, S. Glatt, J.P.K. Bravo, D.W. Heinz, R.N. Jackson, C.L. Beisel, Nature (2026).","ista":"Dmytrenko O, Yuan B, Crosby KT, Krebel M, Chen X, Nowak JS, Chramiec-Głąbik A, Filani B, Gribling-Burrer A-S, van der Toorn W, von Kleist M, Achmedov T, Smyth RP, Glatt S, Bravo JPK, Heinz DW, Jackson RN, Beisel CL. 2026. RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity. Nature.","chicago":"Dmytrenko, Oleg, Biao Yuan, Kadin T. Crosby, Max Krebel, Xiye Chen, Jakub S. Nowak, Andrzej Chramiec-Głąbik, et al. “RNA-Triggered Cas12a3 Cleaves TRNA Tails to Execute Bacterial Immunity.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-025-09852-9\">https://doi.org/10.1038/s41586-025-09852-9</a>.","ama":"Dmytrenko O, Yuan B, Crosby KT, et al. RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity. <i>Nature</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41586-025-09852-9\">10.1038/s41586-025-09852-9</a>","ieee":"O. Dmytrenko <i>et al.</i>, “RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity,” <i>Nature</i>. Springer Nature, 2026."},"has_accepted_license":"1","publisher":"Springer Nature","month":"01","OA_place":"publisher","date_updated":"2026-01-12T10:13:56Z","oa":1,"scopus_import":"1","department":[{"_id":"JaBr"}],"ddc":["570"],"status":"public","_id":"20963"}]