--- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20730' abstract: - lang: eng text: Radio-frequency measurements could satisfy DiVincenzo’s readout criterion in future large-scale solid-state quantum processors, as they allow for high bandwidths and frequency multiplexing. However, the scalability potential of this readout technique can only be leveraged if quantum device tuning is performed using exclusively radio-frequency measurements, that is, without resorting to current measurements. We demonstrate an algorithm that performs automatic coarse tuning of double quantum dots with only radio-frequency measurements by exploiting their bandwidth and impedance matching. The tuning was completed within a few minutes with minimal prior knowledge about the device. Our results show that it is possible to eliminate the need for transport measurements for quantum-dot tuning, paving the way for more scalable device architectures. acknowledged_ssus: - _id: NanoFab acknowledgement: We thank Nicholas Sim for providing help with the rf cavities and David Craig for his feedback on the paper. This work was supported by the Royal Society (URF-R1-191150), the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant (EP/R029229/1), the European Research Council (Grant Agreement 948932), the Scientific Service Units of IST Austria through resources provided by the nanofabrication facility, the FWF-P 30207, and FWF-I 05060 projects, and Grant No. FQXi-IAF19-01 from the Foundational Questions Institute Fund, a donor-advised fund of Silicon Valley Community Foundation. article_number: '054030' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Barnaby full_name: Van Straaten, Barnaby last_name: Van Straaten - first_name: Federico full_name: Fedele, Federico last_name: Fedele - first_name: Florian full_name: Vigneau, Florian last_name: Vigneau - first_name: Joseph full_name: Hickie, Joseph last_name: Hickie - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Andrea full_name: Ballabio, Andrea last_name: Ballabio - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X - first_name: Natalia full_name: Ares, Natalia last_name: Ares citation: ama: Van Straaten B, Fedele F, Vigneau F, et al. All-rf-based coarse-tuning algorithm for quantum devices using machine learning. Physical Review Applied. 2025;24(5). doi:10.1103/v11m-dbhm apa: Van Straaten, B., Fedele, F., Vigneau, F., Hickie, J., Jirovec, D., Ballabio, A., … Ares, N. (2025). All-rf-based coarse-tuning algorithm for quantum devices using machine learning. Physical Review Applied. American Physical Society. https://doi.org/10.1103/v11m-dbhm chicago: Van Straaten, Barnaby, Federico Fedele, Florian Vigneau, Joseph Hickie, Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, Giovanni Isella, Georgios Katsaros, and Natalia Ares. “All-Rf-Based Coarse-Tuning Algorithm for Quantum Devices Using Machine Learning.” Physical Review Applied. American Physical Society, 2025. https://doi.org/10.1103/v11m-dbhm. ieee: B. Van Straaten et al., “All-rf-based coarse-tuning algorithm for quantum devices using machine learning,” Physical Review Applied, vol. 24, no. 5. American Physical Society, 2025. ista: Van Straaten B, Fedele F, Vigneau F, Hickie J, Jirovec D, Ballabio A, Chrastina D, Isella G, Katsaros G, Ares N. 2025. All-rf-based coarse-tuning algorithm for quantum devices using machine learning. Physical Review Applied. 24(5), 054030. mla: Van Straaten, Barnaby, et al. “All-Rf-Based Coarse-Tuning Algorithm for Quantum Devices Using Machine Learning.” Physical Review Applied, vol. 24, no. 5, 054030, American Physical Society, 2025, doi:10.1103/v11m-dbhm. short: B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, G. Katsaros, N. Ares, Physical Review Applied 24 (2025). date_created: 2025-12-07T23:02:01Z date_published: 2025-11-01T00:00:00Z date_updated: 2025-12-09T14:49:35Z day: '01' ddc: - '530' department: - _id: GeKa doi: 10.1103/v11m-dbhm file: - access_level: open_access checksum: 9906b32c7e3c79ed13d05ef88ff15586 content_type: application/pdf creator: dernst date_created: 2025-12-09T13:34:38Z date_updated: 2025-12-09T13:34:38Z file_id: '20748' file_name: 2025_PhysReviewApplied_vanStraaten.pdf file_size: 5754118 relation: main_file success: 1 file_date_updated: 2025-12-09T13:34:38Z fulldoi: https://doi.org/10.1103/v11m-dbhm has_accepted_license: '1' intvolume: ' 24' issue: '5' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins publication: Physical Review Applied publication_identifier: eissn: - 2331-7019 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '20750' relation: research_data status: public scopus_import: '1' status: public title: All-rf-based coarse-tuning algorithm for quantum devices using machine learning 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: 24 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20731' abstract: - lang: eng text: The adult human brain, under resting conditions, consumes approximately 20% of total body glucose, a demand that is even higher during the first decade of life. The brain metabolic landscape is intricately regulated throughout development, and each cell type exhibits distinct metabolic signatures at each specific stage. This picture becomes even more intricate when considering that metabolism is dynamically modulated to sustain critical biological processes, such as cell proliferation and differentiation and synaptic activity–dependent processes. The orchestration between metabolic regulation and the aforementioned physiological processes often relies on metabolism-dependent changes in the epigenetic landscape, which shape gene expression patterns to trigger selected downstream biological responses. Perturbations of brain metabolic pathways are frequently the cause of severe neurodevelopmental disorders. This review explores the latest insights into the regulation of brain metabolism in health and disease. acknowledgement: Funding provided by the European Union (grant 101057429) to G.N. article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Domenico full_name: Marano, Domenico id: 3b004c42-803f-11ed-ab7e-ecee8f08bd58 last_name: Marano - first_name: Vittoria full_name: Mariano, Vittoria id: ee829c33-edb3-11ed-b4fb-c020aaca4b01 last_name: Mariano - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Marano D, Mariano V, Novarino G. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 2025;59:415-434. doi:10.1146/annurev-genet-111523-102424' apa: 'Marano, D., Mariano, V., & Novarino, G. (2025). Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-111523-102424' chicago: 'Marano, Domenico, Vittoria Mariano, and Gaia Novarino. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review of Genetics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-genet-111523-102424.' ieee: 'D. Marano, V. Mariano, and G. Novarino, “Fueling the mind: Brain metabolism in health and neurodevelopmental disorders,” Annual Review of Genetics, vol. 59. Annual Reviews, pp. 415–434, 2025.' ista: 'Marano D, Mariano V, Novarino G. 2025. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 59, 415–434.' mla: 'Marano, Domenico, et al. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review of Genetics, vol. 59, Annual Reviews, 2025, pp. 415–34, doi:10.1146/annurev-genet-111523-102424.' short: D. Marano, V. Mariano, G. Novarino, Annual Review of Genetics 59 (2025) 415–434. corr_author: '1' date_created: 2025-12-07T23:02:01Z date_published: 2025-11-03T00:00:00Z date_updated: 2025-12-09T12:55:11Z day: '03' ddc: - '570' department: - _id: GaNo doi: 10.1146/annurev-genet-111523-102424 external_id: pmid: - '40902207' file: - access_level: open_access checksum: 1000228dc9aca3d48e92605607a99c41 content_type: application/pdf creator: dernst date_created: 2025-12-09T12:53:09Z date_updated: 2025-12-09T12:53:09Z file_id: '20745' file_name: 2025_AnnualRevGenetics_Marano.pdf file_size: 3629986 relation: main_file success: 1 file_date_updated: 2025-12-09T12:53:09Z fulldoi: https://doi.org/10.1146/annurev-genet-111523-102424 has_accepted_license: '1' intvolume: ' 59' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 415-434 pmid: 1 project: - _id: 349d1832-11ca-11ed-8bc3-d79b574010e0 grant_number: '101057429' name: Reducing the impact of major environmental challenges on mental health publication: Annual Review of Genetics publication_identifier: eissn: - 1545-2948 issn: - 0066-4197 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: 'Fueling the mind: Brain metabolism in health and neurodevelopmental disorders' 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: 59 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20732' abstract: - lang: eng text: 'We investigate the real-time dynamics of a quenched quantum impurity immersed in a one-dimensional ultracold Fermi gas, focusing on the breakdown of the adiabatic Born-Oppenheimer approximation due to nonadiabatic effects. Despite a sizable impurity-bath mass imbalance, increasing interactions induce strong nonadiabatic couplings, disrupting adiabatic motion and enabling population transfer between the adiabatic potential energy curves. These transitions are governed by conical intersections arising from the pseudo Jahn-Teller effect, dynamically shaping the impurity''s motion through the bath. Using ab initio simulations via the multilayer multiconfiguration time-dependent Hartree method and a multichannel Born-Oppenheimer framework, we track the impurity''s evolution and directly prove the dynamical manifestation of the pseudo Jahn-Teller effect. We analyze two key scenarios: (i) a small initial shift, where a single avoided crossing drives transitions, and (ii) a large shift, where multiple avoided crossings lead to enhanced nonadiabaticity, self-trapping, and energy redistribution. Our findings establish ultracold fermionic few-body systems as tunable platforms for studying nonadiabatic quantum dynamics, opening new avenues for controlled impurity transport in strongly correlated environments.' acknowledgement: 'This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994. G.K.M. has received funding from the Austrian Science Fund (FWF) [DOI: 10.55776/F1004].' article_number: '033088' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: A. full_name: Becker, A. last_name: Becker - first_name: Georgios full_name: Koutentakis, Georgios id: d7b23d3a-9e21-11ec-b482-f76739596b95 last_name: Koutentakis - first_name: P. full_name: Schmelcher, P. last_name: Schmelcher citation: ama: Becker A, Koutentakis G, Schmelcher P. Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 2025;7(3). doi:10.1103/2fr6-b59y apa: Becker, A., Koutentakis, G., & Schmelcher, P. (2025). Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. American Physical Society. https://doi.org/10.1103/2fr6-b59y chicago: Becker, A., Georgios Koutentakis, and P. Schmelcher. “Dynamical Probe of the Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research. American Physical Society, 2025. https://doi.org/10.1103/2fr6-b59y. ieee: A. Becker, G. Koutentakis, and P. Schmelcher, “Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research, vol. 7, no. 3. American Physical Society, 2025. ista: Becker A, Koutentakis G, Schmelcher P. 2025. Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 7(3), 033088. mla: Becker, A., et al. “Dynamical Probe of the Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research, vol. 7, no. 3, 033088, American Physical Society, 2025, doi:10.1103/2fr6-b59y. short: A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 7 (2025). corr_author: '1' date_created: 2025-12-07T23:02:02Z date_published: 2025-07-01T00:00:00Z date_updated: 2025-12-09T14:16:15Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1103/2fr6-b59y external_id: arxiv: - '2503.09835' file: - access_level: open_access checksum: b9f5ccd6957759b0e578bc817a050532 content_type: application/pdf creator: dernst date_created: 2025-12-09T14:14:46Z date_updated: 2025-12-09T14:14:46Z file_id: '20754' file_name: 2025_PhysReviewResearch_Becker.pdf file_size: 2878032 relation: main_file success: 1 file_date_updated: 2025-12-09T14:14:46Z fulldoi: https://doi.org/10.1103/2fr6-b59y has_accepted_license: '1' intvolume: ' 7' issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3 grant_number: F100403 name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions publication: Physical Review Research publication_identifier: issn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions 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: 7 year: '2025' ... --- OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20733' abstract: - lang: eng text: The conversion of thermal energy into work is usually more efficient in the slow-driving regime, where the power output is vanishingly small. Efficient work extraction for fast-driving protocols remains an outstanding challenge at the nanoscale, where fluctuations play a significant role. In this Letter, we use a quantum-dot Szilard engine to extract work from thermal fluctuations with maximum efficiency over two decades of driving speed. We design and implement a family of optimized protocols ranging from the slow- to the fast-driving regime, and we measure the engine's efficiency as well as the mean and variance of its power output in each case. These optimized protocols exhibit significant improvements in power and efficiency compared to the naive approach. Our results also show that, when optimizing for efficiency, boosting the power output of a Szilard engine inevitably comes at the cost of increased power fluctuations. acknowledgement: We thank Georgios Katsaros for providing the device for this experiment. K.A. and N.A. acknowledge the support provided by funding from the Engineering and Physical Sciences Research Council IAA (Grant No. EP/X525777/1). N.A. acknowledges support from the European Research Council (Grant Agreement No. 948932) and the Royal Society (URF-R1-191150). A.R. is supported by the Swiss National Science Foundation through a Postdoc. Mobility (Grant No. P500PT 225461). M.T.M. is supported by a Royal Society University Research Fellowship. M.P.-L. is supported by the Grant RYC2022-036958-I funded by the Spanish MICIU/AEI/10.13039/501100011033 and by ESF+. This project is cofunded by the European Union and UK Research & Innovation (Quantum Flagship project ASPECTS, Grant Agreement No. 101080167). However, views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union, Research Executive Agency, or UK Research & Innovation. Neither the European Union nor UK Research & Innovation can be held responsible for them. article_number: L032017 article_processing_charge: Yes article_type: letter_note arxiv: 1 author: - first_name: Kushagra full_name: Aggarwal, Kushagra last_name: Aggarwal - first_name: Alberto full_name: Rolandi, Alberto last_name: Rolandi - first_name: Yikai full_name: Yang, Yikai last_name: Yang - first_name: Joseph full_name: Hickie, Joseph last_name: Hickie - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Andrea full_name: Ballabio, Andrea last_name: Ballabio - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Mark T. full_name: Mitchison, Mark T. last_name: Mitchison - first_name: Martí full_name: Perarnau-Llobet, Martí last_name: Perarnau-Llobet - first_name: Natalia full_name: Ares, Natalia last_name: Ares citation: ama: Aggarwal K, Rolandi A, Yang Y, et al. Rapid optimal work extraction from a quantum-dot information engine. Physical Review Research. 2025;7(3). doi:10.1103/q3dx-kyqj apa: Aggarwal, K., Rolandi, A., Yang, Y., Hickie, J., Jirovec, D., Ballabio, A., … Ares, N. (2025). Rapid optimal work extraction from a quantum-dot information engine. Physical Review Research. American Physical Society. https://doi.org/10.1103/q3dx-kyqj chicago: Aggarwal, Kushagra, Alberto Rolandi, Yikai Yang, Joseph Hickie, Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, et al. “Rapid Optimal Work Extraction from a Quantum-Dot Information Engine.” Physical Review Research. American Physical Society, 2025. https://doi.org/10.1103/q3dx-kyqj. ieee: K. Aggarwal et al., “Rapid optimal work extraction from a quantum-dot information engine,” Physical Review Research, vol. 7, no. 3. American Physical Society, 2025. ista: Aggarwal K, Rolandi A, Yang Y, Hickie J, Jirovec D, Ballabio A, Chrastina D, Isella G, Mitchison MT, Perarnau-Llobet M, Ares N. 2025. Rapid optimal work extraction from a quantum-dot information engine. Physical Review Research. 7(3), L032017. mla: Aggarwal, Kushagra, et al. “Rapid Optimal Work Extraction from a Quantum-Dot Information Engine.” Physical Review Research, vol. 7, no. 3, L032017, American Physical Society, 2025, doi:10.1103/q3dx-kyqj. short: K. Aggarwal, A. Rolandi, Y. Yang, J. Hickie, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M.T. Mitchison, M. Perarnau-Llobet, N. Ares, Physical Review Research 7 (2025). date_created: 2025-12-07T23:02:02Z date_published: 2025-07-01T00:00:00Z date_updated: 2025-12-09T14:07:49Z day: '01' ddc: - '530' department: - _id: GeKa doi: 10.1103/q3dx-kyqj external_id: arxiv: - '2412.06916' file: - access_level: open_access checksum: 66f2b572a36a7b5fe611a7639a8b6f12 content_type: application/pdf creator: dernst date_created: 2025-12-09T14:05:56Z date_updated: 2025-12-09T14:05:56Z file_id: '20753' file_name: 2025_PhysReviewResearch_Aggarwal.pdf file_size: 536624 relation: main_file success: 1 file_date_updated: 2025-12-09T14:05:56Z fulldoi: https://doi.org/10.1103/q3dx-kyqj has_accepted_license: '1' intvolume: ' 7' issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Physical Review Research publication_identifier: eissn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - relation: software url: https://doi.org/10.5281/zenodo.14516009 scopus_import: '1' status: public title: Rapid optimal work extraction from a quantum-dot information engine 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: 7 year: '2025' ... --- OA_place: publisher OA_type: diamond PlanS_conform: '1' _id: '20734' abstract: - lang: eng text: We consider the problem of parameter estimation in a high-dimensional generalized linear model. Spectral methods obtained via the principal eigenvector of a suitable data-dependent matrix provide a simple yet surprisingly effective solution. However, despite their wide use, a rigorous performance characterization, as well as a principled way to preprocess the data, are available only for unstructured (i.i.d. Gaussian and Haar orthogonal) designs. In contrast, real-world data matrices are highly structured and exhibit non-trivial correlations. To address the problem, we consider correlated Gaussian designs capturing the anisotropic nature of the features via a covariance matrix Σ. Our main result is a precise asymptotic characterization of the performance of spectral estimators. This allows us to identify the optimal preprocessing that minimizes the number of samples needed for parameter estimation. Surprisingly, such preprocessing is universal across a broad set of designs, which partly addresses a conjecture on optimal spectral estimators for rotationally invariant models. Our principled approach vastly improves upon previous heuristic methods, including for designs common in computational imaging and genetics. The proposed methodology, based on approximate message passing, is broadly applicable and opens the way to the precise characterization of spiked matrices and of the corresponding spectral methods in a variety of settings. acknowledgement: "This work was done when Y. Z. and H. C. J. were at the Institute of Science and Technology Austria. Y. Z. thanks Hugo Latourelle-Vigeant for bringing [53] to the authors’ attention.\r\nY. Z. and M. M. are partially supported by the 2019 Lopez-Loreta Prize and by the Interdisciplinary Projects Committee (IPC) at ISTA. H. C. J. is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331." article_processing_charge: No article_type: original author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 - first_name: Hong Chang full_name: Ji, Hong Chang last_name: Ji - first_name: Ramji full_name: Venkataramanan, Ramji last_name: Venkataramanan - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Zhang Y, Ji HC, Venkataramanan R, Mondelli M. Spectral estimators for structured generalized linear models via approximate message passing. Mathematical Statistics and Learning. 2025;8(3-4):193-304. doi:10.4171/MSL/52 apa: Zhang, Y., Ji, H. C., Venkataramanan, R., & Mondelli, M. (2025). Spectral estimators for structured generalized linear models via approximate message passing. Mathematical Statistics and Learning. EMS Press. https://doi.org/10.4171/MSL/52 chicago: Zhang, Yihan, Hong Chang Ji, Ramji Venkataramanan, and Marco Mondelli. “Spectral Estimators for Structured Generalized Linear Models via Approximate Message Passing.” Mathematical Statistics and Learning. EMS Press, 2025. https://doi.org/10.4171/MSL/52. ieee: Y. Zhang, H. C. Ji, R. Venkataramanan, and M. Mondelli, “Spectral estimators for structured generalized linear models via approximate message passing,” Mathematical Statistics and Learning, vol. 8, no. 3–4. EMS Press, pp. 193–304, 2025. ista: Zhang Y, Ji HC, Venkataramanan R, Mondelli M. 2025. Spectral estimators for structured generalized linear models via approximate message passing. Mathematical Statistics and Learning. 8(3–4), 193–304. mla: Zhang, Yihan, et al. “Spectral Estimators for Structured Generalized Linear Models via Approximate Message Passing.” Mathematical Statistics and Learning, vol. 8, no. 3–4, EMS Press, 2025, pp. 193–304, doi:10.4171/MSL/52. short: Y. Zhang, H.C. Ji, R. Venkataramanan, M. Mondelli, Mathematical Statistics and Learning 8 (2025) 193–304. corr_author: '1' date_created: 2025-12-07T23:02:02Z date_published: 2025-09-02T00:00:00Z date_updated: 2025-12-09T13:53:31Z day: '02' ddc: - '000' department: - _id: MaMo doi: 10.4171/MSL/52 file: - access_level: open_access checksum: 55a1bd9c1b6b0198c42504fb94f4ad4c content_type: application/pdf creator: dernst date_created: 2025-12-09T13:50:03Z date_updated: 2025-12-09T13:50:03Z file_id: '20752' file_name: 2025_MathStatLearning_Zhang.pdf file_size: 1379626 relation: main_file success: 1 file_date_updated: 2025-12-09T13:50:03Z fulldoi: https://doi.org/10.4171/MSL/52 has_accepted_license: '1' intvolume: ' 8' issue: 3-4 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 193-304 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Mathematical Statistics and Learning publication_identifier: eissn: - 2520-2324 issn: - 2520-2316 publication_status: published publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: Spectral estimators for structured generalized linear models via approximate message passing 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: 8 year: '2025' ... --- OA_place: publisher _id: '20737' acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "I also want to thank ISTA and the Austrian Science Fund FWF SFB F78 (F7805) for financially\r\nsupporting my research." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Raquel full_name: Casado Polanco, Raquel id: 15240fc1-dbcd-11ea-9d1d-ac5a786425fd last_name: Casado Polanco orcid: 0000-0001-8293-4568 citation: ama: Casado Polanco R. Role of NOTCH signaling in radial glial progenitor lineage progression. 2025. doi:10.15479/AT-ISTA-20737 apa: Casado Polanco, R. (2025). Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20737 chicago: Casado Polanco, Raquel. “Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20737. ieee: R. Casado Polanco, “Role of NOTCH signaling in radial glial progenitor lineage progression,” Institute of Science and Technology Austria, 2025. ista: Casado Polanco R. 2025. Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria. mla: Casado Polanco, Raquel. Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20737. short: R. Casado Polanco, Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-12-09T09:04:18Z date_published: 2025-12-09T00:00:00Z date_updated: 2026-04-14T08:16:58Z day: '09' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/AT-ISTA-20737 file: - access_level: closed checksum: 71e0fdf4619b0d70d03657ad7348137d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rcasadop date_created: 2025-12-11T09:28:09Z date_updated: 2025-12-11T11:18:37Z file_id: '20793' file_name: 2025_CasadoPolanco_Raquel_Thesis.docx file_size: 78207207 relation: source_file - access_level: closed checksum: 58cf2f25c33567723bc754a019c3e396 content_type: application/pdf creator: rcasadop date_created: 2025-12-11T09:28:04Z date_updated: 2025-12-11T09:28:04Z embargo: 2026-12-01 embargo_to: open_access file_id: '20794' file_name: 2025_CasadoPolanco_Raquel_Thesis.pdf file_size: 6261874 relation: main_file file_date_updated: 2025-12-11T11:18:37Z fulldoi: https://doi.org/10.15479/AT-ISTA-20737 has_accepted_license: '1' keyword: - NOTCH - radial glial progenitor - lineage progression - cortical development language: - iso: eng month: '12' oa_version: Published Version page: '133' project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication_identifier: isbn: - 978-3-99078-072-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Role of NOTCH signaling in radial glial progenitor lineage progression type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: repository OA_type: green _id: '20749' abstract: - lang: eng text: Datasets and code for publication "Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter" article_processing_charge: No author: - first_name: Sue full_name: Shi, Sue id: 5c5b9247-15b2-11ec-abd3-fd958715639c last_name: Shi citation: ama: Shi S. Datasets and code for manuscript “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.” 2025. doi:10.5281/ZENODO.15752991 apa: Shi, S. (2025). Datasets and code for manuscript “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.” Zenodo. https://doi.org/10.5281/ZENODO.15752991 chicago: Shi, Sue. “Datasets and Code for Manuscript ‘Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.’” Zenodo, 2025. https://doi.org/10.5281/ZENODO.15752991. ieee: S. Shi, “Datasets and code for manuscript ‘Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.’” Zenodo, 2025. ista: Shi S. 2025. Datasets and code for manuscript ‘Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter’, Zenodo, 10.5281/ZENODO.15752991. mla: Shi, Sue. Datasets and Code for Manuscript “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.” Zenodo, 2025, doi:10.5281/ZENODO.15752991. short: S. Shi, (2025). contributor: - first_name: Maximilian id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32 last_name: Hübl - first_name: Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X corr_author: '1' date_created: 2025-12-09T13:36:16Z date_published: 2025-11-10T00:00:00Z date_updated: 2026-05-20T08:41:14Z day: '10' ddc: - '530' department: - _id: ScWa - _id: CaGo doi: 10.5281/ZENODO.15752991 fulldoi: https://doi.org/10.5281/ZENODO.15752991 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.15752991 month: '11' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '20727' relation: used_in_publication status: public status: public title: Datasets and code for manuscript "Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '20750' article_processing_charge: No author: - first_name: Barnaby full_name: Van Straaten, Barnaby last_name: Van Straaten - first_name: Federico full_name: Fedele, Federico last_name: Fedele - first_name: Florian full_name: Vigneau, Florian last_name: Vigneau - first_name: Joseph full_name: Hickie, Joseph last_name: Hickie - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Natalia full_name: Ares, Natalia last_name: Ares citation: ama: Van Straaten B, Fedele F, Vigneau F, et al. All rf-based tuning algorithm for quantum devices using machine learning. 2025. doi:10.5281/ZENODO.17352653 apa: Van Straaten, B., Fedele, F., Vigneau, F., Hickie, J., Jirovec, D., Chrastina, D., … Ares, N. (2025). All rf-based tuning algorithm for quantum devices using machine learning. Zenodo. https://doi.org/10.5281/ZENODO.17352653 chicago: Van Straaten, Barnaby, Federico Fedele, Florian Vigneau, Joseph Hickie, Daniel Jirovec, Daniel Chrastina, Giovanni Isella, and Natalia Ares. “All Rf-Based Tuning Algorithm for Quantum Devices Using Machine Learning.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.17352653. ieee: B. Van Straaten et al., “All rf-based tuning algorithm for quantum devices using machine learning.” Zenodo, 2025. ista: Van Straaten B, Fedele F, Vigneau F, Hickie J, Jirovec D, Chrastina D, Isella G, Ares N. 2025. All rf-based tuning algorithm for quantum devices using machine learning, Zenodo, 10.5281/ZENODO.17352653. mla: Van Straaten, Barnaby, et al. All Rf-Based Tuning Algorithm for Quantum Devices Using Machine Learning. Zenodo, 2025, doi:10.5281/ZENODO.17352653. short: B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, D. Chrastina, G. Isella, N. Ares, (2025). date_created: 2025-12-09T13:36:29Z date_published: 2025-10-14T00:00:00Z date_updated: 2025-12-09T14:49:36Z day: '14' ddc: - '530' department: - _id: GeKa doi: 10.5281/ZENODO.17352653 fulldoi: https://doi.org/10.5281/ZENODO.17352653 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.17352653 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '20730' relation: used_in_publication status: public status: public title: All rf-based tuning algorithm for quantum devices using machine learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- _id: '20780' abstract: - lang: eng text: Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Lorena Alexandra full_name: Layana Franco, Lorena Alexandra id: 02814589-eb8f-11eb-b029-a70074f3f18f last_name: Layana Franco orcid: 0000-0002-1253-6297 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:10.15479/AT-ISTA-20780 apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20780 chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20780. ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria, 2025. ista: Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20780. mla: Layana Franco, Lorena Alexandra, et al. Causes and Consequences of Sex-Chromosome Turnovers in Diptera. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20780. short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025). corr_author: '1' date_created: 2025-12-10T23:40:14Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-06-10T08:27:48Z department: - _id: BeVi doi: 10.15479/AT-ISTA-20780 file: - access_level: open_access checksum: 251e7aab01917c2ad2fbccf465492ea1 content_type: application/zip creator: llayanaf date_created: 2025-12-11T10:47:15Z date_updated: 2025-12-11T10:47:15Z file_id: '20799' file_name: Perl_scripts.zip file_size: 4575 relation: main_file success: 1 - access_level: open_access checksum: daf1c03149dd170b14e5c8e109ee3c77 content_type: application/zip creator: llayanaf date_created: 2025-12-11T10:52:17Z date_updated: 2025-12-11T10:52:17Z file_id: '20800' file_name: Supplementary_Datasets.zip file_size: 19052849 relation: main_file success: 1 - access_level: open_access checksum: 658d6e95a361b0a3db058b7b4e1733d4 content_type: application/zip creator: llayanaf date_created: 2025-12-11T10:52:11Z date_updated: 2025-12-11T10:52:11Z file_id: '20801' file_name: Supplementary_Tables.zip file_size: 566476 relation: main_file success: 1 - access_level: open_access checksum: 2a2b92eb9fade0015719190596a8c5b7 content_type: text/plain creator: llayanaf date_created: 2025-12-11T11:00:53Z date_updated: 2025-12-11T11:00:53Z file_id: '20802' file_name: README.txt file_size: 1204 relation: main_file success: 1 file_date_updated: 2025-12-11T11:00:53Z fulldoi: https://doi.org/10.15479/AT-ISTA-20780 has_accepted_license: '1' keyword: - Schizophora - sex chromosomes - sex-chromosome turnover - Diptera - genomic features - out-of-X movement. month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Causes and consequences of sex-chromosome turnovers in Diptera tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- APC_amount: 5651,35 EUR OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20795' abstract: - lang: eng text: The tropical climate variability is characterized by various oscillations across a range of timescales. Oscillations that imprint the tropical mean state are generally attributed to slow processes, such as the seasonal cycle or interannual variability. Here, we identify a pronounced tropics-wide intraseasonal oscillation (TWISO) in satellite observations and reanalyses. This oscillation, with a period of 30 to 60 d, is evident across multiple variables and involves interactions between convection, radiation, surface fluxes, and large-scale circulation. It is primarily manifested as convective perturbations in the tropical Indo-Pacific warm pool accompanied by oscillations in the large-scale tropical overturning circulation. Here, we examine the relationship between TWISO, the Madden–Julian Oscillation (MJO), and the instability of radiative-convective equilibrium. Certain phases of TWISO coincide with specific phases of the MJO, suggesting a potential connection between the two. However, although the MJO can amplify the oscillation amplitude of TWISO, it is not essential for TWISO to occur. Finally, due to its broad manifestation across the tropics, TWISO potentially exerts widespread influence on tropical weather and climate at regional scales. acknowledgement: 'J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement No. 101034413). S.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project Mesoscale organization of tropical convection, grant agreement No 101098063). D.T. acknowledges funding from the Japan Society for the Promotion of Science (JSPS) (Project JSPS Grants-in-Aid for Scientific Research, grant No. JP24K22893). C.M. gratefully acknowledges funding from the ERC under the European Union’s Horizon 2020 research and innovation program (Project organisation of CLoUdS, and implications for Tropical cyclones and for the Energetics of the tropics, in current and in a waRming climate, grant agreement No. 805041). We thank Martin Singh, Steven Sherwood, Bjorn Stevens, and Lokahith Agasthya for helpful discussions. JSPS Core-to-Core Program, “International Core-to-Core Project on Global Storm Resolving Analysis” (Grant Number: JPJSCCA20220001)' article_number: e2511549122 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jiawei full_name: Bao, Jiawei id: bb9a7399-fefd-11ed-be3c-ae648fd1d160 last_name: Bao - first_name: Sandrine full_name: Bony, Sandrine last_name: Bony - first_name: Daisuke full_name: Takasuka, Daisuke last_name: Takasuka - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: Bao J, Bony S, Takasuka D, Muller CJ. Tropics-wide intraseasonal oscillations. Proceedings of the National Academy of Sciences. 2025;122(48). doi:10.1073/pnas.2511549122 apa: Bao, J., Bony, S., Takasuka, D., & Muller, C. J. (2025). Tropics-wide intraseasonal oscillations. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2511549122 chicago: Bao, Jiawei, Sandrine Bony, Daisuke Takasuka, and Caroline J Muller. “Tropics-Wide Intraseasonal Oscillations.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2511549122. ieee: J. Bao, S. Bony, D. Takasuka, and C. J. Muller, “Tropics-wide intraseasonal oscillations,” Proceedings of the National Academy of Sciences, vol. 122, no. 48. National Academy of Sciences, 2025. ista: Bao J, Bony S, Takasuka D, Muller CJ. 2025. Tropics-wide intraseasonal oscillations. Proceedings of the National Academy of Sciences. 122(48), e2511549122. mla: Bao, Jiawei, et al. “Tropics-Wide Intraseasonal Oscillations.” Proceedings of the National Academy of Sciences, vol. 122, no. 48, e2511549122, National Academy of Sciences, 2025, doi:10.1073/pnas.2511549122. short: J. Bao, S. Bony, D. Takasuka, C.J. Muller, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' date_created: 2025-12-11T10:41:13Z date_published: 2025-12-02T00:00:00Z date_updated: 2026-05-20T08:11:56Z day: '02' ddc: - '550' department: - _id: CaMu doi: 10.1073/pnas.2511549122 ec_funded: 1 external_id: pmid: - '41284872' file: - access_level: open_access checksum: 093a8685170e4a1de9176f68ee449493 content_type: application/pdf creator: dernst date_created: 2025-12-15T09:17:33Z date_updated: 2025-12-15T09:17:33Z file_id: '20822' file_name: 2025_PNAS_Bao.pdf file_size: 30890293 relation: main_file success: 1 file_date_updated: 2025-12-15T09:17:33Z fulldoi: https://doi.org/10.1073/pnas.2511549122 has_accepted_license: '1' intvolume: ' 122' issue: '48' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/hidden-in-plain-sight/ scopus_import: '1' status: public title: Tropics-wide intraseasonal 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: 122 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20796' abstract: - lang: eng text: Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements. acknowledgement: We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and Nick Wedige) for training and support in image acquisition. We also thank the members of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B (ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory for helpful discussions. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440). article_number: '10446' article_processing_charge: Yes article_type: original author: - first_name: Dimitra full_name: Paouneskou, Dimitra last_name: Paouneskou - first_name: Antoine full_name: Baudrimont, Antoine last_name: Baudrimont - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Angela full_name: Graf, Angela last_name: Graf - first_name: Shehab full_name: Moukbel Ali Aldawla, Shehab last_name: Moukbel Ali Aldawla - first_name: Claudia full_name: Kölbl, Claudia last_name: Kölbl - first_name: Irene full_name: Tiemann-Boege, Irene last_name: Tiemann-Boege - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Verena full_name: Jantsch, Verena last_name: Jantsch citation: ama: Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 2025;16. doi:10.1038/s41467-025-65420-9 apa: Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65420-9 chicago: Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi, Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65420-9. ieee: D. Paouneskou et al., “BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 16, 10446. mla: Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications, vol. 16, 10446, Springer Nature, 2025, doi:10.1038/s41467-025-65420-9. short: D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications 16 (2025). date_created: 2025-12-11T10:45:06Z date_published: 2025-11-25T00:00:00Z date_updated: 2025-12-15T09:28:37Z day: '25' ddc: - '570' department: - _id: BeVi doi: 10.1038/s41467-025-65420-9 external_id: pmid: - '41290579' file: - access_level: open_access checksum: a952f7ea050242b79008540de49a0e61 content_type: application/pdf creator: dernst date_created: 2025-12-15T09:25:51Z date_updated: 2025-12-15T09:25:51Z file_id: '20823' file_name: 2025_NatureComm_Paouneskou.pdf file_size: 8096309 relation: main_file success: 1 file_date_updated: 2025-12-15T09:25:51Z fulldoi: https://doi.org/10.1038/s41467-025-65420-9 has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity 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: 16 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '20816' abstract: - lang: eng text: "Background: DNA methylation (DNAm) can regulate gene expression, and its genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for complex traits. The relative stability of methylation profiles may enable better assessment of chronic exposures compared to single time-point protein measures. We present the first large-scale epigenetic study of the highly-abundant serum proteome measured via ultra-high throughput mass spectrometry in 14,671 samples from the Generation Scotland cohort. We further demonstrate the first large-scale comparison of protein EpiScores and their respective proteins as predictors of incident cardiovascular disease.\r\n\r\nResults: Marginal epigenome-wide association models, adjusting for age, sex, measurement batch, estimated white cell proportions, BMI, smoking and methylation principal components, reveal 15,855 significant CpG – protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10. Bayesian epigenome-wide association studies of the same 133 proteins reveal 697 CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein EpiScores correlate significantly with their respective protein in a holdout test-set. Of these, sixteen associate significantly with incident all-cause cardiovascular disease (Nevents=191) compared to one measured protein.\r\n\r\nConclusions: We highlight a complex interplay between the blood-based methylome and proteome. Importantly, we show that protein EpiScores correlate with measured proteins and demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically relevant biomarkers. The protein EpiScores demonstrate more significant associations with cardiovascular disease than directly measured proteins, suggesting their potential as clinical biomarkers for monitoring or predicting disease risk. We suggest that biomarker development could be enhanced by the consideration of protein EpiScores alongside measured proteins." acknowledgement: "Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006] and is currently supported by the Wellcome Trust [216767/Z/19/Z]. Genotyping of the Generation Scotland samples was carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, University of Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) Reference 104036/Z/14/Z). The DNA methylation profiling and analysis was supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI: Prof AM McIntosh) and through funding from NARSAD (Ref: 27404; awardee: Dr DM Howard) and the Royal College of Physicians of Edinburgh (Sim Fellowship; Awardee: Prof HC Whalley).\r\nJAR is a University of Edinburgh Clinical Academic Track PhD student, supported by the Wellcome Trust (319878/Z/24/Z). ADC was supported by a Medical Research Council PhD Studentship in Precision Medicine with funding from the Medical Research Council Doctoral Training Program and the University of Edinburgh College of Medicine and Veterinary Medicine. HMS is a student on the University of Edinburgh Translational Neuroscience PhD programme funded by the Wellcome Trust (218493/Z/19/Z). CH was funded by MRC Human Genetics Unit program (QTL in Health and Disease) (grant U.MC_UU_00007/10). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (221890/Z/20/Z). JM and REM were supported by Alzheimer’s Society project grant AS-PG-19b-010." article_number: '417' article_processing_charge: Yes article_type: original author: - first_name: Josephine A. full_name: Robertson, Josephine A. last_name: Robertson - first_name: Jakub full_name: Bajzik, Jakub id: b995e25b-8c4b-11ed-a6d8-f71b7bcd6122 last_name: Bajzik - first_name: Spyros full_name: Vernardis, Spyros last_name: Vernardis - first_name: Aleksandra D. full_name: Chybowska, Aleksandra D. last_name: Chybowska - first_name: Daniel L. full_name: Mccartney, Daniel L. last_name: Mccartney - first_name: Arturas full_name: Grauslys, Arturas last_name: Grauslys - first_name: Jure full_name: Mur, Jure last_name: Mur - first_name: Hannah M. full_name: Smith, Hannah M. last_name: Smith - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Camilla full_name: Drake, Camilla last_name: Drake - first_name: Hannah full_name: Grant, Hannah last_name: Grant - first_name: Jamie full_name: Pearce, Jamie last_name: Pearce - first_name: Tom C. full_name: Russ, Tom C. last_name: Russ - first_name: Poppy full_name: Adkin, Poppy last_name: Adkin - first_name: Matthew full_name: White, Matthew last_name: White - first_name: Charles full_name: Brigden, Charles last_name: Brigden - first_name: Christoph B. full_name: Messner, Christoph B. last_name: Messner - first_name: David J. full_name: Porteous, David J. last_name: Porteous - first_name: Caroline full_name: Hayward, Caroline last_name: Hayward - first_name: Simon R. full_name: Cox, Simon R. last_name: Cox - first_name: Aleksej full_name: Zelezniak, Aleksej last_name: Zelezniak - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni citation: ama: Robertson JA, Bajzik J, Vernardis S, et al. Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. Genome Biology. 2025;26. doi:10.1186/s13059-025-03892-0 apa: Robertson, J. A., Bajzik, J., Vernardis, S., Chybowska, A. D., Mccartney, D. L., Grauslys, A., … Marioni, R. E. (2025). Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-025-03892-0 chicago: Robertson, Josephine A., Jakub Bajzik, Spyros Vernardis, Aleksandra D. Chybowska, Daniel L. Mccartney, Arturas Grauslys, Jure Mur, et al. “Methylome-Wide Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins in 14,671 Generation Scotland Participants.” Genome Biology. Springer Nature, 2025. https://doi.org/10.1186/s13059-025-03892-0. ieee: J. A. Robertson et al., “Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants,” Genome Biology, vol. 26. Springer Nature, 2025. ista: Robertson JA, Bajzik J, Vernardis S, Chybowska AD, Mccartney DL, Grauslys A, Mur J, Smith HM, Campbell A, Drake C, Grant H, Pearce J, Russ TC, Adkin P, White M, Brigden C, Messner CB, Porteous DJ, Hayward C, Cox SR, Zelezniak A, Ralser M, Robinson MR, Marioni RE. 2025. Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. Genome Biology. 26, 417. mla: Robertson, Josephine A., et al. “Methylome-Wide Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins in 14,671 Generation Scotland Participants.” Genome Biology, vol. 26, 417, Springer Nature, 2025, doi:10.1186/s13059-025-03892-0. short: J.A. Robertson, J. Bajzik, S. Vernardis, A.D. Chybowska, D.L. Mccartney, A. Grauslys, J. Mur, H.M. Smith, A. Campbell, C. Drake, H. Grant, J. Pearce, T.C. Russ, P. Adkin, M. White, C. Brigden, C.B. Messner, D.J. Porteous, C. Hayward, S.R. Cox, A. Zelezniak, M. Ralser, M.R. Robinson, R.E. Marioni, Genome Biology 26 (2025). date_created: 2025-12-14T23:02:04Z date_published: 2025-12-08T00:00:00Z date_updated: 2025-12-15T13:19:41Z day: '08' ddc: - '570' department: - _id: MaRo doi: 10.1186/s13059-025-03892-0 external_id: pmid: - '41361833' file: - access_level: open_access checksum: 7c92919af1b5820d01e91e08906a411f content_type: application/pdf creator: dernst date_created: 2025-12-15T13:18:07Z date_updated: 2025-12-15T13:18:07Z file_id: '20825' file_name: 2025_GenomeBiology_Robertson.pdf file_size: 2206991 relation: main_file success: 1 file_date_updated: 2025-12-15T13:18:07Z fulldoi: https://doi.org/10.1186/s13059-025-03892-0 has_accepted_license: '1' intvolume: ' 26' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: eissn: - 1474-760X issn: - 1474-7596 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants 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: 26 year: '2025' ... --- APC_amount: 4910,08 EUR OA_place: publisher OA_type: gold _id: '8125' abstract: - lang: eng text: "Biological memory is known to be flexible—memory formation and recall depend on factors such as the behavioral context of the organism. However, this property is often ignored in associative memory models, leaving it unclear how memories can be organized and recalled when subject to contextual control. Because of the lack of a rigorous analytical framework, it is also unknown how contextual control affects memory stability, storage capacity, and information content. Here, we bring the dynamic nature of memory to the fore by introducing a novel model of associative memory, which we refer to as the context-modular memory network. In our model, stored memory patterns are associated to one of several background network states, or contexts. Memories are accessible when their corresponding context is active, and are otherwise inaccessible. Context modulates the effective network connectivity by imposing a specific\r\nconfiguration of neuronal and synaptic gating—gated neurons (synapses) have their activity (weights) momentarily silenced, thereby reducing interference from memories belonging to other contexts. Memory patterns are randomly and independently chosen, while neuronal and synaptic gates may be selected randomly or optimized through a process of contextual synaptic refinement. Through analytic and numerical results, we show that context-modular memory networks can exhibit both improved memory capacity and differential control of memory stability with random gating (especially for neuronal gating). For contextual synaptic refinement, we devise a method in which synapses are gated off for a given context if they destabilize the memory patterns in that context, drastically improving memory capacity and enabling even more precise control over memory stability. Notably, synaptic refinement allows for patterns to be\r\naccessible in multiple contexts, stabilizing memory patterns even for weight matrices that alone do not contain any information about the memory patterns, such as Gaussian random matrices. Overall, our model integrates recent ideas about context-dependent memory organization with classic associative memory models and proposes a rigorous theory which can act as a framework for future work. Furthermore, our work carries important implications for the understanding of biological memory storage and recall in the brain, such as highlighting an intriguing trade-off between memory capacity and accessibility." acknowledgement: "We thank Helen Barron, Vezha Boboeva, Adam Packer, João Sacramento, Andrew Saxe, Misha Tsodyks, and Friedemann Zenke for helpful comments at various stages of this work, and Rubem Erichsen, Jr. for carefully reading the manuscript and valuable comments. This work was\r\nsupported by a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society [No. WT100000 (W. F. P., E. J. A., and T. P. V.)], a Wellcome Trust Senior Research Fellowship [No. 214316/Z/18/Z (E. J. A. and T. P. V.)], and a Research Project Grant by the Leverhulme Trust\r\n[No. RPG-2016-446 (E. J. A.)]. " article_number: '011057' article_processing_charge: Yes article_type: original author: - first_name: William F. full_name: Podlaski, William F. last_name: Podlaski orcid: 0000-0001-6619-7502 - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes orcid: 0000-0001-7184-7311 - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. Physical Review X. 2025;15. doi:10.1103/PhysRevX.15.011057 apa: Podlaski, W. F., Agnes, E. J., & Vogels, T. P. (2025). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.15.011057 chicago: Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” Physical Review X. American Physical Society, 2025. https://doi.org/10.1103/PhysRevX.15.011057. ieee: W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” Physical Review X, vol. 15. American Physical Society, 2025. ista: Podlaski WF, Agnes EJ, Vogels TP. 2025. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. Physical Review X. 15, 011057. mla: Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” Physical Review X, vol. 15, 011057, American Physical Society, 2025, doi:10.1103/PhysRevX.15.011057. short: W.F. Podlaski, E.J. Agnes, T.P. Vogels, Physical Review X 15 (2025). corr_author: '1' date_created: 2020-07-16T12:24:28Z date_published: 2025-03-13T00:00:00Z date_updated: 2026-05-06T12:44:27Z day: '13' ddc: - '530' department: - _id: TiVo doi: 10.1103/PhysRevX.15.011057 external_id: isi: - '001451378900002' file: - access_level: open_access checksum: 1f27ee469ab51a3e1ce1e2df0022e81d content_type: application/pdf creator: dernst date_created: 2025-03-20T12:47:17Z date_updated: 2025-03-20T12:47:17Z file_id: '19432' file_name: 2025_PhysReviewX_Podlaski.pdf file_size: 1373704 relation: main_file success: 1 file_date_updated: 2025-03-20T12:47:17Z fulldoi: https://doi.org/10.1103/PhysRevX.15.011057 has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng locked: '1' month: '03' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. publication: Physical Review X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/wpodlaski/contextual-memory-nets scopus_import: '1' status: public title: High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating 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: 15 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '8616' abstract: - lang: eng text: The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we report that a substantial proportion of blood vessels in the adult mouse brain sporadically occlude and regress. Their regression proceeds through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels are found to be widespread in mouse, monkey and human brains. We further reveal that blood vessel regression cause a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain. acknowledgement: 'The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies. Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.' article_number: '5840' article_processing_charge: Yes article_type: original author: - first_name: Xiaofei full_name: Gao, Xiaofei last_name: Gao - first_name: Jun-Liszt full_name: Li, Jun-Liszt last_name: Li - first_name: Xingjun full_name: Chen, Xingjun last_name: Chen - first_name: Bo full_name: Ci, Bo last_name: Ci - first_name: Fei full_name: Chen, Fei last_name: Chen - first_name: Nannan full_name: Lu, Nannan last_name: Lu - first_name: Bo full_name: Shen, Bo last_name: Shen - first_name: Lijun full_name: Zheng, Lijun last_name: Zheng - first_name: Jie-Min full_name: Jia, Jie-Min last_name: Jia - first_name: Yating full_name: Yi, Yating last_name: Yi - first_name: Shiwen full_name: Zhang, Shiwen last_name: Zhang - first_name: Ying-Chao full_name: Shi, Ying-Chao last_name: Shi - first_name: Kaibin full_name: Shi, Kaibin last_name: Shi - first_name: Nicholas E full_name: Propson, Nicholas E last_name: Propson - first_name: Yubin full_name: Huang, Yubin last_name: Huang - first_name: Katherine full_name: Poinsatte, Katherine last_name: Poinsatte - first_name: Zhaohuan full_name: Zhang, Zhaohuan last_name: Zhang - first_name: Yuanlei full_name: Yue, Yuanlei last_name: Yue - first_name: Dale B full_name: Bosco, Dale B last_name: Bosco - first_name: Ying-mei full_name: Lu, Ying-mei last_name: Lu - first_name: Shi-bing full_name: Yang, Shi-bing last_name: Yang - first_name: Ralf H. full_name: Adams, Ralf H. last_name: Adams - first_name: Volkhard full_name: Lindner, Volkhard last_name: Lindner - first_name: Fen full_name: Huang, Fen last_name: Huang - first_name: Long-Jun full_name: Wu, Long-Jun last_name: Wu - first_name: Hui full_name: Zheng, Hui last_name: Zheng - first_name: Feng full_name: Han, Feng last_name: Han - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ann M. full_name: Stowe, Ann M. last_name: Stowe - first_name: Bo full_name: Peng, Bo last_name: Peng - first_name: Marta full_name: Margeta, Marta last_name: Margeta - first_name: Xiaoqun full_name: Wang, Xiaoqun last_name: Wang - first_name: Qiang full_name: Liu, Qiang last_name: Liu - first_name: Jakob full_name: Körbelin, Jakob last_name: Körbelin - first_name: Martin full_name: Trepel, Martin last_name: Trepel - first_name: Hui full_name: Lu, Hui last_name: Lu - first_name: Bo O. full_name: Zhou, Bo O. last_name: Zhou - first_name: Hu full_name: Zhao, Hu last_name: Zhao - first_name: Wenzhi full_name: Su, Wenzhi last_name: Su - first_name: Robert M. full_name: Bachoo, Robert M. last_name: Bachoo - first_name: Woo-ping full_name: Ge, Woo-ping last_name: Ge citation: ama: Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. 2025;16. doi:10.1038/s41467-025-60308-0 apa: Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (2025). Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-60308-0 chicago: Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-60308-0. ieee: X. Gao et al., “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. 2025. Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. 16, 5840. mla: Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” Nature Communications, vol. 16, 5840, Springer Nature, 2025, doi:10.1038/s41467-025-60308-0. short: X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, Nature Communications 16 (2025). date_created: 2020-10-06T08:58:59Z date_published: 2025-07-01T00:00:00Z date_updated: 2025-09-04T07:08:37Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1038/s41467-025-60308-0 ec_funded: 1 external_id: isi: - '001523450500035' file: - access_level: open_access checksum: f59748cb67232cfb210035d9aef60836 content_type: application/pdf creator: dernst date_created: 2025-07-07T09:52:46Z date_updated: 2025-07-07T09:52:46Z file_id: '19971' file_name: 2025_NatureComm_Gao.pdf file_size: 17018106 relation: main_file success: 1 file_date_updated: 2025-07-07T09:52:46Z fulldoi: https://doi.org/10.1038/s41467-025-60308-0 has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reduction of neuronal activity mediated by blood-vessel regression in the brain 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18154' abstract: - lang: eng text: 'In 1976, Deligne and Lusztig realized the representation theory of finite groups of Lie type inside étale cohomology of certain algebraic varieties. Recently, a p-adic version of this theory started to emerge: there are p-adic Deligne–Lusztig spaces, whose cohomology encodes representation theoretic information for p-adic groups – for instance, it partially realizes the local Langlands correspondence with characteristic zero coefficients. However, the parallel case of coefficients of positive characteristic ℓ≠p has not been inspected so far. The purpose of this article is to initiate such an inspection. In particular, we relate cohomology of certain p-adic Deligne–Lusztig spaces to Vignéras''s modular local Langlands correspondence for GLn.' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Jakub full_name: Löwit, Jakub id: e3b80ae2-eb8e-11eb-b029-9aef4a9108a0 last_name: Löwit citation: ama: Löwit J. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. Journal of Algebra. 2025;663(2):81-118. doi:10.1016/j.jalgebra.2024.08.033 apa: Löwit, J. (2025). On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2024.08.033 chicago: Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for GLn.” Journal of Algebra. Elsevier, 2025. https://doi.org/10.1016/j.jalgebra.2024.08.033. ieee: J. Löwit, “On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn,” Journal of Algebra, vol. 663, no. 2. Elsevier, pp. 81–118, 2025. ista: Löwit J. 2025. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. Journal of Algebra. 663(2), 81–118. mla: Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for GLn.” Journal of Algebra, vol. 663, no. 2, Elsevier, 2025, pp. 81–118, doi:10.1016/j.jalgebra.2024.08.033. short: J. Löwit, Journal of Algebra 663 (2025) 81–118. corr_author: '1' date_created: 2024-09-29T22:01:37Z date_published: 2025-02-01T00:00:00Z date_updated: 2025-02-27T12:32:40Z day: '01' ddc: - '510' department: - _id: TaHa doi: 10.1016/j.jalgebra.2024.08.033 external_id: arxiv: - '2404.11176' isi: - '001325207800001' file: - access_level: open_access checksum: eb240e93c178e48429ad918c9058f1fe content_type: application/pdf creator: dernst date_created: 2025-01-13T08:57:57Z date_updated: 2025-01-13T08:57:57Z file_id: '18830' file_name: 2024_JourAlgebra_Loewit.pdf file_size: 731175 relation: main_file success: 1 file_date_updated: 2025-01-13T08:57:57Z fulldoi: https://doi.org/10.1016/j.jalgebra.2024.08.033 has_accepted_license: '1' intvolume: ' 663' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 81-118 publication: Journal of Algebra publication_identifier: eissn: - 1090-266X issn: - 0021-8693 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn 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: 663 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18169' abstract: - lang: eng text: "As the complexity and criticality of software increase every year, so does the importance of runtime monitoring. Third-party and best-effort monitoring are especially valuable, yet under-explored areas of runtime monitoring. In this context, third-party monitoring means monitoring with a limited knowledge of the monitored software (as it has been developed by a third party). Best-effort monitoring keeps pace with the monitored software at the cost of possibly imprecise verdicts when keeping up with the monitored software would not be feasible. Most existing monitoring frameworks do not support the combination of third-party and best-effort monitoring because they either require the full access to the monitored code or the ability to process all observable events, or both.\r\nWe present a middleware framework, Vamos, for the runtime monitoring of software. Vamos is explicitly designed to support third-party and best-effort scenarios. The design goals of Vamos are (i) efficiency (tracing events with low overhead), (ii) flexibility (the ability to monitor a variety of different event channels, and to connect to a wide range of monitors), and (iii) ease-of-use. To achieve its goals, Vamos combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for Vamos and conducted a set of experiments demonstrating the usability of the scheme. The results indicate that Vamos enables writing useful yet efficient monitors, and simplifies key aspects of setting up a monitoring system from scratch." acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the STTT reviewers for their valuable feedback and suggestions. article_number: '103212' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Marek full_name: Chalupa, Marek id: 87e34708-d6c6-11ec-9f5b-9391e7be2463 last_name: Chalupa - first_name: Fabian full_name: Mühlböck, Fabian id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425 last_name: Mühlböck orcid: 0000-0003-1548-0177 - first_name: Stefanie full_name: Muroya Lei, Stefanie id: a376de31-8972-11ed-ae7b-d0251c13c8ff last_name: Muroya Lei - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for best-effort third-party monitoring. Science of Computer Programming. 2025;240(2). doi:10.1016/j.scico.2024.103212' apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2025). VAMOS: Middleware for best-effort third-party monitoring. Science of Computer Programming. Elsevier. https://doi.org/10.1016/j.scico.2024.103212' chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “VAMOS: Middleware for Best-Effort Third-Party Monitoring.” Science of Computer Programming. Elsevier, 2025. https://doi.org/10.1016/j.scico.2024.103212.' ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “VAMOS: Middleware for best-effort third-party monitoring,” Science of Computer Programming, vol. 240, no. 2. Elsevier, 2025.' ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2025. VAMOS: Middleware for best-effort third-party monitoring. Science of Computer Programming. 240(2), 103212.' mla: 'Chalupa, Marek, et al. “VAMOS: Middleware for Best-Effort Third-Party Monitoring.” Science of Computer Programming, vol. 240, no. 2, 103212, Elsevier, 2025, doi:10.1016/j.scico.2024.103212.' short: M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, Science of Computer Programming 240 (2025). corr_author: '1' date_created: 2024-10-06T22:01:10Z date_published: 2025-02-01T00:00:00Z date_updated: 2025-09-09T12:25:29Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1016/j.scico.2024.103212 ec_funded: 1 external_id: isi: - '001327852600001' file: - access_level: open_access checksum: cd93c0c356e479ffccfbe8499b6ba8e2 content_type: application/pdf creator: dernst date_created: 2025-01-13T09:02:47Z date_updated: 2025-01-13T09:02:47Z file_id: '18831' file_name: 2024_ScienceCompProg_Chalupa.pdf file_size: 1173677 relation: main_file success: 1 file_date_updated: 2025-01-13T09:02:47Z fulldoi: https://doi.org/10.1016/j.scico.2024.103212 has_accepted_license: '1' intvolume: ' 240' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Science of Computer Programming publication_identifier: issn: - 0167-6423 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '12856' relation: earlier_version status: public scopus_import: '1' status: public title: 'VAMOS: Middleware for best-effort third-party monitoring' 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: 240 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18170' abstract: - lang: eng text: 'This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.' acknowledgement: 'This research was funded in whole by the Austrian Science Fund (FWF) [P 35103-B, Grant-DOI: 10.55776/P35103]. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. We would like to thank Olfert Landt for advice on ssDNA probe design; Rui Qiang Chen, Jennifer Stock, and Christine Wukotitsch for their excellent support with ONT sequencing; Christoph Köppl and Andreas Fischer for excellent support in recombinant N protein expression and purification; and the whole team at the division of clinical virology for their support with standard diagnostics.' article_number: '116807' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Anna Nele full_name: Herdina, Anna Nele last_name: Herdina - first_name: Anil full_name: Bozdogan, Anil last_name: Bozdogan - first_name: Patrik full_name: Aspermair, Patrik last_name: Aspermair - first_name: Jakub full_name: Dostalek, Jakub last_name: Dostalek - first_name: Miriam full_name: Klausberger, Miriam last_name: Klausberger - first_name: Nico full_name: Lingg, Nico last_name: Lingg - first_name: Monika full_name: Cserjan-Puschmann, Monika last_name: Cserjan-Puschmann - first_name: Patricia Pereira full_name: Aguilar, Patricia Pereira last_name: Aguilar - first_name: Simone full_name: Auer, Simone last_name: Auer - first_name: Halil full_name: Demirtas, Halil last_name: Demirtas - first_name: Jakob full_name: Andersson, Jakob id: 3a5f4167-9bd9-11ed-bd12-a1446d38776f last_name: Andersson - first_name: Felix full_name: Lötsch, Felix last_name: Lötsch - first_name: Barbara full_name: Holzer, Barbara last_name: Holzer - first_name: Adi full_name: Steinrigl, Adi last_name: Steinrigl - first_name: Florian full_name: Thalhammer, Florian last_name: Thalhammer - first_name: Julia full_name: Schellnegger, Julia last_name: Schellnegger - first_name: Monika full_name: Breuer, Monika last_name: Breuer - first_name: Wolfgang full_name: Knoll, Wolfgang last_name: Knoll - first_name: Robert full_name: Strassl, Robert last_name: Strassl citation: ama: 'Herdina AN, Bozdogan A, Aspermair P, et al. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. Biosensors and Bioelectronics. 2025;267. doi:10.1016/j.bios.2024.116807' apa: 'Herdina, A. N., Bozdogan, A., Aspermair, P., Dostalek, J., Klausberger, M., Lingg, N., … Strassl, R. (2025). Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. Biosensors and Bioelectronics. Elsevier. https://doi.org/10.1016/j.bios.2024.116807' chicago: 'Herdina, Anna Nele, Anil Bozdogan, Patrik Aspermair, Jakub Dostalek, Miriam Klausberger, Nico Lingg, Monika Cserjan-Puschmann, et al. “Bridging Basic Science and Applied Diagnostics: Comprehensive Viral Diagnostics Enabled by Graphene-Based Electronic Biosensor Technology Advancements.” Biosensors and Bioelectronics. Elsevier, 2025. https://doi.org/10.1016/j.bios.2024.116807.' ieee: 'A. N. Herdina et al., “Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements,” Biosensors and Bioelectronics, vol. 267. Elsevier, 2025.' ista: 'Herdina AN, Bozdogan A, Aspermair P, Dostalek J, Klausberger M, Lingg N, Cserjan-Puschmann M, Aguilar PP, Auer S, Demirtas H, Andersson J, Lötsch F, Holzer B, Steinrigl A, Thalhammer F, Schellnegger J, Breuer M, Knoll W, Strassl R. 2025. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. Biosensors and Bioelectronics. 267, 116807.' mla: 'Herdina, Anna Nele, et al. “Bridging Basic Science and Applied Diagnostics: Comprehensive Viral Diagnostics Enabled by Graphene-Based Electronic Biosensor Technology Advancements.” Biosensors and Bioelectronics, vol. 267, 116807, Elsevier, 2025, doi:10.1016/j.bios.2024.116807.' short: A.N. Herdina, A. Bozdogan, P. Aspermair, J. Dostalek, M. Klausberger, N. Lingg, M. Cserjan-Puschmann, P.P. Aguilar, S. Auer, H. Demirtas, J. Andersson, F. Lötsch, B. Holzer, A. Steinrigl, F. Thalhammer, J. Schellnegger, M. Breuer, W. Knoll, R. Strassl, Biosensors and Bioelectronics 267 (2025). date_created: 2024-10-06T22:01:11Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-02-27T12:34:07Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.bios.2024.116807 external_id: isi: - '001328413700001' pmid: - '39341071' file: - access_level: open_access checksum: 208ac27dab27af792d198fcb74af8756 content_type: application/pdf creator: dernst date_created: 2025-01-13T11:14:32Z date_updated: 2025-01-13T11:14:32Z file_id: '18843' file_name: 2025_BiosensorsBioelectronics_Herdina.pdf file_size: 4135372 relation: main_file success: 1 file_date_updated: 2025-01-13T11:14:32Z fulldoi: https://doi.org/10.1016/j.bios.2024.116807 has_accepted_license: '1' intvolume: ' 267' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Biosensors and Bioelectronics publication_identifier: eissn: - 1873-4235 issn: - 0956-5663 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements' 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: 267 year: '2025' ... --- OA_place: publisher OA_type: gold _id: '22120' article_number: EGU25-17446 article_processing_charge: No author: - first_name: José M full_name: Muñoz Hermosilla, José M id: e1037a6d-646e-11ef-b402-e0ed9ab0901e last_name: Muñoz Hermosilla orcid: 0000-0002-1990-8508 - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Michael full_name: McCarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: McCarthy - first_name: Florian full_name: Hardmeier, Florian last_name: Hardmeier - first_name: Juan Vicente full_name: Melo Velasco, Juan Vicente id: 2611dec0-b9c6-11ed-9bea-a81c2b17a549 last_name: Melo Velasco - first_name: Guillaume full_name: Jouvet, Guillaume last_name: Jouvet - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: 'Muñoz Hermosilla JM, Miles E, McCarthy M, et al. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In: EGU General Assembly 2025. European Geosciences Union; 2025. doi:10.5194/egusphere-egu25-17446' apa: 'Muñoz Hermosilla, J. M., Miles, E., McCarthy, M., Hardmeier, F., Melo Velasco, J. V., Jouvet, G., & Pellicciotti, F. (2025). Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In EGU General Assembly 2025. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu25-17446' chicago: Muñoz Hermosilla, José M, Evan Miles, Michael McCarthy, Florian Hardmeier, Juan Vicente Melo Velasco, Guillaume Jouvet, and Francesca Pellicciotti. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” In EGU General Assembly 2025. European Geosciences Union, 2025. https://doi.org/10.5194/egusphere-egu25-17446. ieee: J. M. Muñoz Hermosilla et al., “Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier,” in EGU General Assembly 2025, Vienna, Austria & Virtual, 2025. ista: Muñoz Hermosilla JM, Miles E, McCarthy M, Hardmeier F, Melo Velasco JV, Jouvet G, Pellicciotti F. 2025. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. EGU General Assembly 2025. EGU General Assembly, EGU25-17446. mla: Muñoz Hermosilla, José M., et al. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” EGU General Assembly 2025, EGU25-17446, European Geosciences Union, 2025, doi:10.5194/egusphere-egu25-17446. short: J.M. Muñoz Hermosilla, E. Miles, M. McCarthy, F. Hardmeier, J.V. Melo Velasco, G. Jouvet, F. Pellicciotti, in:, EGU General Assembly 2025, European Geosciences Union, 2025. conference: end_date: 2025-05-02 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2025-04-27 date_created: 2026-06-22T12:17:47Z date_published: 2025-05-14T00:00:00Z date_updated: 2026-07-02T06:41:43Z day: '14' ddc: - '550' department: - _id: FrPe - _id: GradSch doi: 10.5194/egusphere-egu25-17446 fulldoi: https://doi.org/10.5194/egusphere-egu25-17446 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5194/egusphere-egu25-17446 month: '05' oa: 1 oa_version: Published Version publication: EGU General Assembly 2025 publication_status: published publisher: European Geosciences Union status: public title: Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: diamond PlanS_conform: '1' _id: '21263' abstract: - lang: eng text: Two landmark results in combinatorial random matrix theory, due to Komlós and Costello–Tao–Vu, show that discrete random matrices and symmetric discrete random matrices are typically nonsingular. In particular, in the language of graph theory, when p is a fixed constant, the biadjacency matrix of a random Erdős–Rényi bipartite graph G(n,n,p) and the adjacency matrix of an Erdős–Rényi random graph G(n,p) are both nonsingular with high probability. However, very sparse random graphs (i.e., where p is allowed to decay rapidly with n) are typically singular, due to the presence of “local” dependencies such as isolated vertices and pairs of degree-1 vertices with the same neighbour. In this paper, we give a combinatorial description of the rank of a sparse random graph G(n,n,c/n) or G(n,c/n) in terms of such local dependencies, for all constants c=e (and we present some evidence that the situation is very different for c=e). This gives an essentially complete answer to a question raised by Vu (2014). As applications of our main theorem and its proof, we also determine the asymptotic singularity probability of the 2-core of a sparse random graph, we show that the rank of a sparse random graph is extremely well approximated by its matching number, and we deduce a central limit theorem for the rank of G(n,c/n). acknowledgement: "We would like to thank Noga Alon for suggesting that our main result gives\r\na linear-time algorithm for computing the rank. We also thank the referees for a number of thoughtful comments and suggestions. Glasgow was supported by NSF graduate research fellowship program award DGE1656518. Kwan was supported by ERC Starting Grant “RANDSTRUCT” No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302.\r\n" article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Margalit full_name: Glasgow, Margalit last_name: Glasgow - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Ashwin full_name: Sah, Ashwin last_name: Sah - first_name: Mehtaab full_name: Sawhney, Mehtaab last_name: Sawhney citation: ama: Glasgow M, Kwan MA, Sah A, Sawhney M. The exact rank of sparse random graphs. Journal of the European Mathematical Society. 2025. doi:10.4171/jems/1692 apa: Glasgow, M., Kwan, M. A., Sah, A., & Sawhney, M. (2025). The exact rank of sparse random graphs. Journal of the European Mathematical Society. EMS Press. https://doi.org/10.4171/jems/1692 chicago: Glasgow, Margalit, Matthew Alan Kwan, Ashwin Sah, and Mehtaab Sawhney. “The Exact Rank of Sparse Random Graphs.” Journal of the European Mathematical Society. EMS Press, 2025. https://doi.org/10.4171/jems/1692. ieee: M. Glasgow, M. A. Kwan, A. Sah, and M. Sawhney, “The exact rank of sparse random graphs,” Journal of the European Mathematical Society. EMS Press, 2025. ista: Glasgow M, Kwan MA, Sah A, Sawhney M. 2025. The exact rank of sparse random graphs. Journal of the European Mathematical Society. mla: Glasgow, Margalit, et al. “The Exact Rank of Sparse Random Graphs.” Journal of the European Mathematical Society, EMS Press, 2025, doi:10.4171/jems/1692. short: M. Glasgow, M.A. Kwan, A. Sah, M. Sawhney, Journal of the European Mathematical Society (2025). corr_author: '1' das_tickbox: '1' date_created: 2026-02-17T07:41:59Z date_published: 2025-09-02T00:00:00Z date_updated: 2026-07-06T11:51:31Z day: '02' ddc: - '510' department: - _id: MaKw doi: 10.4171/jems/1692 external_id: arxiv: - '2303.05435' fulldoi: https://doi.org/10.4171/jems/1692 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4171/JEMS/1692 month: '09' oa: 1 oa_version: Published Version project: - _id: bd95085b-d553-11ed-ba76-e55d3349be45 grant_number: '101076777' name: Randomness and structure in combinatorics publication: Journal of the European Mathematical Society publication_identifier: eissn: - 1435-9863 issn: - 1435-9855 publication_status: epub_ahead publisher: EMS Press quality_controlled: '1' status: public title: The exact rank of sparse random graphs 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 year: '2025' ... --- OA_place: publisher _id: '20441' abstract: - lang: eng text: "Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 citation: ama: Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:10.15479/AT-ISTA-20441 apa: Naik, S. (2025). Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20441 chicago: Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20441. ieee: S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025. ista: Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. mla: Naik, Suyash. Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20441. short: S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-10T14:58:30Z date_published: 2025-10-12T00:00:00Z date_updated: 2026-07-06T12:51:41Z day: '12' ddc: - '596' - '597' - '532' degree_awarded: PhD department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-20441 file: - access_level: open_access checksum: 2892f04d4a5c18677871c3e06ac1244a content_type: application/pdf creator: snaik date_created: 2025-10-28T13:10:08Z date_updated: 2025-10-28T13:10:08Z file_id: '20567' file_name: Thesis_PDFA_.pdf file_size: 6846189 relation: main_file success: 1 - access_level: open_access checksum: 15934d4465cd0e9b7c32678da9a33a2f content_type: application/zip creator: snaik date_created: 2025-10-28T13:10:26Z date_updated: 2025-10-28T13:10:26Z file_id: '20568' file_name: Thesis.zip file_size: 8839300 relation: source_file file_date_updated: 2025-10-28T13:10:26Z fulldoi: https://doi.org/10.15479/AT-ISTA-20441 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '105' project: - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 25AA5F24-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W 1250-B20 name: Nano-Analytics of Cellular Systems publication_identifier: isbn: - 978-3-99078-069-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20465' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Keratins act as global coordinators of tissue spreading through mechanosensitive feedback 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ...