--- OA_place: publisher OA_type: hybrid _id: '20729' abstract: - lang: eng text: 'Persistence modules (defined as a sequence of vector spaces and linear maps between them) are a key tool in topological data analysis. They are easy to interpret and fast to compute. However, when considering persistence maps (i.e. maps between persistence modules), these properties are lost. We propose a new invariant for persistence maps consisting of a partial matching such that: it is easy to interpret, it is more discriminative than the image of the persistence map, and can be calculated with cubical complexity.' acknowledgement: Álvaro Torras-Casas contract is funded by the French Agence Nationale de la Recherche through the project reference ANR-22-CPJ1-0047-01. Rocio Gonzalez-Diaz is partially funded by the European Union under grant agreement no. 101070028-2 (REXASI-PRO). article_processing_charge: Yes (in subscription journal) author: - first_name: Rocio full_name: Gonzalez-Diaz, Rocio last_name: Gonzalez-Diaz - first_name: Manuel full_name: Soriano Trigueros, Manuel id: 15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8 last_name: Soriano Trigueros orcid: 0000-0003-2449-1433 - first_name: Alvaro full_name: Torras-Casas, Alvaro last_name: Torras-Casas citation: ama: 'Gonzalez-Diaz R, Soriano Trigueros M, Torras-Casas A. Additive partial matchings for persistent homology. In: Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation. Association for Computing Machinery; 2025:188-196. doi:10.1145/3747199.3747561' apa: 'Gonzalez-Diaz, R., Soriano Trigueros, M., & Torras-Casas, A. (2025). Additive partial matchings for persistent homology. In Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation (pp. 188–196). Guanajuato, Mexico: Association for Computing Machinery. https://doi.org/10.1145/3747199.3747561' chicago: Gonzalez-Diaz, Rocio, Manuel Soriano Trigueros, and Alvaro Torras-Casas. “Additive Partial Matchings for Persistent Homology.” In Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation, 188–96. Association for Computing Machinery, 2025. https://doi.org/10.1145/3747199.3747561. ieee: R. Gonzalez-Diaz, M. Soriano Trigueros, and A. Torras-Casas, “Additive partial matchings for persistent homology,” in Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation, Guanajuato, Mexico, 2025, pp. 188–196. ista: 'Gonzalez-Diaz R, Soriano Trigueros M, Torras-Casas A. 2025. Additive partial matchings for persistent homology. Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation. ISSAC: International Symposium on Symbolic and Algebraic Computation, 188–196.' mla: Gonzalez-Diaz, Rocio, et al. “Additive Partial Matchings for Persistent Homology.” Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation, Association for Computing Machinery, 2025, pp. 188–96, doi:10.1145/3747199.3747561. short: R. Gonzalez-Diaz, M. Soriano Trigueros, A. Torras-Casas, in:, Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation, Association for Computing Machinery, 2025, pp. 188–196. conference: end_date: 2025-08-01 location: Guanajuato, Mexico name: 'ISSAC: International Symposium on Symbolic and Algebraic Computation' start_date: 2025-07-28 corr_author: '1' date_created: 2025-12-07T23:02:01Z date_published: 2025-11-10T00:00:00Z date_updated: 2025-12-09T13:46:42Z day: '10' ddc: - '510' department: - _id: HeEd doi: 10.1145/3747199.3747561 file: - access_level: open_access checksum: 1c299cca165a20e2518afe4fda63dbf1 content_type: application/pdf creator: dernst date_created: 2025-12-09T13:43:17Z date_updated: 2025-12-09T13:43:17Z file_id: '20751' file_name: 2025_ISSAC_GonzalezDiaz.pdf file_size: 761617 relation: main_file success: 1 file_date_updated: 2025-12-09T13:43:17Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 188-196 publication: Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation publication_identifier: isbn: - '9798400720758' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Additive partial matchings for persistent homology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- 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 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 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 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 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 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 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: publisher _id: '20741' abstract: - lang: eng text: "Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. \r\n\r\nFirstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. \r\n\r\nNext, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. \r\n\r\nFinally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. " acknowledged_ssus: - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marko full_name: Kojic, Marko id: 73e7ecd4-dc85-11ea-9058-88a16394b160 last_name: Kojic orcid: 0000-0001-7244-8128 citation: ama: Kojic M. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. 2025. doi:10.15479/AT-ISTA-20741 apa: Kojic, M. (2025). Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20741 chicago: Kojic, Marko. “Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20741. ieee: M. Kojic, “Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria,” Institute of Science and Technology Austria, 2025. ista: Kojic M. 2025. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria. mla: Kojic, Marko. Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20741. short: M. Kojic, Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-12-09T13:08:11Z date_published: 2025-12-09T00:00:00Z date_updated: 2026-04-07T12:27:58Z day: '09' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: MaLo doi: 10.15479/AT-ISTA-20741 file: - access_level: closed checksum: a3643d07e93134b2490a566b02a4517d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mkojic date_created: 2025-12-10T13:09:58Z date_updated: 2025-12-10T13:09:58Z file_id: '20774' file_name: 2025_marko_kojic_thesis.docx file_size: 142876975 relation: source_file - access_level: open_access checksum: 0a096f0af6ccc3a8329d5bb8797ad533 content_type: application/pdf creator: mkojic date_created: 2025-12-10T13:09:38Z date_updated: 2025-12-10T13:09:38Z file_id: '20775' file_name: 2025_marko_kojic_thesis.pdf file_size: 8597045 relation: main_file success: 1 file_date_updated: 2025-12-10T13:09:58Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication_identifier: isbn: - 978-3-99078-073-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15118' relation: part_of_dissertation status: public status: public supervisor: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 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 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 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' ... --- OA_place: publisher OA_type: hybrid _id: '20755' abstract: - lang: eng text: We report the development of a continuous flow approach to nitrogen atom insertion. The setup is modular, enabling the rapid optimization of reaction conditions for a wide range of substrates. The milder reaction conditions led to an improved substrate scope and functional group tolerance compared to batch conditions. The reactions can also be safely scaled up to preparative scale. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sooyeon full_name: Moon, Sooyeon last_name: Moon - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Ann-Sophie K. full_name: Paschke, Ann-Sophie K. last_name: Paschke - first_name: Alessandro full_name: Scotto, Alessandro last_name: Scotto - first_name: Luca full_name: Terraneo, Luca last_name: Terraneo - first_name: Niklas full_name: Brenner, Niklas last_name: Brenner - first_name: Quentin full_name: Lefebvre, Quentin last_name: Lefebvre - first_name: Thomas C. full_name: Fessard, Thomas C. last_name: Fessard - first_name: Bill full_name: Morandi, Bill last_name: Morandi citation: ama: Moon S, Reisenbauer J, Paschke A-SK, et al. Efficient optimization and synthesis of diverse azaarenes via nitrogen atom insertion under continuous flow conditions. Chemical Communications. 2025;61(87):16993-16996. doi:10.1039/d5cc03194j apa: Moon, S., Reisenbauer, J., Paschke, A.-S. K., Scotto, A., Terraneo, L., Brenner, N., … Morandi, B. (2025). Efficient optimization and synthesis of diverse azaarenes via nitrogen atom insertion under continuous flow conditions. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/d5cc03194j chicago: Moon, Sooyeon, Julia Reisenbauer, Ann-Sophie K. Paschke, Alessandro Scotto, Luca Terraneo, Niklas Brenner, Quentin Lefebvre, Thomas C. Fessard, and Bill Morandi. “Efficient Optimization and Synthesis of Diverse Azaarenes via Nitrogen Atom Insertion under Continuous Flow Conditions.” Chemical Communications. Royal Society of Chemistry, 2025. https://doi.org/10.1039/d5cc03194j. ieee: S. Moon et al., “Efficient optimization and synthesis of diverse azaarenes via nitrogen atom insertion under continuous flow conditions,” Chemical Communications, vol. 61, no. 87. Royal Society of Chemistry, pp. 16993–16996, 2025. ista: Moon S, Reisenbauer J, Paschke A-SK, Scotto A, Terraneo L, Brenner N, Lefebvre Q, Fessard TC, Morandi B. 2025. Efficient optimization and synthesis of diverse azaarenes via nitrogen atom insertion under continuous flow conditions. Chemical Communications. 61(87), 16993–16996. mla: Moon, Sooyeon, et al. “Efficient Optimization and Synthesis of Diverse Azaarenes via Nitrogen Atom Insertion under Continuous Flow Conditions.” Chemical Communications, vol. 61, no. 87, Royal Society of Chemistry, 2025, pp. 16993–96, doi:10.1039/d5cc03194j. short: S. Moon, J. Reisenbauer, A.-S.K. Paschke, A. Scotto, L. Terraneo, N. Brenner, Q. Lefebvre, T.C. Fessard, B. Morandi, Chemical Communications 61 (2025) 16993–16996. date_created: 2025-12-09T14:22:09Z date_published: 2025-10-06T00:00:00Z date_updated: 2026-03-16T08:31:23Z day: '06' ddc: - '540' doi: 10.1039/d5cc03194j extern: '1' has_accepted_license: '1' intvolume: ' 61' issue: '87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/D5CC03194J month: '10' oa: 1 oa_version: Published Version page: 16993-16996 publication: Chemical Communications publication_identifier: eissn: - 1364-548X issn: - 1359-7345 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Efficient optimization and synthesis of diverse azaarenes via nitrogen atom insertion under continuous flow conditions 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: 61 year: '2025' ... --- OA_type: closed access _id: '20767' abstract: - lang: eng text: Chemistry education at the graduate level and beyond faces the formidable challenge of a boundless and constantly expanding frontier of knowledge on many fronts. While modern learners have an increasingly broad range of resources available at their disposal (including open access text-based references, online videos, training problems, and other digital learning materials), there are comparatively fewer such materials aimed at the highest levels of study. With the goal of producing widely accessible graduate-level learning content, we created a community-based approach to online course design that is easily digestible to meet the expectations of modern learners. Herein, we report the development of an open access Advanced Organic Chemistry video-based online course and several other specialized minicourses using the Synthesis Workshop YouTube channel. article_processing_charge: No article_type: original author: - first_name: Matthew A. full_name: Horwitz, Matthew A. last_name: Horwitz - first_name: Reem full_name: Al-Ahmad, Reem last_name: Al-Ahmad - first_name: Xingfeng full_name: Bai, Xingfeng last_name: Bai - first_name: Matteo full_name: Balletti, Matteo last_name: Balletti - first_name: Peter full_name: Bellotti, Peter last_name: Bellotti - first_name: Yael full_name: Ben-Tal, Yael last_name: Ben-Tal - first_name: Mark W. full_name: Campbell, Mark W. last_name: Campbell - first_name: Kathleen full_name: Cheasty, Kathleen last_name: Cheasty - first_name: Steven W. M. full_name: Crossley, Steven W. M. last_name: Crossley - first_name: Craig S. full_name: Day, Craig S. last_name: Day - first_name: Patrick J. full_name: Deneny, Patrick J. last_name: Deneny - first_name: Katherine C. full_name: Forbes, Katherine C. last_name: Forbes - first_name: Emma S. full_name: Gogarnoiu, Emma S. last_name: Gogarnoiu - first_name: Phillip S. full_name: Grant, Phillip S. last_name: Grant - first_name: Riya full_name: Halder, Riya last_name: Halder - first_name: Georgia R. full_name: Harris, Georgia R. last_name: Harris - first_name: Pol full_name: Hernández-Lladó, Pol last_name: Hernández-Lladó - first_name: Morgan full_name: Jouanneau, Morgan last_name: Jouanneau - first_name: Vera full_name: Jost, Vera last_name: Jost - first_name: Dennis A. full_name: Kutateladze, Dennis A. last_name: Kutateladze - first_name: Gabriele full_name: Laudadio, Gabriele last_name: Laudadio - first_name: Chun full_name: Liu, Chun last_name: Liu - first_name: Aidan P. full_name: Looby, Aidan P. last_name: Looby - first_name: Aitor full_name: Maestro, Aitor last_name: Maestro - first_name: Terry full_name: McCallum, Terry last_name: McCallum - first_name: Maximilian D. full_name: Palkowitz, Maximilian D. last_name: Palkowitz - first_name: Joshua M. full_name: Paolillo, Joshua M. last_name: Paolillo - first_name: Matthew W. D. full_name: Perry, Matthew W. D. last_name: Perry - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Cesar full_name: Reyes, Cesar last_name: Reyes - first_name: Hayden A. full_name: Sharma, Hayden A. last_name: Sharma - first_name: Fu Kit full_name: Sheong, Fu Kit last_name: Sheong - first_name: Benjamin full_name: Thoma, Benjamin last_name: Thoma - first_name: Andrew V. full_name: Tran, Andrew V. last_name: Tran - first_name: Duc N. full_name: Tran, Duc N. last_name: Tran - first_name: Francisco José full_name: Aguilar Troyano, Francisco José last_name: Aguilar Troyano - first_name: Thomas full_name: Verheyen, Thomas last_name: Verheyen - first_name: Mark P. full_name: Walsh, Mark P. last_name: Walsh - first_name: Alicia full_name: Wagner, Alicia last_name: Wagner - first_name: Emily R. full_name: Wearing, Emily R. last_name: Wearing - first_name: Georg full_name: Wuitschik, Georg last_name: Wuitschik citation: ama: 'Horwitz MA, Al-Ahmad R, Bai X, et al. Reimagining advanced chemistry education: A community-based approach to course design for modern learners. Journal of Chemical Education. 2025;102(9):3777-3783. doi:10.1021/acs.jchemed.5c00555' apa: 'Horwitz, M. A., Al-Ahmad, R., Bai, X., Balletti, M., Bellotti, P., Ben-Tal, Y., … Wuitschik, G. (2025). Reimagining advanced chemistry education: A community-based approach to course design for modern learners. Journal of Chemical Education. American Chemical Society. https://doi.org/10.1021/acs.jchemed.5c00555' chicago: 'Horwitz, Matthew A., Reem Al-Ahmad, Xingfeng Bai, Matteo Balletti, Peter Bellotti, Yael Ben-Tal, Mark W. Campbell, et al. “Reimagining Advanced Chemistry Education: A Community-Based Approach to Course Design for Modern Learners.” Journal of Chemical Education. American Chemical Society, 2025. https://doi.org/10.1021/acs.jchemed.5c00555.' ieee: 'M. A. Horwitz et al., “Reimagining advanced chemistry education: A community-based approach to course design for modern learners,” Journal of Chemical Education, vol. 102, no. 9. American Chemical Society, pp. 3777–3783, 2025.' ista: 'Horwitz MA, Al-Ahmad R, Bai X, Balletti M, Bellotti P, Ben-Tal Y, Campbell MW, Cheasty K, Crossley SWM, Day CS, Deneny PJ, Forbes KC, Gogarnoiu ES, Grant PS, Halder R, Harris GR, Hernández-Lladó P, Jouanneau M, Jost V, Kutateladze DA, Laudadio G, Liu C, Looby AP, Maestro A, McCallum T, Palkowitz MD, Paolillo JM, Perry MWD, Reisenbauer J, Reyes C, Sharma HA, Sheong FK, Thoma B, Tran AV, Tran DN, Aguilar Troyano FJ, Verheyen T, Walsh MP, Wagner A, Wearing ER, Wuitschik G. 2025. Reimagining advanced chemistry education: A community-based approach to course design for modern learners. Journal of Chemical Education. 102(9), 3777–3783.' mla: 'Horwitz, Matthew A., et al. “Reimagining Advanced Chemistry Education: A Community-Based Approach to Course Design for Modern Learners.” Journal of Chemical Education, vol. 102, no. 9, American Chemical Society, 2025, pp. 3777–83, doi:10.1021/acs.jchemed.5c00555.' short: M.A. Horwitz, R. Al-Ahmad, X. Bai, M. Balletti, P. Bellotti, Y. Ben-Tal, M.W. Campbell, K. Cheasty, S.W.M. Crossley, C.S. Day, P.J. Deneny, K.C. Forbes, E.S. Gogarnoiu, P.S. Grant, R. Halder, G.R. Harris, P. Hernández-Lladó, M. Jouanneau, V. Jost, D.A. Kutateladze, G. Laudadio, C. Liu, A.P. Looby, A. Maestro, T. McCallum, M.D. Palkowitz, J.M. Paolillo, M.W.D. Perry, J. Reisenbauer, C. Reyes, H.A. Sharma, F.K. Sheong, B. Thoma, A.V. Tran, D.N. Tran, F.J. Aguilar Troyano, T. Verheyen, M.P. Walsh, A. Wagner, E.R. Wearing, G. Wuitschik, Journal of Chemical Education 102 (2025) 3777–3783. date_created: 2025-12-09T14:27:11Z date_published: 2025-08-15T00:00:00Z date_updated: 2025-12-16T12:13:49Z day: '15' doi: 10.1021/acs.jchemed.5c00555 extern: '1' intvolume: ' 102' issue: '9' language: - iso: eng month: '08' oa_version: None page: 3777-3783 publication: Journal of Chemical Education publication_identifier: eissn: - 1938-1328 issn: - 0021-9584 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Reimagining advanced chemistry education: A community-based approach to course design for modern learners' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 102 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 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 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 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 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' ... --- OA_place: publisher OA_type: gold _id: '20817' abstract: - lang: eng text: We present Mechanistic PDE Networks -- a model for discovery of governing partial differential equations from data. Mechanistic PDE Networks represent spatiotemporal data as space-time dependent linear partial differential equations in neural network hidden representations. The represented PDEs are then solved and decoded for specific tasks. The learned PDE representations naturally express the spatiotemporal dynamics in data in neural network hidden space, enabling increased modeling power. Solving the PDE representations in a compute and memory-efficient way, however, is a significant challenge. We develop a native, GPU-capable, parallel, sparse and differentiable multigrid solver specialized for linear partial differential equations that acts as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose a discovery architecture that can discovers nonlinear PDEs in complex settings, while being robust to noise. We validate PDE discovery on a number of PDEs including reaction-diffusion and Navier-Stokes equations. acknowledgement: "AP. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.\r\nFL. This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/COE12. For open access purposes, the author has applied a CC BY public\r\ncopyright license to any author accepted manuscript version arising from this submission." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Adeel A full_name: Pervez, Adeel A id: fca6d90c-d47f-11ee-bc87-93ff51604981 last_name: Pervez - first_name: Efstratios full_name: Gavves, Efstratios last_name: Gavves - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Pervez AA, Gavves E, Locatello F. Mechanistic PDE networks for discovery of governing equations. In: 42nd International Conference on Machine Learning. Vol 267. ML Research Press; 2025:48962-48973.' apa: 'Pervez, A. A., Gavves, E., & Locatello, F. (2025). Mechanistic PDE networks for discovery of governing equations. In 42nd International Conference on Machine Learning (Vol. 267, pp. 48962–48973). Vancouver, Canada: ML Research Press.' chicago: Pervez, Adeel A, Efstratios Gavves, and Francesco Locatello. “Mechanistic PDE Networks for Discovery of Governing Equations.” In 42nd International Conference on Machine Learning, 267:48962–73. ML Research Press, 2025. ieee: A. A. Pervez, E. Gavves, and F. Locatello, “Mechanistic PDE networks for discovery of governing equations,” in 42nd International Conference on Machine Learning, Vancouver, Canada, 2025, vol. 267, pp. 48962–48973. ista: 'Pervez AA, Gavves E, Locatello F. 2025. Mechanistic PDE networks for discovery of governing equations. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 48962–48973.' mla: Pervez, Adeel A., et al. “Mechanistic PDE Networks for Discovery of Governing Equations.” 42nd International Conference on Machine Learning, vol. 267, ML Research Press, 2025, pp. 48962–73. short: A.A. Pervez, E. Gavves, F. Locatello, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 48962–48973. conference: end_date: 2025-07-19 location: Vancouver, Canada name: 'ICML: International Conference on Machine Learning' start_date: 2025-07-13 corr_author: '1' date_created: 2025-12-14T23:02:04Z date_published: 2025-05-01T00:00:00Z date_updated: 2025-12-16T12:24:55Z day: '01' ddc: - '000' department: - _id: FrLo ec_funded: 1 external_id: arxiv: - '2502.18377' file: - access_level: open_access checksum: 933cb673fb41416f537278fb990df6c3 content_type: application/pdf creator: dernst date_created: 2025-12-16T12:21:49Z date_updated: 2025-12-16T12:21:49Z file_id: '20827' file_name: 2025_ICML_Pervez.pdf file_size: 993381 relation: main_file success: 1 file_date_updated: 2025-12-16T12:21:49Z has_accepted_license: '1' intvolume: ' 267' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 48962-48973 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: 42nd International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ alpz/mech-nn-discovery-pde scopus_import: '1' status: public title: Mechanistic PDE networks for discovery of governing equations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 267 year: '2025' ... --- OA_place: publisher OA_type: gold _id: '20819' abstract: - lang: eng text: "Clustering is a cornerstone of data analysis that is particularly suited to identifying coherent subgroups or substructures in unlabeled data, as are generated continuously in large amounts these days. However, in many cases traditional clustering methods are not applicable, because data are increasingly being produced and stored in a distributed way, e.g. on edge devices, and privacy concerns prevent it from being transferred to a central server. To address this challenge, we present FedDP-KMeans, a new algorithm for \r\n-means clustering that is fully-federated as well as differentially private. Our approach leverages (potentially small and out-of-distribution) server-side data to overcome the primary challenge of differentially private clustering methods: the need for a good initialization. Combining our initialization with a simple federated DP-Lloyds algorithm we obtain an algorithm that achieves excellent results on synthetic and real-world benchmark tasks. We also provide a theoretical analysis of our method that provides bounds on the convergence speed and cluster identification success." acknowledged_ssus: - _id: ScienComp acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF) [10.55776/COE12] and supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).\r\n" alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: David full_name: Saulpic, David id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964 last_name: Saulpic citation: ama: 'Scott JA, Lampert C, Saulpic D. Differentially private federated k-means clustering with server-side data. In: 42nd International Conference on Machine Learning. Vol 267. ML Research Press; 2025:53757-53790.' apa: 'Scott, J. A., Lampert, C., & Saulpic, D. (2025). Differentially private federated k-means clustering with server-side data. In 42nd International Conference on Machine Learning (Vol. 267, pp. 53757–53790). Vancouver, Canada: ML Research Press.' chicago: Scott, Jonathan A, Christoph Lampert, and David Saulpic. “Differentially Private Federated K-Means Clustering with Server-Side Data.” In 42nd International Conference on Machine Learning, 267:53757–90. ML Research Press, 2025. ieee: J. A. Scott, C. Lampert, and D. Saulpic, “Differentially private federated k-means clustering with server-side data,” in 42nd International Conference on Machine Learning, Vancouver, Canada, 2025, vol. 267, pp. 53757–53790. ista: 'Scott JA, Lampert C, Saulpic D. 2025. Differentially private federated k-means clustering with server-side data. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 53757–53790.' mla: Scott, Jonathan A., et al. “Differentially Private Federated K-Means Clustering with Server-Side Data.” 42nd International Conference on Machine Learning, vol. 267, ML Research Press, 2025, pp. 53757–90. short: J.A. Scott, C. Lampert, D. Saulpic, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 53757–53790. conference: end_date: 2025-07-19 location: Vancouver, Canada name: 'ICML: International Conference on Machine Learning' start_date: 2025-07-13 corr_author: '1' date_created: 2025-12-14T23:02:05Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-04-07T11:46:11Z day: '01' ddc: - '000' department: - _id: ChLa - _id: MoHe external_id: arxiv: - '2506.05408' file: - access_level: open_access checksum: 815b32b463023ca21e569c2158745c15 content_type: application/pdf creator: dernst date_created: 2025-12-16T12:38:29Z date_updated: 2025-12-16T12:38:29Z file_id: '20829' file_name: 2025_ICML_Scott.pdf file_size: 746612 relation: main_file success: 1 file_date_updated: 2025-12-16T12:38:29Z has_accepted_license: '1' intvolume: ' 267' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 53757-53790 publication: 42nd International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '21198' relation: dissertation_contains status: public scopus_import: '1' status: public title: Differentially private federated k-means clustering with server-side data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 267 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '10045' abstract: - lang: eng text: "Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n" acknowledgement: We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2025;209:279-322. doi:10.1007/s10107-024-02064-5 apa: Dvorak, M., & Kolmogorov, V. (2025). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5 chicago: Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2025. https://doi.org/10.1007/s10107-024-02064-5. ieee: M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming, vol. 209. Springer Nature, pp. 279–322, 2025. ista: Dvorak M, Kolmogorov V. 2025. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 209, 279–322. mla: Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, vol. 209, Springer Nature, 2025, pp. 279–322, doi:10.1007/s10107-024-02064-5. short: M. Dvorak, V. Kolmogorov, Mathematical Programming 209 (2025) 279–322. corr_author: '1' date_created: 2021-09-27T10:48:23Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-05-19T13:52:10Z day: '01' ddc: - '004' department: - _id: GradSch - _id: VlKo doi: 10.1007/s10107-024-02064-5 external_id: arxiv: - '2109.10203' isi: - '001176563300001' file: - access_level: open_access checksum: 25d9bd490719b45eca84f4d93a06c69f content_type: application/pdf creator: dernst date_created: 2025-04-16T09:36:08Z date_updated: 2025-04-16T09:36:08Z file_id: '19578' file_name: 2025_MathProgramming_Dvorak.pdf file_size: 839510 relation: main_file success: 1 file_date_updated: 2025-04-16T09:36:08Z has_accepted_license: '1' intvolume: ' 209' isi: 1 keyword: - minimum 0-extension problem - metric labeling problem - discrete metric spaces - metric extensions - computational complexity - valued constraint satisfaction problems - discrete convex analysis - L-convex functions language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 279-322 publication: Mathematical Programming publication_identifier: eissn: - 1436-4646 issn: - 0025-5610 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Generalized minimum 0-extension problem and discrete convexity 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: 209 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 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' ...