--- OA_type: closed access _id: '21996' abstract: - lang: eng text: In this issue of Cell Host & Microbe, Osterman et al. discover aRES,1 a new family of bacterial immune proteins that deplete cellular NAD+, generating cleavage products that cannot be utilized by canonical phage NAD+ regeneration pathways. They identify the invader-specific trigger for aRES and characterize two distinct evolutionary countermeasures employed by phages to resist aRES. acknowledgement: This work was supported by the Austrian Science Fund (FWF) (10.55776/PAT1617625). article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Williams-Jones, Daniel id: 128eaab9-b327-11f0-bdbe-e02d5abac73b last_name: Williams-Jones - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 citation: ama: 'Williams-Jones D, Bravo JPK. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. 2026;34(6):978-980. doi:10.1016/j.chom.2026.05.013' apa: 'Williams-Jones, D., & Bravo, J. P. K. (2026). NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. Cell Press. https://doi.org/10.1016/j.chom.2026.05.013' chicago: 'Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” Cell Host & Microbe. Cell Press, 2026. https://doi.org/10.1016/j.chom.2026.05.013.' ieee: 'D. Williams-Jones and J. P. K. Bravo, “NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back,” Cell Host & Microbe, vol. 34, no. 6. Cell Press, pp. 978–980, 2026.' ista: 'Williams-Jones D, Bravo JPK. 2026. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. 34(6), 978–980.' mla: 'Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” Cell Host & Microbe, vol. 34, no. 6, Cell Press, 2026, pp. 978–80, doi:10.1016/j.chom.2026.05.013.' short: D. Williams-Jones, J.P.K. Bravo, Cell Host & Microbe 34 (2026) 978–980. corr_author: '1' das_tickbox: '1' date_created: 2026-06-14T22:01:42Z date_published: 2026-06-10T00:00:00Z date_updated: 2026-10-20T09:04:35Z day: '10' department: - _id: JaBr doi: 10.1016/j.chom.2026.05.013 external_id: pmid: - '42269584' fulldoi: https://doi.org/10.1016/j.chom.2026.05.013 intvolume: ' 34' issue: '6' language: - iso: eng month: '06' oa_version: None page: 978-980 pmid: 1 project: - _id: 9f295cab-ad08-11f1-bc83-9e197d0f6d50 grant_number: PAT1617625 name: 'Search & Destroy: Mechanisms of anti-plasmid immunity' publication: Cell Host & Microbe publication_identifier: eissn: - 1934-6069 issn: - 1931-3128 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: 'NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2026' ... --- OA_place: repository OA_type: green _id: '22104' abstract: - lang: eng text: ' Modern computer systems store vast amounts of personal data, enabling advances in AI and ML but risking user privacy and trust. For privacy reasons, it is sometimes desired for an ML model to forget part of the data it was trained on. In this paper, we introduce a novel unlearning approach based on Forgetting Neural Networks (FNNs), a neuroscience-inspired architecture that explicitly encodes forgetting through multiplicative decay factors. While FNNs had previously been studied as a theoretical construct, we provide the first concrete implementation and demonstrate their effectiveness for targeted unlearning. We propose several variants with per-neuron forgetting factors, including rank-based assignments guided by activation levels, and evaluate them on MNIST and Fashion-MNIST benchmarks. Our method systematically removes information associated with forget sets while preserving performance on retained data. Membership inference attacks confirm the effectiveness of FNN-based unlearning in erasing information about the training data from the neural network. These results establish FNNs as a promising foundation for efficient and interpretable unlearning.' acknowledgement: "This work has been supported by the European Research\r\nCouncil under Grant No.: ERC-2020-AdG\r\n101020093. We thank Brian Subirana for the original\r\nideation of the concept of forgetting neural networks\r\nand his belief in their potential." article_processing_charge: No arxiv: 1 author: - first_name: Amartya full_name: Hatua, Amartya last_name: Hatua - first_name: Trung T. full_name: Nguyen, Trung T. last_name: Nguyen - first_name: Filip full_name: Cano Cordoba, Filip id: 708cad98-e86a-11ef-8098-bdae2d7c6af1 last_name: Cano Cordoba orcid: 0000-0002-0783-904X - first_name: Andrew H. full_name: Sung, Andrew H. last_name: Sung citation: ama: 'Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. Machine unlearning using forgetting neural networks. In: Proceedings of the 18th International Conference on Agents and Artificial Intelligence. Vol 2. Science and Technology Publications; 2026:1536-1546. doi:10.5220/0014326500004052' apa: 'Hatua, A., Nguyen, T. T., Cano Cordoba, F., & Sung, A. H. (2026). Machine unlearning using forgetting neural networks. In Proceedings of the 18th International Conference on Agents and Artificial Intelligence (Vol. 2, pp. 1536–1546). Marbella, Spain: Science and Technology Publications. https://doi.org/10.5220/0014326500004052' chicago: Hatua, Amartya, Trung T. Nguyen, Filip Cano Cordoba, and Andrew H. Sung. “Machine Unlearning Using Forgetting Neural Networks.” In Proceedings of the 18th International Conference on Agents and Artificial Intelligence, 2:1536–46. Science and Technology Publications, 2026. https://doi.org/10.5220/0014326500004052. ieee: A. Hatua, T. T. Nguyen, F. Cano Cordoba, and A. H. Sung, “Machine unlearning using forgetting neural networks,” in Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Marbella, Spain, 2026, vol. 2, pp. 1536–1546. ista: 'Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. 2026. Machine unlearning using forgetting neural networks. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 2, 1536–1546.' mla: Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” Proceedings of the 18th International Conference on Agents and Artificial Intelligence, vol. 2, Science and Technology Publications, 2026, pp. 1536–46, doi:10.5220/0014326500004052. short: A. Hatua, T.T. Nguyen, F. Cano Cordoba, A.H. Sung, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Science and Technology Publications, 2026, pp. 1536–1546. conference: end_date: 2026-03-08 location: Marbella, Spain name: 'ICAART: International Conference on Agents and Artificial Intelligence' start_date: 2026-03-05 das_tickbox: '0' date_created: 2026-06-21T22:03:01Z date_published: 2026-04-01T00:00:00Z date_updated: 2026-10-20T14:05:02Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.5220/0014326500004052 ec_funded: 1 external_id: arxiv: - '2410.22374' file: - access_level: open_access checksum: d0f5212846c8f3129509b081648465cb content_type: application/pdf creator: dernst date_created: 2026-10-20T14:00:27Z date_updated: 2026-10-20T14:00:27Z file_id: '23178' file_name: 2026_CAART_Hatua.pdf file_size: 779692 relation: main_file success: 1 file_date_updated: 2026-10-20T14:00:27Z fulldoi: https://doi.org/10.5220/0014326500004052 has_accepted_license: '1' intvolume: ' 2' keyword: - Machine Unlearning - Neuroscience-Inspired Machine Learning - Membership Inference Attacks language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: 1536-1546 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Proceedings of the 18th International Conference on Agents and Artificial Intelligence publication_identifier: eissn: - 2184-433X isbn: - '9789897587962' issn: - 2184-3589 publication_status: published publisher: Science and Technology Publications quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Machine unlearning using forgetting neural networks tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2026' ... --- OA_place: repository OA_type: green _id: '22359' abstract: - lang: eng text: We prove a mesoscopic central limit theorem for linear eigenvalue statistics of correlated Hermitian random matrices. The class considered here includes Wigner and Wigner-type matrices, as well as models whose entry correlations decay polynomially in the distance between index pairs. The proof combines a multivariate cumulant expansion with multi-resolvent local laws and a detailed analysis of the resulting variance kernel on the operator-level. acknowledgement: Supported by ERC Advanced Grant “RMTBeyond” No. 101020331 article_number: '2607.05848' article_processing_charge: No arxiv: 1 author: - first_name: Jaehun full_name: Lee, Jaehun id: 96155047-f36a-11ef-b766-8b5ae7cecd49 last_name: Lee - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv. doi:10.48550/arXiv.2607.05848 apa: Lee, J., & Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. arXiv. https://doi.org/10.48550/arXiv.2607.05848 chicago: Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2607.05848. ieee: J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices,” arXiv. . ista: Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv, 2607.05848. mla: Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” ArXiv, 2607.05848, doi:10.48550/arXiv.2607.05848. short: J. Lee, L. Erdös, ArXiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-07-18T08:59:02Z date_published: 2026-07-07T00:00:00Z date_updated: 2026-10-20T10:06:12Z day: '07' department: - _id: LaEr doi: 10.48550/arXiv.2607.05848 ec_funded: 1 external_id: arxiv: - '2607.05848' fulldoi: https://doi.org/10.48550/arXiv.2607.05848 keyword: - Central limit theorem - universality - matrix Dyson equation - multi-resolvent local law language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2607.05848 month: '07' oa: 1 oa_version: Preprint project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: arXiv publication_status: submitted status: public title: Mesoscopic eigenvalue statistics for correlated random matrices type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: diamond PlanS_conform: '1' _id: '22381' abstract: - lang: eng text: "Context. X-ray binaries exhibit complex variability patterns studied in the power spectrum. These include the broadband noise (BBN)\r\ncomponents and various types of narrow components called quasi-periodic oscillations (QPOs). There is currently no consensus about\r\nwhat determines the presence or absence of the BBN or what generates the QPOs. Many believe that QPO generation is due to framedragging effects caused by Lense–Thirring torques.\r\nAims. We investigated the potential impact of frame-dragging effects on the accretion disk itself. In particular, we focused on its\r\nimpact on the observed variability and on the presence (and types) of associated QPOs.\r\nMethods. We made analytical estimates to assess the potential presence of a geometric warp in the inner accretion disk during state\r\ntransitions.\r\nResults. We show that the presence of a warp can modify the spectral-timing properties in a way that matches the observed transition\r\nbetween QPO types during outbursts. We also discuss the peculiar case of Cyg X-1, as well as how the hard-to-soft transition could\r\nbe driven by the warp itself.\r\nConclusions. The (expected) emergence of a warp provides a consistent explanation for the evolution of both the BBN and the QPO\r\nproperties during state transitions. This offers a first path toward unifying the variability of black hole X-ray binaries." acknowledgement: "GM acknowledges support from the Polish National Science Center grant 2023/48/Q/ST9/00138 and the Academy of Finland grant 355672. The authors thank the Editor for their insightful comments and effective stewardship of the review process. SGDT acknowledges support under\r\nSTFC Grant ST/X001113/1. This work made use of the python packages\r\nMatplotlib (Hunter 2007), NumPy (Harris et al. 2020), and Stingray v2.2\r\n(Huppenkothen et al. 2019; Bachetti et al. 2024b,a)." article_number: A387 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: G. full_name: Marcel, G. last_name: Marcel - first_name: S. G. D. full_name: Turner, S. G. D. last_name: Turner - first_name: B. J. full_name: Ricketts, B. J. last_name: Ricketts - first_name: V. full_name: López-Barquero, V. last_name: López-Barquero - first_name: D. J. K. full_name: Buisson, D. J. K. last_name: Buisson - first_name: F. full_name: Vincentelli, F. last_name: Vincentelli - first_name: M. full_name: Middleton, M. last_name: Middleton - first_name: C.S. full_name: Reynolds, C.S. last_name: Reynolds - first_name: Mark full_name: Avara, Mark id: c9b42585-7787-11f0-9bdd-bf7d947cf79d last_name: Avara citation: ama: 'Marcel G, Turner SGD, Ricketts BJ, et al. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. Astronomy & Astrophysics. 2026;710. doi:10.1051/0004-6361/202558103' apa: 'Marcel, G., Turner, S. G. D., Ricketts, B. J., López-Barquero, V., Buisson, D. J. K., Vincentelli, F., … Avara, M. (2026). Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202558103' chicago: 'Marcel, G., S. G. D. Turner, B. J. Ricketts, V. López-Barquero, D. J. K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, and Mark Avara. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” Astronomy & Astrophysics. EDP Sciences, 2026. https://doi.org/10.1051/0004-6361/202558103.' ieee: 'G. Marcel et al., “Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations,” Astronomy & Astrophysics, vol. 710. EDP Sciences, 2026.' ista: 'Marcel G, Turner SGD, Ricketts BJ, López-Barquero V, Buisson DJK, Vincentelli F, Middleton M, Reynolds CS, Avara M. 2026. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. Astronomy & Astrophysics. 710, A387.' mla: 'Marcel, G., et al. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” Astronomy & Astrophysics, vol. 710, A387, EDP Sciences, 2026, doi:10.1051/0004-6361/202558103.' short: G. Marcel, S.G.D. Turner, B.J. Ricketts, V. López-Barquero, D.J.K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, M. Avara, Astronomy & Astrophysics 710 (2026). das_tickbox: '0' date_created: 2026-07-21T10:29:36Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-10-21T06:33:09Z day: '01' ddc: - '520' department: - _id: ZoHa doi: 10.1051/0004-6361/202558103 external_id: arxiv: - '2511.10474' file: - access_level: open_access checksum: 95c1695f3c7183b2ad9d58167500b18d content_type: application/pdf creator: dernst date_created: 2026-07-21T12:20:49Z date_updated: 2026-07-21T12:20:49Z file_id: '22382' file_name: 2026_AstronomyAstrophysics_Marcel.pdf file_size: 3286905 relation: main_file success: 1 file_date_updated: 2026-07-21T12:20:49Z fulldoi: https://doi.org/10.1051/0004-6361/202558103 has_accepted_license: '1' intvolume: ' 710' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '06' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 710 year: '2026' ... --- OA_place: publisher _id: '22399' alternative_title: - ISTA Master’s Thesis article_processing_charge: No author: - first_name: Aleksa full_name: Spasić, Aleksa id: ecee9d38-4040-11ef-8843-b941efb445d6 last_name: Spasić citation: ama: Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:10.15479/AT-ISTA-22399 apa: Spasić, A. (2026). Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22399 chicago: Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22399. ieee: A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026. ista: Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria. mla: Spasić, Aleksa. Studying the Evolutionary Systems Biology of the Lac Operon. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22399. short: A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '0' date_created: 2026-07-25T13:08:32Z date_published: 2026-07-27T00:00:00Z date_updated: 2026-10-21T07:47:08Z day: '27' ddc: - '576' degree_awarded: MS department: - _id: GradSch - _id: GaTk - _id: CaGu doi: 10.15479/AT-ISTA-22399 doi_confirm: '1' file: - access_level: closed checksum: c29880dd71fcc37f23ac6e2843066ede content_type: application/pdf creator: aspasic date_created: 2026-07-27T13:00:07Z date_updated: 2026-10-20T08:47:40Z embargo: 2027-07-30 embargo_to: open_access file_id: '22588' file_name: Aleksa_Spasic_Thesis_final.pdf file_size: 1986078 relation: main_file - access_level: closed checksum: 4ebe3bd2d833d913c0756343cca5e5f0 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: aspasic date_created: 2026-07-27T13:00:22Z date_updated: 2026-07-27T13:07:23Z file_id: '22589' file_name: Thesis_final.docx file_size: 1868853 relation: source_file file_date_updated: 2026-10-20T08:47:40Z fulldoi: https://doi.org/10.15479/AT-ISTA-22399 has_accepted_license: '1' language: - iso: eng month: '07' oa_version: Published Version page: '32' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Studying the evolutionary systems biology of the lac operon type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22281' abstract: - lang: eng text: "In this thesis, we took a look at networks, and more specifically, at networks that change over time, whether those are networks in the distributed algorithms sense of the word, or the graph algorithm sense. \r\n\r\nIn distributed algorithms, we looked at two main problems. First, the broadcast problem: given n agents, each agent is tasked to forward a (unique) message to every other agent. Agents collaborate and can copy and forward all messages they have received up until that point. Broadcast is achieved when one agent has successfully broadcast its message to everyone else. We studied the case where the communication network is controlled by an adversary, under the condition that the graph is rooted in every round of communication. We show that the adversary can delay broadcast for at most l\r\n(1 + √\r\n2)n\r\nm\r\n rounds, improving on the $O(n\\log\\log n)$ previous upper bound~\\cite{fugger2020radius}, and asymptotically matching the $\\sim 1.5n$ lower bound~\\cite{schwarz2017linear}.\r\n\r\nWe then looked at the stochastic version of the problem: here, the adversary -- parametrized by $k$ where $k=0$ signifies that the adversary has no control, and $k=n$ that the adversary has full control -- can choose parts of the graph, and the graph is then completed stochastically. Here, we are able to look at a stronger version of broadcast: instead of having $n$ messages trying to be broadcast in parallel, we can assume that only one message needs to be broadcasted. We show the bound $\\Theta(k+\\log n)$.\r\n\r\nThen, we looked at undecided states dynamics in population protocols: given a population of $n$ agents, where each initially holds an opinion among $k$ different ones. In each round, two agents are chosen uniformly at random, and can interact. If they have different opinions, they forget their opinions and become undecided. If one of them is undecided while the other has an opinion, they undecided agent copies they opinion of the decided one. The question is then, how many interactions does it take for the whole population to share the same opinion? We show a $\\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})$ lower bound \ for any $k = o\\left(\\frac {\\sqrt n}{\\log n}\\right)$.\r\nThis is tight for any $ k \\le n^{\\frac 1 2 - \\epsilon}$, where $\\epsilon >0$ can be any small constant, matching the known $O(kn\\log n)$ upper bound for $k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)$~\\cite{DBLP:conf/podc/AmirABBHKL23}.\r\n\r\nFinally, in dynamic algorithms, we study the minimum cut problem: we are given a graph, whose vertex set we want to partition into two subsets such that the number of edges crossing from one subset to the other is minimized. Then, the graph can be updated via edge insertions or deletions, and we must update the solution without recomputing everything from scratch. We present an exact fully-dynamic minimum cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum cut size is at most $2^{\\Theta(\\log^{3/4-c}n)}$ for any $c>0$, improving on the previous algorithm~\\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit is $(\\log n)^{o(1)}$. Using sparsification and randomization techniques, we are able to extend this to all values of the minimum cut in weighted graphs, at the cost of a $(1+o(1))$-approximation ratio." acknowledgement: "This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564)\r\n\"The Design and Evaluation of Modern Fully Dynamic Data Structures\" , from the\r\nAustrian Science Fund (FWF) grant DOI 10.55776/I5982 \"Static and Dynamic Hierarchical\r\nGraph Decompositions\", and from the Austrian Science Fund (FWF) and netIDEE SCIENCE\r\nproject P 33775-N, \"Fast Algorithms for a Reactive Network Layer\".\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Antoine full_name: El-Hayek, Antoine id: 888a098e-fcac-11ee-aff7-d347be57b725 last_name: El-Hayek orcid: 0000-0003-4268-7368 citation: ama: 'El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:10.15479/AT-ISTA-22281' apa: 'El-Hayek, A. (2026). Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22281' chicago: 'El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22281.' ieee: 'A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026.' ista: 'El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.' mla: 'El-Hayek, Antoine. Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22281.' short: 'A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-07-13T09:39:59Z date_published: 2026-07-13T00:00:00Z date_updated: 2026-10-21T08:05:35Z day: '13' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: MoHe doi: 10.15479/AT-ISTA-22281 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 923e4ca769c9ef2f6b0b005444faf462 content_type: application/pdf creator: aelhayek date_created: 2026-07-17T11:39:47Z date_updated: 2026-07-17T11:39:47Z file_id: '22356' file_name: 2026_El-Hayek_Antoine_Thesis.pdf file_size: 5465973 relation: main_file success: 1 - access_level: closed checksum: 262689f9df27dd6c2c7c7861f1de7329 content_type: application/x-zip-compressed creator: aelhayek date_created: 2026-07-17T11:40:34Z date_updated: 2026-07-20T11:29:38Z file_id: '22357' file_name: 2026_El-Hayek_Antoine_Thesis.zip file_size: 9116107 relation: source_file file_date_updated: 2026-07-20T11:29:38Z fulldoi: https://doi.org/10.15479/AT-ISTA-22281 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '244' project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: bda196b2-d553-11ed-ba76-8e8ee6c21103 grant_number: I05982 name: Static and Dynamic Hierarchical Graph Decompositions - _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe grant_number: P33775 name: Fast Algorithms for a Reactive Network Layer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved. related_material: record: - id: '20051' relation: part_of_dissertation status: public - id: '19982' relation: part_of_dissertation status: public - id: '21720' relation: part_of_dissertation status: public - id: '22374' relation: part_of_dissertation status: public - id: '22373' relation: part_of_dissertation status: public - id: '18557' relation: part_of_dissertation status: public status: public supervisor: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 title: 'Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '20991' abstract: - lang: eng text: "Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms." acknowledgement: "I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Diego Fernando full_name: Garcia Castillo, Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo citation: ama: Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:10.15479/AT-ISTA-20991 apa: Garcia Castillo, D. F. (2026). The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20991 chicago: Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20991. ieee: D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026. ista: Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. mla: Garcia Castillo, Diego Fernando. The Genomic Architecture of Local Adaptation in Introduced Populations. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20991. short: D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-01-16T09:47:59Z date_published: 2026-01-16T00:00:00Z date_updated: 2026-10-21T08:18:21Z day: '16' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20991 file: - access_level: closed checksum: 841f1bc073d667125729b2a017f8c37a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20996' file_name: 2026_Garcia_Diego_Thesis.docx file_size: 22456421 relation: source_file - access_level: open_access checksum: a1f33d4f183ce7072eee42a6ccf5340b content_type: application/pdf creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20997' file_name: 2026_Garcia_Diego_Thesis.pdf file_size: 9556719 relation: main_file success: 1 - access_level: closed checksum: 98a80691067174c30fe53f38ce7344e6 content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z description: Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis. file_id: '20998' file_name: 2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar file_size: 54491433 relation: supplementary_material - access_level: open_access checksum: 99a3cab2fa36666b9a92eefc27d586da content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z file_id: '20999' file_name: 2026_DiegoGarcia_Thesis-Supplementary_Material.rar file_size: 7982811 relation: supplementary_material - access_level: open_access checksum: 255fdf56b2932c46bf27c63aa6106a4f content_type: text/plain creator: dgarciac date_created: 2026-01-16T13:08:59Z date_updated: 2026-01-16T13:08:59Z file_id: '21000' file_name: README.txt file_size: 732 relation: supplementary_material file_date_updated: 2026-01-16T13:08:59Z fulldoi: https://doi.org/10.15479/AT-ISTA-20991 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '01' oa: 1 oa_version: Published Version page: '199' publication_identifier: isbn: - 978-3-99078-077-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18498' relation: research_data status: public - id: '18491' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 title: The genomic architecture of local adaptation in introduced populations tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: publisher _id: '22684' abstract: - lang: eng text: "Contact electrification (CE) is a simple yet elusive phenomenon that occurs when two materials come into contact and separate, leaving behind net electrical charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In this thesis, we investigate CE from three complementary perspectives: developing a quantitative method to measure charge at the nanoscale, exploring the dynamic behavior of charge on insulating surfaces, and uncovering the role of mechanical history in forming a triboelectric series.\r\n\r\nIn the first part, we establish a rigorous framework for converting qualitative Kelvin probe force microscopy (KPFM) voltage maps into quantitative charge density distributions. Using finite element method (FEM) simulations, we determine the point-spread function of the KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed by numerical deconvolution. This procedure enables the recovery of both the magnitude and sign of charge density with high fidelity, resolving nanoscale features that are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces, we show that existing analytical approximations, such as parallel plate or spherical models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM approach therefore provides a fast and general method to convert qualitative KPFM signals into quantitative charge data, enabling nanoscale charge mapping under realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal stability of CE-induced charges and identify the key material factors that determine whether KPFM can capture meaningful charge patterns. Through time-resolved experiments combining a custom-built transfer system with both microscopic and macroscopic measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve CE charge long enough for stationary imaging. For less conductive polymers, such as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction. Using a simple capacitor-based model, we reproduce the observed decay dynamics and confirm that the transferred charge decays characteristic to the sample's bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn the third part, we address the question: can we form a triboelectric series with identical materials? Using controlled repetitive contact experiments, we show that nominally identical materials can progressively order themselves into a triboelectric series, where surfaces with more contact history charge negatively relative to fresher ones. By constructing a minimal model based on this ``contact bias'', we replicate the evolution from random to ordered charging observed in experiments. Supporting surface analyses, including atomic force microscopy, reveal that repeated contact induces nanoscale morphological changes, suggesting a mechanism tightly coupled to mechanical strain. These results highlight the crucial role of surface history and nanoscale mechanics in dictating charge transfer, motivating further exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric polarization." acknowledged_ssus: - _id: NanoFab - _id: ScienComp - _id: LifeSc - _id: M-Shop - _id: EM-Fac acknowledgement: "This project has received financing from the European Research Council grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and innovation programme.\r\nThis research was supported by the Scientific Service Units of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility, the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina Strugaru for help with testing the device for Young’s modulus measurements.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Felix full_name: Pertl, Felix id: 6313aec0-15b2-11ec-abd3-ed67d16139af last_name: Pertl orcid: 0000-0003-0463-5794 citation: ama: Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:10.15479/AT-ISTA-22684 apa: Pertl, F. (2026). Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22684 chicago: Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22684. ieee: F. Pertl, “Experimental probing of nanoscale charge features and surface morphology changes during tribocharging,” Institute of Science and Technology Austria, 2026. ista: Pertl F. 2026. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria. mla: Pertl, Felix. Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22684. short: F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-08-12T09:44:40Z date_published: 2026-08-12T00:00:00Z date_updated: 2026-10-21T08:39:24Z day: '12' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-22684 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 0a4f5a941c40b921447e72291d72bc6f content_type: application/x-zip-compressed creator: fpertl date_created: 2026-08-12T13:04:21Z date_updated: 2026-08-12T13:04:21Z file_id: '22690' file_name: 2026_Pertl_Felix_Thesis.zip file_size: 31192621 relation: source_file - access_level: open_access checksum: ae60dcdb363222138886b2857643d4e3 content_type: application/pdf creator: fpertl date_created: 2026-08-12T13:04:21Z date_updated: 2026-08-12T13:04:21Z file_id: '22691' file_name: 2026_Pertl_Felix_Thesis.pdf file_size: 27882509 relation: main_file file_date_updated: 2026-08-12T13:04:21Z fulldoi: https://doi.org/10.15479/AT-ISTA-22684 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '107' project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication_identifier: isbn: - 978-3-99078-083-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20481' relation: part_of_dissertation status: public - id: '12109' relation: part_of_dissertation status: public - id: '19278' relation: part_of_dissertation status: public - id: '17373' relation: part_of_dissertation status: public status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 title: Experimental probing of nanoscale charge features and surface morphology changes during tribocharging tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '17437' abstract: - lang: eng text: We prove that the zero-fiber of the moment map of a totally negative quiver has rational singularities. Our proof consists in generalizing dimension bounds on jet spaces of this fiber, which were introduced by Budur. We also transfer the rational singularities property to other moduli spaces of objects in 2-Calabi-Yau categories, based on recent work of Davison. This has interesting arithmetic applications on quiver moment maps and moduli spaces of objects in 2-Calabi-Yau categories. First, we generalize results of Wyss on the asymptotic behaviour of counts of jets of quiver moment maps over finite fields. Moreover, we interpret the limit of counts of jets on a given moduli space as its p-adic volume under a canonical measure analogous to the measure built by Carocci, Orecchia and Wyss on certain moduli spaces of coherent sheaves. acknowledgement: "I would like to warmly thank Dimitri Wyss for his guidance and supervision and Nero Budur for helpful discussions and answering all my questions on his previous works. I would also like to thank Francesca Carocci, Ben Davison, Lucien Hennecart and Olivier Schiffmann for helpful remarks and discussions during the writing of this paper. Finally, I would like to thank the anonymous referees for their careful reading and suggesting improvements in the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This work was supported by the Swiss National Science Foundation [No. 196960]. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Tanguy full_name: Vernet, Tanguy id: 19f1e3bf-c59a-11ee-a1af-ed269948817b last_name: Vernet citation: ama: Vernet T. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 2026;31:1047-1083. doi:10.1007/s00031-024-09873-0 apa: Vernet, T. (2026). Rational singularities for moment maps of totally negative quivers. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-024-09873-0 chicago: Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” Transformation Groups. Springer Nature, 2026. https://doi.org/10.1007/s00031-024-09873-0. ieee: T. Vernet, “Rational singularities for moment maps of totally negative quivers,” Transformation Groups, vol. 31. Springer Nature, pp. 1047–1083, 2026. ista: Vernet T. 2026. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 31, 1047–1083. mla: Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” Transformation Groups, vol. 31, Springer Nature, 2026, pp. 1047–83, doi:10.1007/s00031-024-09873-0. short: T. Vernet, Transformation Groups 31 (2026) 1047–1083. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Not applicable. date_created: 2024-08-18T22:01:04Z date_published: 2026-03-01T00:00:00Z date_updated: 2026-10-21T10:55:21Z day: '01' ddc: - '510' department: - _id: TaHa doi: 10.1007/s00031-024-09873-0 ec_funded: 1 external_id: isi: - '001287455300001' file: - access_level: open_access checksum: 8985b4154b730284d3412ddc9e55d965 content_type: application/pdf creator: dernst date_created: 2026-07-23T05:50:09Z date_updated: 2026-07-23T05:50:09Z file_id: '22385' file_name: 2026_TransformationGroups_Vernet.pdf file_size: 912029 relation: main_file success: 1 file_date_updated: 2026-07-23T05:50:09Z fulldoi: https://doi.org/10.1007/s00031-024-09873-0 has_accepted_license: '1' intvolume: ' 31' isi: 1 language: - iso: eng mathsc: - 14B05 - 14D23 - 14G20 - 16G20 month: '03' oa: 1 oa_version: Published Version page: 1047-1083 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Transformation Groups publication_identifier: eissn: - 1531-586X issn: - 1083-4362 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: no title: Rational singularities for moment maps of totally negative quivers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 31 year: '2026' ... --- OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22247' abstract: - lang: eng text: "A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, …, k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring).\r\nHere, we investigate the complexity of approximating the “linearly ordered chromatic number” of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023)." acknowledgement: "This research was supported by the Charles University project PRIMUS/21/SCI/014, by the Ministry of Education, Youth\r\nand Sports of the Czech Republic under the project MSCAfellow5_MUNI (CZ.02.01.01/00/22_010/0003229), and by the\r\nAustrian Science Fund (FWF project P31312-N35). This research was funded by UKRI EP/X024431/1 and by a Clarendon\r\nFund Scholarship. This project has received funding from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No 101034413.\r\n" article_number: '10' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Marek full_name: Filakovský, Marek id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87 last_name: Filakovský - first_name: Tamio Vesa full_name: Nakajima, Tamio Vesa last_name: Nakajima - first_name: Jakub full_name: Opršal, Jakub id: ec596741-c539-11ec-b829-c79322a91242 last_name: Opršal orcid: 0000-0003-1245-3456 - first_name: Gianluca full_name: Tasinato, Gianluca id: 0433290C-AF8F-11E9-A4C7-F729E6697425 last_name: Tasinato - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. ACM Transactions on Computation Theory. 2026;18(2). doi:10.1145/3779121 apa: Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U. (2026). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. ACM Transactions on Computation Theory. Association for Computing Machinery. https://doi.org/10.1145/3779121 chicago: Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” ACM Transactions on Computation Theory. Association for Computing Machinery, 2026. https://doi.org/10.1145/3779121. ieee: M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” ACM Transactions on Computation Theory, vol. 18, no. 2. Association for Computing Machinery, 2026. ista: Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2026. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. ACM Transactions on Computation Theory. 18(2), 10. mla: Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” ACM Transactions on Computation Theory, vol. 18, no. 2, 10, Association for Computing Machinery, 2026, doi:10.1145/3779121. short: M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, ACM Transactions on Computation Theory 18 (2026). corr_author: '1' das_tickbox: '0' date_created: 2026-07-05T22:01:37Z date_published: 2026-05-04T00:00:00Z date_updated: 2026-10-21T13:23:55Z day: '04' ddc: - '500' department: - _id: UlWa doi: 10.1145/3779121 ec_funded: 1 external_id: arxiv: - '2312.12981' file: - access_level: open_access checksum: 0399ab94085878fc810084845eabd627 content_type: application/pdf creator: dernst date_created: 2026-07-06T09:03:02Z date_updated: 2026-07-06T09:03:02Z file_id: '22252' file_name: 2026_TransactionsGraphics_Filakovsky.pdf file_size: 941518 relation: main_file success: 1 file_date_updated: 2026-07-06T09:03:02Z fulldoi: https://doi.org/10.1145/3779121 has_accepted_license: '1' intvolume: ' 18' issue: '2' keyword: - Constraint satisfaction problem - hypergraph colouring - promise problem - topological methods language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26611F5C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31312 name: Algorithms for Embeddings and Homotopy Theory - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: ACM Transactions on Computation Theory publication_identifier: eissn: - 1942-3462 issn: - 1942-3454 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '15168' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19860' abstract: - lang: eng text: "An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in R^3\r\n consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in R^3 admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument. We prove the following variant of this result: any mass distribution (or point set) in R^3 admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction. Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in R^3 (with prescribed normal direction of one of the planes) in time O(n^7/3). A preliminary version of this work appeared in SoCG’24 (Aronov et al., 40th International Symposium on Computational Geometry, 2024)." acknowledgement: Work by BA was supported by NSF grants CCF 15-40656 and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of this research was conducted while BA was visiting ISTA in the summers of 2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting Professorship. Research of BA also partially supported by ERC grant no. 882971, “GeoScape,” and by the Erdős Center. Work by AB was supported by Australian Research Council grant DP220102212. Work by IR was supported by a Tandon School of Engineering Fellowship and by NSF Grant CCF-20-08551. BA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work. Open Access funding enabled and organized by CAUL and its Member Institutions. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Boris full_name: Aronov, Boris last_name: Aronov - first_name: Abdul full_name: Basit, Abdul last_name: Basit - first_name: Indu full_name: Ramesh, Indu last_name: Ramesh - first_name: Gianluca full_name: Tasinato, Gianluca id: 0433290C-AF8F-11E9-A4C7-F729E6697425 last_name: Tasinato - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. Discrete & Computational Geometry. 2026;75:1331-1355. doi:10.1007/s00454-025-00739-0 apa: Aronov, B., Basit, A., Ramesh, I., Tasinato, G., & Wagner, U. (2026). Eight-partitioning points in 3D, and efficiently too. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-025-00739-0 chicago: Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” Discrete & Computational Geometry. Springer Nature, 2026. https://doi.org/10.1007/s00454-025-00739-0. ieee: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” Discrete & Computational Geometry, vol. 75. Springer Nature, pp. 1331–1355, 2026. ista: Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2026. Eight-partitioning points in 3D, and efficiently too. Discrete & Computational Geometry. 75, 1331–1355. mla: Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” Discrete & Computational Geometry, vol. 75, Springer Nature, 2026, pp. 1331–55, doi:10.1007/s00454-025-00739-0. short: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, Discrete & Computational Geometry 75 (2026) 1331–1355. das_tickbox: '0' date_created: 2025-06-22T22:02:07Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-10-21T13:38:17Z day: '01' ddc: - '500' department: - _id: UlWa doi: 10.1007/s00454-025-00739-0 external_id: arxiv: - '2403.02627' isi: - '001506904300001' file: - access_level: open_access checksum: a32774a0d14f46cafbd77bfb9d9ac4b6 content_type: application/pdf creator: dernst date_created: 2026-07-23T11:14:05Z date_updated: 2026-07-23T11:14:05Z file_id: '22395' file_name: 2026_DiscreteCompGeom_Aronov.pdf file_size: 525281 relation: main_file success: 1 file_date_updated: 2026-07-23T11:14:05Z fulldoi: https://doi.org/10.1007/s00454-025-00739-0 has_accepted_license: '1' intvolume: ' 75' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1331-1355 publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/s00454-025-00759-w record: - id: '20339' relation: dissertation_contains status: public - id: '18917' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Eight-partitioning points in 3D, and efficiently too tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2026' ... --- OA_place: repository OA_type: green _id: '21763' abstract: - lang: eng text: Reactive oxygen species (ROS) have been implicated in multiple signaling processes in plants, but the underlying mechanisms and roles remain enigmatic. In this study, we developed a method of live imaging of apoplastic ROS at the root surface. Distinct signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts. Genetic and optogenetic manipulations of Arabidopsis identified calcium transients as necessary and sufficient for ROS bursts through activation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS bursts are not required, but they do limit gravity-induced root bending. Root bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH oxidase activation. The resulting ROS production stiffens cell walls to facilitate soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility and stiffness to navigate soil. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "We gratefully acknowledge the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) (both of ISTA) and the Hounsfield CT Facility (University of Nottingham) for support with imaging and the Growth Facility (IPMB) for plant cultivation. We thank M. Fendrych and his team for help with the microfluidics upgrades and J. Atkinson at the University of Nottingham MakerSpace for 3D printing of Arabidopsis mini-soil columns.\r\nThis project received funding from the European Research Council (ERC; 101142681 CYNIPS) and the Austrian Science Fund (FWF; P 37051-B). I.K. was cofunded by the European Union, Horizon Europe, project MOLIPEC, ID 101087030 and CSF project 25-16449S. L.V. and B.K.P. acknowledge funding from UK Research and Innovation (UKRI) Frontiers Research (EP/Y036697/1). M.J.B. acknowledges funding from ERC SYNERGY (grant 101118769 HYDROSENSING). The study was partially supported by the Université Paris Cité, Idex ANR-18-IDEX-0001, funded by the French Government through its “Investments for the Future” program and also by the projects “Mecha-Nuc” ANR-20-CE13-0025-03 and “scEm-bryoMech” ANR-21-CE13-0046. P.D. acknowledges support by Human Frontier Science Program Organization grant 2022-RG107. P.V. acknowledges support provided by “Programme blanc” of the Graduate School BIOSPHERA, Université Paris-Saclay. Phytohormonal analysis was performed using the service laboratory funded by Toward Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the European Regional Development Fund (ERDF) program Johannes Amos Comenius. This research was funded in whole or in part by the Austrian Science Fund (P 37051-B) and UK Research and Innovation (EP/Y036697/1), cOAlition S organizations, and by the European Research Council (101142681 CYNIPS, 101118769 HYDROSENSING); as required, the author will make the Author Accepted Manuscript (AAM) version available under a CC BY public copyright license." article_processing_charge: No article_type: original author: - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Shiqiang full_name: Gao, Shiqiang last_name: Gao - first_name: Matteo full_name: Citterico, Matteo last_name: Citterico - first_name: Kai R. full_name: Konrad, Kai R. last_name: Konrad - first_name: Georg full_name: Nagel, Georg last_name: Nagel - first_name: Michael full_name: Wrzaczek, Michael last_name: Wrzaczek - first_name: Léa full_name: Cascaro, Léa last_name: Cascaro - first_name: Pauline full_name: Vinet, Pauline last_name: Vinet - first_name: Pauline full_name: Durand, Pauline last_name: Durand - first_name: Atef full_name: Asnacios, Atef last_name: Asnacios - first_name: Lokesh full_name: Verma, Lokesh last_name: Verma - first_name: Malcolm J. full_name: Bennett, Malcolm J. last_name: Bennett - first_name: Bipin K. full_name: Pandey, Bipin K. last_name: Pandey - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. 2026;392(6795):296-300. doi:10.1126/science.adu8197 apa: Kulich, I., Vladimirtsev, D., Randuch, M., Gao, S., Citterico, M., Konrad, K. R., … Friml, J. (2026). Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. AAAS. https://doi.org/10.1126/science.adu8197 chicago: Kulich, Ivan, Dmitrii Vladimirtsev, Marek Randuch, Shiqiang Gao, Matteo Citterico, Kai R. Konrad, Georg Nagel, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” Science. AAAS, 2026. https://doi.org/10.1126/science.adu8197. ieee: I. Kulich et al., “Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation,” Science, vol. 392, no. 6795. AAAS, pp. 296–300, 2026. ista: Kulich I, Vladimirtsev D, Randuch M, Gao S, Citterico M, Konrad KR, Nagel G, Wrzaczek M, Cascaro L, Vinet P, Durand P, Asnacios A, Verma L, Bennett MJ, Pandey BK, Friml J. 2026. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. 392(6795), 296–300. mla: Kulich, Ivan, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” Science, vol. 392, no. 6795, AAAS, 2026, pp. 296–300, doi:10.1126/science.adu8197. short: I. Kulich, D. Vladimirtsev, M. Randuch, S. Gao, M. Citterico, K.R. Konrad, G. Nagel, M. Wrzaczek, L. Cascaro, P. Vinet, P. Durand, A. Asnacios, L. Verma, M.J. Bennett, B.K. Pandey, J. Friml, Science 392 (2026) 296–300. corr_author: '1' date_created: 2026-04-26T22:01:47Z date_published: 2026-04-16T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '16' ddc: - '580' department: - _id: JiFr - _id: GradSch doi: 10.1126/science.adu8197 external_id: pmid: - '41990180' file: - access_level: open_access checksum: eb5b29247832ecdc53c8146da0509bbe content_type: application/pdf creator: dernst date_created: 2026-05-07T05:54:43Z date_updated: 2026-05-07T05:54:43Z file_id: '21832' file_name: 2026_Science_Kulich_accepted.pdf file_size: 6150733 relation: main_file success: 1 file_date_updated: 2026-05-07T05:54:43Z fulldoi: https://doi.org/10.1126/science.adu8197 has_accepted_license: '1' intvolume: ' 392' issue: '6795' language: - iso: eng month: '04' oa: 1 oa_version: Accepted Version page: 296-300 pmid: 1 project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' related_material: record: - id: '23145' relation: dissertation_contains status: public scopus_import: '1' status: public title: Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 392 year: '2026' ... --- OA_place: publisher _id: '23145' acknowledged_ssus: - _id: LifeSc - _id: M-Shop - _id: CampIT - _id: Bio acknowledgement: "European Research Council (101142681 CYNIPS), Cyclic nucleotides as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors, \r\nDOI: https://doi.org/10.55776/P37051 " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch citation: ama: 'Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:10.15479/AT-ISTA-23145' apa: 'Randuch, M. (2026). Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-23145' chicago: 'Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-23145.' ieee: 'M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.' ista: 'Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria.' mla: 'Randuch, Marek. Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-23145.' short: 'M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-10-16T17:14:40Z date_published: 2026-10-18T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '18' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-23145 doi_confirm: '1' file: - access_level: closed checksum: 4ace20ba4f1bb0f8dcc3f8eb45eb68fa content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mranduch date_created: 2026-10-20T09:17:28Z date_updated: 2026-10-20T11:48:37Z file_id: '23176' file_name: 2026_Marek_Randuch_Thesis.docx file_size: 89544771 relation: source_file - access_level: closed checksum: fc630c7e8d795e7f13000cbb428424b3 content_type: application/pdf creator: mranduch date_created: 2026-10-20T09:17:20Z date_updated: 2026-10-20T11:48:37Z embargo: 2027-10-20 embargo_to: open_access file_id: '23177' file_name: 2026_Marek_Randuch_Thesis.pdf file_size: 28321059 relation: main_file file_date_updated: 2026-10-20T11:48:37Z fulldoi: https://doi.org/10.15479/AT-ISTA-23145 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa_version: Published Version page: '289' project: - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '21763' relation: part_of_dissertation status: public - id: '23175' relation: part_of_dissertation status: public - id: '23174' relation: part_of_dissertation status: public - id: '20656' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Fast growth responses in plants: Growth regulation and phospho-proteomic ' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '23175' abstract: - lang: eng text: Plants must continually balance growth with arrest, especially under stress. Auxin signaling acts as a central regulatory hub in this process, yet the mechanisms that dynamically tune early auxin signalling in real time remain unknown. Here, we used the light-gated, Ca2+-permeable Channelrhodopsin 2 variant XXM2.0 to optogenetically impose defined Ca2+ signatures on Arabidopsis root cells. Repetitive light activation triggered cytosolic Ca2+ signals that in turn suppressed auxin-induced membrane depolarization and Ca2+ transients. Moreover, prolonged optogenetic Ca2+ stimulation affects auxin-responsive transcriptional reprogramming. As phenotypic output, reversible inhibition of root growth by suppressing cell division and elongation was observed. We further identify a candidate CaM7–CNGC14 module that likely mediates Ca2+-dependent gating of early auxin signalling. Our study thus introduces a synthetic biology approach to decompose calcium–auxin crosstalk in plant cells, and demonstrates that optogenetically imposed cytosolic Ca2+ signals act as dynamic regulators of auxin susceptibility in roots. acknowledgement: "We would like to thank Dirk Becker (University of Wuerzburg) for his help in making the optogenetic constructs and for his comments on the manuscript. We also appreciate Rob Roelfsema (University of Wuerzburg) for his feedback on the manuscript. We sincerely thank the anonymous reviewers for the thoughtful and inspiring suggestions that helped broaden the discussion and identify important future research directions. Funding\r\nNational Key R&D Program of China, 2025YFA0923400 (RH)\r\n\r\nNational Natural Science Foundation of China (NSFC), W2531024 (RH); 32271501(NL)\r\n\r\nNSFC-Excellent Young Scientists Fund Program (overseas) (SH)\r\n\r\nNSFC-RFIS, ZB2025101410702 (RH)\r\n\r\nGuangdong Pearl River Talents Program, 2023ZT10N033\r\n\r\nChina Scholarship Council no. 202306510063 (HS)\r\n\r\nThe European Research Council grant 101142681 CYNIPS (JF)\r\n\r\nAustrian Science Fund grant FWF; P 37051-B (JF)\r\n\r\nGerman Research Foundation grant CRC 1644 (512328399; 512328399) (KK, ZH)\r\n\r\nERC Synergy project STARMORPH, reg. no. 101166880 (AP, ON)" article_processing_charge: No author: - first_name: Huifang full_name: Song, Huifang last_name: Song - first_name: Angel full_name: Baudon, Angel last_name: Baudon - first_name: Matthias full_name: Freund, Matthias last_name: Freund - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Novák full_name: Ondřej, Novák last_name: Ondřej - first_name: Zhaohui full_name: He, Zhaohui last_name: He - first_name: Kerstin full_name: Kaufmann, Kerstin last_name: Kaufmann - first_name: 'Nan' full_name: Li, Nan last_name: Li - first_name: Matthew full_name: Gilliham, Matthew last_name: Gilliham - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Rainer full_name: Hedrich, Rainer last_name: Hedrich - first_name: Shouguang full_name: Huang, Shouguang last_name: Huang biorxivid: 1 citation: ama: Song H, Baudon A, Freund M, et al. Ca2+ signature gates early auxin signaling in Arabidopsis roots. bioRxiv. doi:10.1101/2025.10.04.680446 apa: Song, H., Baudon, A., Freund, M., Randuch, M., Pěnčík, A., Ondřej, N., … Huang, S. (n.d.). Ca2+ signature gates early auxin signaling in Arabidopsis roots. bioRxiv. https://doi.org/10.1101/2025.10.04.680446 chicago: Song, Huifang, Angel Baudon, Matthias Freund, Marek Randuch, Aleš Pěnčík, Novák Ondřej, Zhaohui He, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis Roots.” BioRxiv, n.d. https://doi.org/10.1101/2025.10.04.680446. ieee: H. Song et al., “Ca2+ signature gates early auxin signaling in Arabidopsis roots,” bioRxiv. . ista: Song H, Baudon A, Freund M, Randuch M, Pěnčík A, Ondřej N, He Z, Kaufmann K, Li N, Gilliham M, Friml J, Hedrich R, Huang S. Ca2+ signature gates early auxin signaling in Arabidopsis roots. bioRxiv, 10.1101/2025.10.04.680446. mla: Song, Huifang, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis Roots.” BioRxiv, doi:10.1101/2025.10.04.680446. short: H. Song, A. Baudon, M. Freund, M. Randuch, A. Pěnčík, N. Ondřej, Z. He, K. Kaufmann, N. Li, M. Gilliham, J. Friml, R. Hedrich, S. Huang, BioRxiv (n.d.). corr_author: '1' date_created: 2026-10-19T11:51:47Z date_published: 2026-08-26T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '26' department: - _id: JiFr doi: 10.1101/2025.10.04.680446 external_id: biorxivid: - 10.1101/2025.10.04.680446 fulldoi: https://doi.org/10.1101/2025.10.04.680446 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.10.04.680446 month: '08' oa: 1 oa_version: Preprint project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: bioRxiv publication_status: draft related_material: record: - id: '23145' relation: dissertation_contains status: public status: public title: Ca2+ signature gates early auxin signaling in Arabidopsis roots tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_type: closed access _id: '23197' abstract: - lang: eng text: We develop a quantum theory of light-matter interactions in 229Th nanophotonic resonators pumped via the optonuclear quadrupolar effect, predicting detectable photon fluxes with realistic platforms and revealing how collective dynamics shape the future nuclear clock performance. alternative_title: - Technical Digest Series article_number: FTU1B.4 article_processing_charge: No author: - first_name: Karen full_name: Mamian, Karen id: d21e88e4-b0a3-11f1-8f28-b033c1af3b5a last_name: Mamian - first_name: Jan full_name: De Haan, Jan last_name: De Haan - first_name: Toby full_name: Bi, Toby last_name: Bi - first_name: Swadheen full_name: Dubey, Swadheen last_name: Dubey - first_name: Georgy A. full_name: Kazakov, Georgy A. last_name: Kazakov - first_name: Kjeld full_name: Beeks, Kjeld last_name: Beeks - first_name: Christoph full_name: Marquardt, Christoph last_name: Marquardt - first_name: Sandro full_name: Kraemer, Sandro last_name: Kraemer - first_name: Lino M.C. full_name: Pereira, Lino M.C. last_name: Pereira - first_name: Pascal full_name: Del’Haye, Pascal last_name: Del’Haye - first_name: Kasper full_name: Van Gasse, Kasper last_name: Van Gasse - first_name: Thorsten full_name: Schumm, Thorsten last_name: Schumm - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes citation: ama: 'Mamian K, De Haan J, Bi T, et al. Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. In: CLEO Fundamental Science Proceedings. Optica Publishing Group; 2026. doi:10.1364/CLEO_FS.2026.FTU1B.4' apa: 'Mamian, K., De Haan, J., Bi, T., Dubey, S., Kazakov, G. A., Beeks, K., … Roques-Carmes, C. (2026). Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. In CLEO Fundamental Science Proceedings. Long Beach, CA, United States: Optica Publishing Group. https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4' chicago: Mamian, Karen, Jan De Haan, Toby Bi, Swadheen Dubey, Georgy A. Kazakov, Kjeld Beeks, Christoph Marquardt, et al. “Collective Optonuclear Cavity Quantum Electrodynamics in 229Th Nanophotonic Resonators.” In CLEO Fundamental Science Proceedings. Optica Publishing Group, 2026. https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4. ieee: K. Mamian et al., “Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators,” in CLEO Fundamental Science Proceedings, Long Beach, CA, United States, 2026. ista: 'Mamian K, De Haan J, Bi T, Dubey S, Kazakov GA, Beeks K, Marquardt C, Kraemer S, Pereira LMC, Del’Haye P, Van Gasse K, Schumm T, Roques-Carmes C. 2026. Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. CLEO Fundamental Science Proceedings. CLEO: Fundamental Science, Technical Digest Series, , FTU1B.4.' mla: Mamian, Karen, et al. “Collective Optonuclear Cavity Quantum Electrodynamics in 229Th Nanophotonic Resonators.” CLEO Fundamental Science Proceedings, FTU1B.4, Optica Publishing Group, 2026, doi:10.1364/CLEO_FS.2026.FTU1B.4. short: K. Mamian, J. De Haan, T. Bi, S. Dubey, G.A. Kazakov, K. Beeks, C. Marquardt, S. Kraemer, L.M.C. Pereira, P. Del’Haye, K. Van Gasse, T. Schumm, C. Roques-Carmes, in:, CLEO Fundamental Science Proceedings, Optica Publishing Group, 2026. conference: end_date: 2026-05-06 location: Long Beach, CA, United States name: 'CLEO: Fundamental Science' start_date: 2026-05-02 corr_author: '1' date_created: 2026-10-25T23:02:24Z date_published: 2026-05-15T00:00:00Z date_updated: 2026-10-27T10:53:59Z day: '15' department: - _id: ChRo doi: 10.1364/CLEO_FS.2026.FTU1B.4 fulldoi: https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4 language: - iso: eng month: '05' oa_version: None publication: CLEO Fundamental Science Proceedings publication_identifier: isbn: - '9781957171586' publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21983' abstract: - lang: eng 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.' 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' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Elia full_name: Mascolo, Elia id: 776a6ed0-a053-11f0-8635-80b95e0e0d53 last_name: Mascolo orcid: 0000-0003-2977-7844 - first_name: Reka E full_name: Körei, Reka E id: 50FDE43E-AA30-11E9-A72B-8A12E6697425 last_name: Körei - first_name: Santiago full_name: Herrera-Álvarez, Santiago last_name: Herrera-Álvarez - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: 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. Current Opinion in Genetics & Development. 2026;99. doi:10.1016/j.gde.2026.102483' apa: 'Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., 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 & Development. Elsevier. https://doi.org/10.1016/j.gde.2026.102483' 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.” Current Opinion in Genetics & Development. Elsevier, 2026. https://doi.org/10.1016/j.gde.2026.102483.' 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,” Current Opinion in Genetics & Development, vol. 99. Elsevier, 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 & Development. 99, 102483.' mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” Current Opinion in Genetics & Development, vol. 99, 102483, Elsevier, 2026, doi:10.1016/j.gde.2026.102483.' short: E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics & Development 99 (2026). corr_author: '1' date_created: 2026-06-10T07:37:12Z date_published: 2026-05-09T00:00:00Z date_updated: 2026-10-27T13:12:27Z day: '09' ddc: - '570' department: - _id: GradSch - _id: CaGu - _id: GaTk doi: 10.1016/j.gde.2026.102483 external_id: arxiv: - '2601.19681' fulldoi: https://doi.org/10.1016/j.gde.2026.102483 has_accepted_license: '1' intvolume: ' 99' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.gde.2026.102483 month: '05' oa: 1 oa_version: Published Version publication: Current Opinion in Genetics & Development publication_identifier: eissn: - 1879-0380 issn: - 0959-437X publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '23198' abstract: - lang: eng text: Small RNAs (sRNAs) are widespread across diverse flowering plant species and play important roles regulating reproduction and environmental responses. However, how sRNAs exert their function is largely unknown, likely due to their typical origin in non-genic regions, the lack of distinct gene targets, and the sparse characterization of their associated Argonaute (AGO) effector proteins. Here we show that Arabidopsis male reproductive sRNAs associate with AGO4, 5, 6 and 9, all of which are enriched in meiocytes along with RNA Polymerase V (Pol V). This enables these sRNAs to methylate loci with imperfect sequence homology. AGO4, AGO6 and AGO9 predominantly load 24-nucleotide (nt) Pol IV-derived sRNAs and mediate DNA methylation in meiocytes in a dosage-dependent manner. Despite closer homology to microRNA-associated AGO1 and AGO10, AGO5 primarily binds CLSY3- and Pol IV-derived 21-24 nt sRNAs. Transcriptomic and methylomic analyses of meiocytes from single and compound ago mutants demonstrate distinct yet complementary roles of AGO4/6/9 and AGO5 in regulating protein-coding genes and silencing transposons in the germline. These molecular disruptions are accompanied by significant meiotic defects. Together, our findings reveal how AGO4/6/9-mediated DNA methylation and AGO5, likely acting through post-transcriptional gene silencing, work together to promote male germline development. acknowledgement: We thank Michael J. Axtell for generously sharing ago4-4 ago6-2, ago6-2 ago9-1 double and ago4-4 ago6-2 ago9-1 triple mutants. We thank the John Innes Centre Bioimaging Facility and ISTA Imaging and Optics Facility for their assistance with the confocal microscopy, and the ISTA Scientific Computing Facility for high performance computing resources. This work was funded by a Marie Curie Postdoctoral Fellowship (101153710; C.Y.), a European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (ISTA Bridge Fellowship) (S.X.), a DFG grant (FOR 5235 CSCS; A.S.), a European Research Council (ERC) Starting Grant (804981; X.F) and an ERC Consolidator Grant (101126201; C.Y. and XF). article_number: '10758' article_processing_charge: Yes article_type: original author: - first_name: Jincheng full_name: Long, Jincheng last_name: Long - first_name: Chao full_name: Yang, Chao id: 082e3e6e-8069-11ed-8390-c8cce7b1aaca last_name: Yang - first_name: Shujuan full_name: Xu, Shujuan id: 9724dd9d-f591-11ee-bd51-e97ed0652286 last_name: Xu - first_name: Joke G full_name: De Jaeger-Braet, Joke G id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5 last_name: De Jaeger-Braet - first_name: Wenjing full_name: She, Wenjing last_name: She - first_name: Seijiro full_name: Ono, Seijiro last_name: Ono - first_name: James full_name: Walker, James last_name: Walker - first_name: Ygor full_name: de Souza Vieira, Ygor id: af019b77-d2a9-11f1-9e65-c47a5932b764 last_name: de Souza Vieira - first_name: Arp full_name: Schnittger, Arp last_name: Schnittger - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: Long J, Yang C, Xu S, et al. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. 2026;17. doi:10.1038/s41467-026-77326-1 apa: Long, J., Yang, C., Xu, S., De Jaeger-Braet, J. G., She, W., Ono, S., … Feng, X. (2026). Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-026-77326-1 chicago: Long, Jincheng, Chao Yang, Shujuan Xu, Joke G De Jaeger-Braet, Wenjing She, Seijiro Ono, James Walker, Ygor de Souza Vieira, Arp Schnittger, and Xiaoqi Feng. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-77326-1. ieee: J. Long et al., “Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline,” Nature Communications, vol. 17. Springer Nature, 2026. ista: Long J, Yang C, Xu S, De Jaeger-Braet JG, She W, Ono S, Walker J, de Souza Vieira Y, Schnittger A, Feng X. 2026. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. 17, 10758. mla: Long, Jincheng, et al. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” Nature Communications, vol. 17, 10758, Springer Nature, 2026, doi:10.1038/s41467-026-77326-1. short: J. Long, C. Yang, S. Xu, J.G. De Jaeger-Braet, W. She, S. Ono, J. Walker, Y. de Souza Vieira, A. Schnittger, X. Feng, Nature Communications 17 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Illumina sequencing data (RIP-seq, BS-seq, and RNA-seq) generated in this study have been deposited in the NCBI BioProject and are accessible under accession number PRJNA1192978. Published BS-seq data of Arabidopsis meiocyte used in this study for Fig. 4a are available in the NCBI GEO database under accession code GSE161625. All custom codes are available via the request to the corresponding author. date_created: 2026-10-27T10:38:56Z date_published: 2026-10-14T00:00:00Z date_updated: 2026-10-28T08:43:20Z day: '14' ddc: - '580' department: - _id: XiFe doi: 10.1038/s41467-026-77326-1 ec_funded: 1 external_id: pmid: - '42869904' file: - access_level: open_access checksum: f24efcba89d880d48fef04b780923780 content_type: application/pdf creator: dernst date_created: 2026-10-28T08:41:06Z date_updated: 2026-10-28T08:41:06Z file_id: '23204' file_name: 2026_NatureComm_Long.pdf file_size: 4220128 relation: main_file success: 1 file_date_updated: 2026-10-28T08:41:06Z fulldoi: https://doi.org/10.1038/s41467-026-77326-1 has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 8e917275-16d5-11f0-9cad-fee255fa62e0 grant_number: '101153710' name: The moleculaR mEchAnismS Of dNa methylatIon reprogrammiNg in Arabidopsis sexual lineaGe - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: bdb51a6e-d553-11ed-ba76-c2025f3d5725 call_identifier: H2020 grant_number: '804981' name: Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants - _id: 7c012eb8-9f16-11ee-852c-dc2b6371d5a0 grant_number: '101126201' name: Mechanisms and biological functions of H3K27me3 reprogramming in plant microspores publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '23200' abstract: - lang: eng text: "We investigate the low-ionization electron density in the interstellar medium (ISM) of galaxies across 0 < z < 8,\r\nderived with the [O II] λλ3727, 3730 and [S II] λλ6718, 6733 doublets, using both deep JWST/NIRCam/grism\r\nand NIRSpec/MSA spectroscopy. Along with ancillary density samples from the literature at 0 < z < 6, we\r\nassemble three samples containing a total of 703 galaxies spanning 3.7 < z < 7.8 at 〈z〉 ∼ 5.6; 691 galaxies in the\r\nluminosity-complete NIRCam/grism programs CONGRESS and FRESCO at 〈z〉 ∼ 4.3 and ∼5.3, respectively;\r\nand 12 galaxies with high-resolution NIRSpec/MSA spectra from the GO 1871 and GLASS programs. We find\r\nmedian electron densities of ne[S II] = + 463 203 cm 281 3\r\nfor CONGRESS, ne[S II] = + 301 206 cm 388 3\r\nfor FRESCO, and\r\nne[O II] = + 202 102 cm 145 3\r\nfor the NIRSpec/MSA sample. The median low-ionization ne increases from z = 0 to 4,\r\nin agreement with previous studies and those using JWST observations. However, beyond z ∼ 4 median ne begins\r\nto deviate from a monotonically increasing evolution with z. We find a positive, but shallow, correlation between\r\nO32 (a proxy for the ionization parameter) and ne, while also confirming a positive correlation between O32 and z.\r\nWe suggest that these trends are possibly due to an evolving ISM gas density and ionization structure, and\r\npropose a toy model where the gas clumping evolves with z to explain the observed density and ionization\r\nvariations." acknowledgement: "We are grateful for the support for programs GO 1871, GO 1895, and GO 3577 provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. This work is based in part on observations made with the NASA/ESA/CSA JWST. 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 GO 1324, GO 1871, GO 1895 and GO 3577. The specific observations analyzed can be accessed via DOI: 10.17909/01dt-fm17.\r\n\r\nA.S.L. acknowledges support from Knut and Alice Wallenberg Foundation. T.A.H. acknowledges support from an appointment to the NASA Postdoctoral Program at the NASA Goddard Space, administered by Oak Ridge Associated Universities under contract with NASA, as well as the University of Maryland Baltimore County and the Center for Space Sciences and Technology. N.G.G. and Y.I.I. and acknowledge support from the joint Ukrainian-Swiss project No. 224866. This work has received funding from the Swiss State Secretariat for Education, Research, and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140.\r\n\r\nFacility: JWST (NIRCam - , NIRSpec).\r\n\r\nSoftware: numpy (v.1.24.3; C. R. Harris et al. 2020), scipy (v.1.13.1; P. Virtanen et al. 2020), astropy (Astropy Collaboration et al. 2013, 2018, 2022), pyneb (v.1.1.24; V. Luridiana et al. 2013, 2015; C. Morisset et al. 2020), msaexp (v.0.8.4; G. B. Brammer 2022), msafit (A. de Graaff et al. 2024), grizli (G. Brammer 2018), EAZY (G. B. Brammer et al. 2008), BAGPIPES (A. C. Carnall et al. 2018), Prospector (B. D. Johnson et al. 2019, 2021), pysersic (I. Pasha & T. B. Miller 2023), GALFIT (C. Y. Peng et al. 2002, 2010), kendall (S. R. Flury et al. 2022; S. R. Flury 2023)." article_number: '184' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Mabel G. full_name: Stephenson, Mabel G. last_name: Stephenson - first_name: John full_name: Chisholm, John last_name: Chisholm - first_name: A. full_name: Saldana-Lopez, A. last_name: Saldana-Lopez - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Alaina full_name: Henry, Alaina last_name: Henry - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Sophia R. full_name: Flury, Sophia R. last_name: Flury - first_name: Taylor A. full_name: Hutchison, Taylor A. last_name: Hutchison - first_name: Steven L. full_name: Finkelstein, Steven L. last_name: Finkelstein - first_name: Natalia G. full_name: Guseva, Natalia G. last_name: Guseva - first_name: Yuri I. full_name: Izotov, Yuri I. last_name: Izotov - first_name: Rui full_name: Marques-Chaves, Rui last_name: Marques-Chaves - first_name: Pascal A. full_name: Oesch, Pascal A. last_name: Oesch - first_name: Naveen A. full_name: Reddy, Naveen A. last_name: Reddy - first_name: Daniel full_name: Schaerer, Daniel last_name: Schaerer citation: ama: Stephenson MG, Chisholm J, Saldana-Lopez A, et al. The evolution of low-ionization electron densities in galaxies across cosmic epochs. The Astrophysical Journal. 2026;1010(2). doi:10.3847/1538-4357/ae9eb7 apa: Stephenson, M. G., Chisholm, J., Saldana-Lopez, A., Matthee, J. J., Henry, A., Naidu, R. P., … Schaerer, D. (2026). The evolution of low-ionization electron densities in galaxies across cosmic epochs. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ae9eb7 chicago: Stephenson, Mabel G., John Chisholm, A. Saldana-Lopez, Jorryt J Matthee, Alaina Henry, Rohan P. Naidu, Sophia R. Flury, et al. “The Evolution of Low-Ionization Electron Densities in Galaxies across Cosmic Epochs.” The Astrophysical Journal. IOP Publishing, 2026. https://doi.org/10.3847/1538-4357/ae9eb7. ieee: M. G. Stephenson et al., “The evolution of low-ionization electron densities in galaxies across cosmic epochs,” The Astrophysical Journal, vol. 1010, no. 2. IOP Publishing, 2026. ista: Stephenson MG, Chisholm J, Saldana-Lopez A, Matthee JJ, Henry A, Naidu RP, Flury SR, Hutchison TA, Finkelstein SL, Guseva NG, Izotov YI, Marques-Chaves R, Oesch PA, Reddy NA, Schaerer D. 2026. The evolution of low-ionization electron densities in galaxies across cosmic epochs. The Astrophysical Journal. 1010(2), 184. mla: Stephenson, Mabel G., et al. “The Evolution of Low-Ionization Electron Densities in Galaxies across Cosmic Epochs.” The Astrophysical Journal, vol. 1010, no. 2, 184, IOP Publishing, 2026, doi:10.3847/1538-4357/ae9eb7. short: M.G. Stephenson, J. Chisholm, A. Saldana-Lopez, J.J. Matthee, A. Henry, R.P. Naidu, S.R. Flury, T.A. Hutchison, S.L. Finkelstein, N.G. Guseva, Y.I. Izotov, R. Marques-Chaves, P.A. Oesch, N.A. Reddy, D. Schaerer, The Astrophysical Journal 1010 (2026). das_tickbox: '0' date_created: 2026-10-27T10:40:40Z date_published: 2026-10-15T00:00:00Z date_updated: 2026-10-28T08:05:42Z day: '15' ddc: - '520' department: - _id: JoMa doi: 10.3847/1538-4357/ae9eb7 external_id: arxiv: - '2608.23846' file: - access_level: open_access checksum: 6968c85ac6ccc997a30dab818dc04e42 content_type: application/pdf creator: dernst date_created: 2026-10-28T08:02:57Z date_updated: 2026-10-28T08:02:57Z file_id: '23202' file_name: 2026_AstrophysicalJour_Stephenson.pdf file_size: 4194012 relation: main_file success: 1 file_date_updated: 2026-10-28T08:02:57Z fulldoi: https://doi.org/10.3847/1538-4357/ae9eb7 has_accepted_license: '1' intvolume: ' 1010' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: The evolution of low-ionization electron densities in galaxies across cosmic epochs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1010 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '23199' abstract: - lang: eng text: The physics governing the morphology of radio-loud active galactic nucleus (AGN) jets is not fully understood. We investigate how magnetization, flickering jet power and the interplay between them affects the morphology of radio galaxies. We present a grid of relativistic magnetohydrodynamic simulations using the pluto code covering constant and variable jets with two levels of magnetization. We find that the constant high-magnetization jets can lead to highly asymmetrical cocoon morphologies, while the variable high-magnetization jet can exhibit a broken morphology, caused by a discontinuous jet beam. Our work highlights the importance of magnetization and variability on the stability and resulting morphology of radio-loud AGN jets, suggesting both are significant factors in addition to jet power or environment. Furthermore, we show that the interaction between magnetization and variability can lead to the development of localized kink instabilities along the jet beam. Finally, we discuss the effects of hydrodynamic mixing in low-magnetization jets and the role of viewing-angle dependence in comparisons between our simulations and observed sources. To facilitate this comparison we present a library of simulated radio images at different times in the simulations and from various viewing angles, which highlight a diverse set of complex morphologies. acknowledgement: 'JHM and ELE acknowledge funding from a Royal Society University Research Fellowship (URF\R1\221062). AJC acknowledges support from the Oxford Hintze Centre for Astrophysical Surveys, which is funded through generous support from the Hintze Family Charitable Foundation. HW acknowledges funding by the Science and Technology Facilities Council Grant Number ST/W000903/1 and the ISTA-Fellow programme. The authors acknowledge the use of resources provided by the Isambard 3 Tier-2 HPC Facility. Isambard 3 is hosted by the University of Bristol and operated by the GW4 Alliance (https://gw4.ac.uk) and is funded by UK Research and Innovation and the Engineering and Physical Sciences Research Council (EP/X039137/1). The authors would like to acknowledge the use of the University of Oxford Advanced Research Computing (ARC) facility in carrying out this work (https://doi.org/10.5281/zenodo.22558). We are grateful for the use of the following software packages: pluto (A. Mignone et al. 2007) and matplotlib (J. D. Hunter 2007). We are grateful to Dipanjan Mukherjee, Imogen Whittam, Matt Jarvis, Judith Croston and Fraser Cowie for useful discussions. The authors wish to thank the anonymous referee for their helpful and constructive comments which have improved the quality of this manuscript.' article_number: stag1798 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Emma L full_name: Elley, Emma L last_name: Elley - first_name: James H full_name: Matthews, James H last_name: Matthews - first_name: Henry William full_name: Whitehead, Henry William id: b5363ed7-0345-11f1-8029-eef7ff5d6bfc last_name: Whitehead orcid: 0009-0006-0716-0965 - first_name: Alex J full_name: Cooper, Alex J last_name: Cooper citation: ama: Elley EL, Matthews JH, Whitehead HW, Cooper AJ. The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. Monthly Notices of the Royal Astronomical Society. 2026;552(4). doi:10.1093/mnras/stag1798 apa: Elley, E. L., Matthews, J. H., Whitehead, H. W., & Cooper, A. J. (2026). The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stag1798 chicago: Elley, Emma L, James H Matthews, Henry William Whitehead, and Alex J Cooper. “The Impact of Flickering Variability and Magnetization on the Dynamics, Stability, and Morphology of Radio-Loud AGN Jets.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2026. https://doi.org/10.1093/mnras/stag1798. ieee: E. L. Elley, J. H. Matthews, H. W. Whitehead, and A. J. Cooper, “The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets,” Monthly Notices of the Royal Astronomical Society, vol. 552, no. 4. Oxford University Press, 2026. ista: Elley EL, Matthews JH, Whitehead HW, Cooper AJ. 2026. The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. Monthly Notices of the Royal Astronomical Society. 552(4), stag1798. mla: Elley, Emma L., et al. “The Impact of Flickering Variability and Magnetization on the Dynamics, Stability, and Morphology of Radio-Loud AGN Jets.” Monthly Notices of the Royal Astronomical Society, vol. 552, no. 4, stag1798, Oxford University Press, 2026, doi:10.1093/mnras/stag1798. short: E.L. Elley, J.H. Matthews, H.W. Whitehead, A.J. Cooper, Monthly Notices of the Royal Astronomical Society 552 (2026). das_tickbox: '1' dataavailabilitystatement: The data underlying this article are available from the authors on reasonable request. Furthermore, the data for the simulated radio images from various angles as discussed in Section 2.3 are publicly available as FITS files from https://doi.org/10.5281/zenodo.20140021. date_created: 2026-10-27T10:39:59Z date_published: 2026-11-01T00:00:00Z date_updated: 2026-10-28T08:19:37Z day: '01' ddc: - '520' department: - _id: ZoHa doi: 10.1093/mnras/stag1798 external_id: arxiv: - '2605.13469' file: - access_level: open_access checksum: 57e15f531d22d18eaeca96d58b2ab911 content_type: application/pdf creator: dernst date_created: 2026-10-28T08:19:16Z date_updated: 2026-10-28T08:19:16Z file_id: '23203' file_name: 2026_MonthNoticesRAS_Elley.pdf file_size: 8344810 relation: main_file success: 1 file_date_updated: 2026-10-28T08:19:16Z fulldoi: https://doi.org/10.1093/mnras/stag1798 has_accepted_license: '1' intvolume: ' 552' issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 552 year: '2026' ... --- OA_type: closed access _id: '23196' abstract: - lang: eng text: We introduce an experimental realization of the measurement, processing, and generation of partially coherent light on a photonic chip. This device relies on self-configuring networks optimized sequentially to learn the coherency matrix of input light. alternative_title: - Technical Digest Series article_number: STU2F.1 article_processing_charge: No author: - first_name: Paul Alexis full_name: Mor, Paul Alexis last_name: Mor - first_name: Annie R. full_name: Kroo, Annie R. last_name: Kroo - first_name: Carson G. full_name: Valdez, Carson G. last_name: Valdez - first_name: Marko full_name: Šimić, Marko last_name: Šimić - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Gabriele full_name: Cavicchioli, Gabriele last_name: Cavicchioli - first_name: Zhanghao full_name: Sun, Zhanghao last_name: Sun - first_name: Vittorio full_name: Grimaldi, Vittorio last_name: Grimaldi - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan - first_name: Olav full_name: Solgaard, Olav last_name: Solgaard - first_name: David A.B. full_name: Miller, David A.B. last_name: Miller - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes citation: ama: 'Mor PA, Kroo AR, Valdez CG, et al. Variational processing of partially coherent light in a photonic integrated circuit. In: CLEO Science and Innovations Proceedings. Optica Publishing Group; 2026. doi:10.1364/CLEO_SI.2026.STU2F.1' apa: 'Mor, P. A., Kroo, A. R., Valdez, C. G., Šimić, M., Karnieli, A., Cavicchioli, G., … Roques-Carmes, C. (2026). Variational processing of partially coherent light in a photonic integrated circuit. In CLEO Science and Innovations Proceedings. Long Beach, CA, United States: Optica Publishing Group. https://doi.org/10.1364/CLEO_SI.2026.STU2F.1' chicago: Mor, Paul Alexis, Annie R. Kroo, Carson G. Valdez, Marko Šimić, Aviv Karnieli, Gabriele Cavicchioli, Zhanghao Sun, et al. “Variational Processing of Partially Coherent Light in a Photonic Integrated Circuit.” In CLEO Science and Innovations Proceedings. Optica Publishing Group, 2026. https://doi.org/10.1364/CLEO_SI.2026.STU2F.1. ieee: P. A. Mor et al., “Variational processing of partially coherent light in a photonic integrated circuit,” in CLEO Science and Innovations Proceedings, Long Beach, CA, United States, 2026. ista: 'Mor PA, Kroo AR, Valdez CG, Šimić M, Karnieli A, Cavicchioli G, Sun Z, Grimaldi V, Fan S, Solgaard O, Miller DAB, Roques-Carmes C. 2026. Variational processing of partially coherent light in a photonic integrated circuit. CLEO Science and Innovations Proceedings. CLEO: Conference on Lasers and Electro-Optics, Technical Digest Series, , STU2F.1.' mla: Mor, Paul Alexis, et al. “Variational Processing of Partially Coherent Light in a Photonic Integrated Circuit.” CLEO Science and Innovations Proceedings, STU2F.1, Optica Publishing Group, 2026, doi:10.1364/CLEO_SI.2026.STU2F.1. short: P.A. Mor, A.R. Kroo, C.G. Valdez, M. Šimić, A. Karnieli, G. Cavicchioli, Z. Sun, V. Grimaldi, S. Fan, O. Solgaard, D.A.B. Miller, C. Roques-Carmes, in:, CLEO Science and Innovations Proceedings, Optica Publishing Group, 2026. conference: end_date: 2026-05-06 location: Long Beach, CA, United States name: 'CLEO: Conference on Lasers and Electro-Optics' start_date: 2026-05-02 date_created: 2026-10-25T23:02:24Z date_published: 2026-05-15T00:00:00Z date_updated: 2026-10-28T07:57:55Z day: '15' department: - _id: ChRo doi: 10.1364/CLEO_SI.2026.STU2F.1 fulldoi: https://doi.org/10.1364/CLEO_SI.2026.STU2F.1 language: - iso: eng month: '05' oa_version: None publication: CLEO Science and Innovations Proceedings publication_identifier: isbn: - '9781957171586' publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Variational processing of partially coherent light in a photonic integrated circuit type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ...