[{"publication":"ACS Nano","issue":"11","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"doi":"10.1021/acsnano.4c18078","year":"2025","date_created":"2025-03-23T23:01:26Z","main_file_link":[{"url":"https://hal.science/hal-04682818v2","open_access":"1"}],"quality_controlled":"1","pmid":1,"OA_place":"repository","volume":19,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Carrasco, Celso","first_name":"Celso","last_name":"Carrasco"},{"first_name":"Quentin","last_name":"Martinet","full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"last_name":"Shen","first_name":"Zaiyi","full_name":"Shen, Zaiyi"},{"last_name":"Lintuvuori","first_name":"Juho","full_name":"Lintuvuori, Juho"},{"first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"}],"title":"Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers","abstract":[{"text":"Catalytic microswimmers convert the chemical energy from fuel into motion. They sustain chemical gradients and fluid flows that propel them by phoresis. This leads to unconventional behavior and collective dynamics, such as self-organization into complex structures. Characterizing the nonequilibrium interactions of microswimmers is crucial for advancing our understanding of active systems. However, this remains a challenge owing to the importance of fluctuations at the microscale and the difficulty in disentangling the different contributions to the interactions. Here, we show a massive dependence of the nonequilibrium interactions on the shape of catalytic microswimmers. We perform tracking experiments at high throughput to map interactions between nanocolloidal tracers and dimeric microswimmers of various aspect ratios. Our method leverages dual tracers with differing phoretic mobilities to quantitatively disentangle phoretic motion from hydrodynamic advection. This approach is validated through experiments on single chemically active sites and on immobilized catalytic microswimmers. We further investigate the activity-driven interactions of free microswimmers and directly measure their phoretic interactions. When compared to standard models, our findings highlight the important role of osmotic flows for microswimmers near surfaces and reveal an enhanced contribution of hydrodynamic advection relative to phoretic motion as the size of the microswimmer increases. Our study provides robust measurements of the nonequilibrium interactions from catalytic microswimmers and lays the groundwork for a realistic description of active systems.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001443359300001"],"pmid":["40069094"]},"page":"11133-11145","article_processing_charge":"No","day":"11","status":"public","OA_type":"green","project":[{"name":"Emergent Behavior in Spinning Active Matter","_id":"eb99c9bb-77a9-11ec-83b8-9f8cffa20a35","grant_number":"P35206"}],"citation":{"ama":"Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. 2025;19(11):11133-11145. doi:<a href=\"https://doi.org/10.1021/acsnano.4c18078\">10.1021/acsnano.4c18078</a>","ista":"Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. 2025. Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. ACS Nano. 19(11), 11133–11145.","short":"C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J.A. Palacci, A. Aubret, ACS Nano 19 (2025) 11133–11145.","ieee":"C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J. A. Palacci, and A. Aubret, “Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers,” <i>ACS Nano</i>, vol. 19, no. 11. American Chemical Society, pp. 11133–11145, 2025.","mla":"Carrasco, Celso, et al. “Characterization of Nonequilibrium Interactions of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>, vol. 19, no. 11, American Chemical Society, 2025, pp. 11133–45, doi:<a href=\"https://doi.org/10.1021/acsnano.4c18078\">10.1021/acsnano.4c18078</a>.","chicago":"Carrasco, Celso, Quentin Martinet, Zaiyi Shen, Juho Lintuvuori, Jérémie A Palacci, and Antoine Aubret. “Characterization of Nonequilibrium Interactions of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acsnano.4c18078\">https://doi.org/10.1021/acsnano.4c18078</a>.","apa":"Carrasco, C., Martinet, Q., Shen, Z., Lintuvuori, J., Palacci, J. A., &#38; Aubret, A. (2025). Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c18078\">https://doi.org/10.1021/acsnano.4c18078</a>"},"_id":"19441","scopus_import":"1","type":"journal_article","acknowledgement":"The authors thank M. Perrin and A. Allard for enlightening discussions. This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/P35206]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No. 886024.","article_type":"original","oa_version":"Submitted Version","intvolume":"        19","publisher":"American Chemical Society","department":[{"_id":"JePa"}],"date_updated":"2025-10-16T10:26:59Z","month":"03","language":[{"iso":"eng"}],"date_published":"2025-03-11T00:00:00Z","oa":1,"isi":1},{"title":"Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?","publication_status":"published","external_id":{"isi":["001443422900001"]},"abstract":[{"lang":"eng","text":"1. Climate change is expected to induce shifts in the composition, structure and functioning of Arctic tundra ecosystems. Increases in the frequency and severity of tundra fires have the potential to catalyse vegetation transitions with far-reaching local, regional and global consequences.\r\n2. We propose that post-fire tundra recovery, coupled with climate change, may not necessarily lead to pre-fire conditions. Our hypothesis, based on surveys and literature, suggests two climate–fire driven trajectories. One trajectory results in increased woody vegetation under low fire frequency; the other results in grass dominance under high frequency.\r\n3. Future research should address uncertainties regarding possible tundra ecosystem shifts linked to fires, using methods that encompass greater temporal and spatial scales than previously addressed. More case studies, especially in underrepresented regions and ecosystem types, are essential to broaden the empirical basis for forecasts and potential fire management strategies.\r\n4. Synthesis. Our review synthesises current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems, highlighting potential transitions and alternative ecosystem states and their implications. We discuss challenges in defining and predicting these trajectories as well as future directions."}],"article_processing_charge":"Yes (via OA deal)","page":"1042-1056","OA_place":"publisher","volume":113,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Heim, Ramona Julia","first_name":"Ramona Julia","last_name":"Heim"},{"first_name":"Adrian V.","last_name":"Rocha","full_name":"Rocha, Adrian V."},{"last_name":"Zemlianskii","first_name":"Vitalii","full_name":"Zemlianskii, Vitalii"},{"full_name":"Barrett, Kirsten","first_name":"Kirsten","last_name":"Barrett"},{"first_name":"Helga","last_name":"Bültmann","full_name":"Bültmann, Helga"},{"full_name":"Breen, Amy","last_name":"Breen","first_name":"Amy"},{"full_name":"Frost, Gerald Verner","last_name":"Frost","first_name":"Gerald Verner"},{"last_name":"Hollingsworth","first_name":"Teresa Nettleton","full_name":"Hollingsworth, Teresa Nettleton"},{"first_name":"Randi","last_name":"Jandt","full_name":"Jandt, Randi"},{"first_name":"Maria","last_name":"Kozlova","full_name":"Kozlova, Maria"},{"first_name":"Anastasiya","last_name":"Kurka","full_name":"Kurka, Anastasiya"},{"full_name":"Jorgenson, Mark Torre","last_name":"Jorgenson","first_name":"Mark Torre"},{"full_name":"Landhäusser, Simon M.","first_name":"Simon M.","last_name":"Landhäusser"},{"full_name":"Loranty, Michael Mark","last_name":"Loranty","first_name":"Michael Mark"},{"full_name":"Miller, Eric A.","first_name":"Eric A.","last_name":"Miller"},{"first_name":"Kenji","last_name":"Narita","full_name":"Narita, Kenji"},{"full_name":"Pravdolyubova, Evgeniya","id":"0b30719b-13f0-11ed-ab2a-94498bc6a278","first_name":"Evgeniya","last_name":"Pravdolyubova"},{"last_name":"Hölzel","first_name":"Norbert","full_name":"Hölzel, Norbert"},{"first_name":"Gabriela","last_name":"Schaepman-Strub","full_name":"Schaepman-Strub, Gabriela"}],"ddc":["550","570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"file_id":"20890","relation":"main_file","checksum":"e2785ae265e211b4dc7fc9c5b7744948","access_level":"open_access","date_updated":"2025-12-30T08:08:18Z","file_size":2662766,"date_created":"2025-12-30T08:08:18Z","content_type":"application/pdf","file_name":"2025_JournEcology_Heim.pdf","creator":"dernst","success":1}],"publication":"Journal of Ecology","doi":"10.1111/1365-2745.70022","publication_identifier":{"eissn":["1365-2745"],"issn":["0022-0477"]},"issue":"5","date_created":"2025-03-23T23:01:27Z","year":"2025","date_updated":"2025-12-30T08:09:47Z","department":[{"_id":"NiBa"}],"publisher":"Wiley","date_published":"2025-05-01T00:00:00Z","language":[{"iso":"eng"}],"month":"05","file_date_updated":"2025-12-30T08:08:18Z","oa":1,"isi":1,"scopus_import":"1","_id":"19442","acknowledgement":"We would like to express our sincere gratitude to all the data providers who carried out fieldwork in different regions of the Arctic and published their data, which we used for our meta-analysis. We recognise the hard work and dedication of these individuals, without whom this paper would not have been possible. We are grateful to the editor and the anonymous reviewer for their time and valuable feedback on this manuscript. We particularly appreciate the detailed and constructive comments provided by reviewer Mara Baudena, which significantly strengthened our work. We also acknowledge the Indigenous peoples and rural communities of the Arctic, whose traditional knowledge, rights, and interests are integral to the stewardship and study of these ecosystems. This work was funded in part by the U.S. National Aeronautics and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled and organized by Projekt DEAL.","type":"journal_article","oa_version":"Published Version","intvolume":"       113","article_type":"review","citation":{"ama":"Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. 2025;113(5):1042-1056. doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>","ista":"Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV, Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? Journal of Ecology. 113(5), 1042–1056.","ieee":"R. J. Heim <i>et al.</i>, “Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?,” <i>Journal of Ecology</i>, vol. 113, no. 5. Wiley, pp. 1042–1056, 2025.","short":"R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen, G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson, S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel, G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.","mla":"Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>, vol. 113, no. 5, Wiley, 2025, pp. 1042–56, doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>.","chicago":"Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett, Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>.","apa":"Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen, A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>"},"PlanS_conform":"1","day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid"},{"date_created":"2025-03-23T23:01:27Z","year":"2025","doi":"10.1016/j.str.2025.01.020","publication_identifier":{"eissn":["1878-4186"],"issn":["0969-2126"]},"issue":"4","publication":"Structure","corr_author":"1","file":[{"date_updated":"2025-08-05T12:15:13Z","file_size":4367530,"access_level":"open_access","checksum":"f346bc357a66a88cca3d0eb95793fb73","relation":"main_file","file_id":"20130","success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2025_Structure_Harar.pdf","date_created":"2025-08-05T12:15:13Z"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["570"],"author":[{"last_name":"Harar","first_name":"Pavol","full_name":"Harar, Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","orcid":"0000-0001-5206-1794"},{"first_name":"Lukas","last_name":"Herrmann","full_name":"Herrmann, Lukas"},{"last_name":"Grohs","first_name":"Philipp","full_name":"Grohs, Philipp"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":33,"OA_place":"publisher","pmid":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/paloha/faket/"}]},"article_processing_charge":"Yes (in subscription journal)","page":"820-827.e4","publication_status":"published","external_id":{"pmid":["39947174"],"isi":["001463196100001"]},"abstract":[{"text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.","lang":"eng"}],"title":"FakET: Simulating cryo-electron tomograms with neural style transfer","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","status":"public","day":"03","citation":{"ista":"Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4.","ama":"Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. 2025;33(4):820-827.e4. doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>","ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Elsevier, p. 820–827.e4, 2025.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4, doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>.","chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>.","apa":"Harar, P., Herrmann, L., Grohs, P., &#38; Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>"},"PlanS_conform":"1","oa_version":"Published Version","intvolume":"        33","article_type":"original","type":"journal_article","acknowledgement":"The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions.","scopus_import":"1","_id":"19443","isi":1,"file_date_updated":"2025-08-05T12:15:13Z","oa":1,"date_published":"2025-04-03T00:00:00Z","month":"04","language":[{"iso":"eng"}],"date_updated":"2025-09-30T11:13:02Z","department":[{"_id":"AlMi"}],"publisher":"Elsevier"},{"quality_controlled":"1","year":"2025","date_created":"2025-03-23T23:01:27Z","issue":"8054","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"doi":"10.1038/s41586-024-08487-6","publication":"Nature","page":"315-320","article_processing_charge":"No","abstract":[{"lang":"eng","text":"As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards."}],"publication_status":"published","external_id":{"pmid":["39653126"],"isi":["001437461900001"]},"title":"A framework for neural organoids, assembloids and transplantation studies","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Pașca","first_name":"Sergiu P.","full_name":"Pașca, Sergiu P."},{"full_name":"Arlotta, Paola","first_name":"Paola","last_name":"Arlotta"},{"first_name":"Helen S.","last_name":"Bateup","full_name":"Bateup, Helen S."},{"last_name":"Camp","first_name":"J. Gray","full_name":"Camp, J. Gray"},{"full_name":"Cappello, Silvia","first_name":"Silvia","last_name":"Cappello"},{"full_name":"Gage, Fred H.","last_name":"Gage","first_name":"Fred H."},{"first_name":"Jürgen A.","last_name":"Knoblich","full_name":"Knoblich, Jürgen A."},{"full_name":"Kriegstein, Arnold R.","last_name":"Kriegstein","first_name":"Arnold R."},{"last_name":"Lancaster","first_name":"Madeline A.","full_name":"Lancaster, Madeline A."},{"full_name":"Ming, Guo Li","first_name":"Guo Li","last_name":"Ming"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"},{"first_name":"Hideyuki","last_name":"Okano","full_name":"Okano, Hideyuki"},{"first_name":"Malin","last_name":"Parmar","full_name":"Parmar, Malin"},{"last_name":"Park","first_name":"In Hyun","full_name":"Park, In Hyun"},{"full_name":"Reiner, Orly","first_name":"Orly","last_name":"Reiner"},{"full_name":"Song, Hongjun","last_name":"Song","first_name":"Hongjun"},{"full_name":"Studer, Lorenz","last_name":"Studer","first_name":"Lorenz"},{"first_name":"Jun","last_name":"Takahashi","full_name":"Takahashi, Jun"},{"full_name":"Temple, Sally","last_name":"Temple","first_name":"Sally"},{"full_name":"Testa, Giuseppe","last_name":"Testa","first_name":"Giuseppe"},{"last_name":"Treutlein","first_name":"Barbara","full_name":"Treutlein, Barbara"},{"full_name":"Vaccarino, Flora M.","last_name":"Vaccarino","first_name":"Flora M."},{"last_name":"Vanderhaeghen","first_name":"Pierre","full_name":"Vanderhaeghen, Pierre"},{"last_name":"Young-Pearse","first_name":"Tracy","full_name":"Young-Pearse, Tracy"}],"volume":639,"pmid":1,"citation":{"ama":"Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. 2025;639(8054):315-320. doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>","ista":"Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH, Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids and transplantation studies. Nature. 639(8054), 315–320.","ieee":"S. P. Pașca <i>et al.</i>, “A framework for neural organoids, assembloids and transplantation studies,” <i>Nature</i>, vol. 639, no. 8054. Springer Nature, pp. 315–320, 2025.","short":"S.P. Pașca, P. Arlotta, H.S. Bateup, J.G. Camp, S. Cappello, F.H. Gage, J.A. Knoblich, A.R. Kriegstein, M.A. Lancaster, G.L. Ming, G. Novarino, H. Okano, M. Parmar, I.H. Park, O. Reiner, H. Song, L. Studer, J. Takahashi, S. Temple, G. Testa, B. Treutlein, F.M. Vaccarino, P. Vanderhaeghen, T. Young-Pearse, Nature 639 (2025) 315–320.","mla":"Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>, vol. 639, no. 8054, Springer Nature, 2025, pp. 315–20, doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>.","chicago":"Pașca, Sergiu P., Paola Arlotta, Helen S. Bateup, J. Gray Camp, Silvia Cappello, Fred H. Gage, Jürgen A. Knoblich, et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>.","apa":"Pașca, S. P., Arlotta, P., Bateup, H. S., Camp, J. G., Cappello, S., Gage, F. H., … Young-Pearse, T. (2025). A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>"},"OA_type":"closed access","status":"public","day":"13","isi":1,"language":[{"iso":"eng"}],"month":"03","date_published":"2025-03-13T00:00:00Z","department":[{"_id":"GaNo"}],"publisher":"Springer Nature","date_updated":"2025-09-30T11:13:47Z","article_type":"original","oa_version":"None","intvolume":"       639","type":"journal_article","acknowledgement":"The authors thank members of their laboratories who provided feedback on earlier versions of this manuscript, including A. Jourdon, V. Mariano, T. L. Li, N. Caporale, E. Villa and M. Sutcliffe.","_id":"19444","scopus_import":"1"},{"article_processing_charge":"No","page":"244-265","external_id":{"isi":["001537885900016"],"arxiv":["2411.12582"]},"publication_status":"published","abstract":[{"lang":"eng","text":"In reconfiguration, we are given two solutions to a graph problem, such as Vertex Cover or Dominating Set, with each solution represented by a placement of tokens on vertices of the graph. Our task is to reconfigure one into the other using small steps while ensuring the intermediate configurations of tokens are also valid solutions. The two commonly studied settings are Token Jumping and Token Sliding, which allows moving a single token to an arbitrary or an adjacent vertex, respectively.\r\n\r\nWe introduce new rules that generalize Token Jumping, parameterized by the number of tokens allowed to move at once and by the maximum distance of each move. Our main contribution is identifying minimal rules that allow reconfiguring any possible given solution into any other for Independent Set, Vertex Cover, and Dominating Set. For each minimal rule, we also provide an efficient algorithm that finds a corresponding reconfiguration sequence.\r\n\r\nWe further focus on the rule that allows each token to move to an adjacent vertex in a single step. This natural variant turns out to be the minimal rule that guarantees reconfigurability for Vertex Cover. We determine the computational complexity of deciding whether a (shortest) reconfiguration sequence exists under this rule for the three studied problems. While reachability for Vertex Cover is shown to be in P, finding a shortest sequence is shown to be NP-complete. For Independent Set and Dominating Set, even reachability is shown to be PSPACE-complete."}],"title":"Reconfiguration using generalized token jumping","author":[{"full_name":"Křišťan, Jan Matyáš","first_name":"Jan Matyáš","last_name":"Křišťan"},{"full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":15411,"OA_place":"repository","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2411.12582","open_access":"1"}],"conference":{"start_date":"2025-02-28","name":"WALCOM: International Conference and Workshops on Algorithms and Computation","end_date":"2025-03-02","location":"Chengdu, China"},"date_created":"2025-03-23T23:01:27Z","year":"2025","publication_identifier":{"eissn":["1611-3349"],"isbn":["9789819628445"],"issn":["0302-9743"]},"doi":"10.1007/978-981-96-2845-2_16","publication":"19th International Conference and Workshops on Algorithms and Computation","isi":1,"oa":1,"date_published":"2025-02-20T00:00:00Z","language":[{"iso":"eng"}],"month":"02","date_updated":"2025-09-30T11:14:33Z","arxiv":1,"publisher":"Springer Nature","department":[{"_id":"KrCh"}],"oa_version":"Preprint","intvolume":"     15411","acknowledgement":"J. M. Křišťan acknowledges the support of the Czech Science Foundation Grant No. 24-12046S. This work was supported by the Grant Agency of the Czech Technical University in Prague, grant No. SGS23/205/OHK3/3T/18. J. Svoboda acknowledges the support of the ERC CoG 863818 (ForM-SMArt) grant.","type":"conference","scopus_import":"1","_id":"19445","citation":{"apa":"Křišťan, J. M., &#38; Svoboda, J. (2025). Reconfiguration using generalized token jumping. In <i>19th International Conference and Workshops on Algorithms and Computation</i> (Vol. 15411, pp. 244–265). Chengdu, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">https://doi.org/10.1007/978-981-96-2845-2_16</a>","chicago":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized Token Jumping.” In <i>19th International Conference and Workshops on Algorithms and Computation</i>, 15411:244–65. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">https://doi.org/10.1007/978-981-96-2845-2_16</a>.","mla":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized Token Jumping.” <i>19th International Conference and Workshops on Algorithms and Computation</i>, vol. 15411, Springer Nature, 2025, pp. 244–65, doi:<a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">10.1007/978-981-96-2845-2_16</a>.","short":"J.M. Křišťan, J. Svoboda, in:, 19th International Conference and Workshops on Algorithms and Computation, Springer Nature, 2025, pp. 244–265.","ieee":"J. M. Křišťan and J. Svoboda, “Reconfiguration using generalized token jumping,” in <i>19th International Conference and Workshops on Algorithms and Computation</i>, Chengdu, China, 2025, vol. 15411, pp. 244–265.","ista":"Křišťan JM, Svoboda J. 2025. Reconfiguration using generalized token jumping. 19th International Conference and Workshops on Algorithms and Computation. WALCOM: International Conference and Workshops on Algorithms and Computation, LNCS, vol. 15411, 244–265.","ama":"Křišťan JM, Svoboda J. Reconfiguration using generalized token jumping. In: <i>19th International Conference and Workshops on Algorithms and Computation</i>. Vol 15411. Springer Nature; 2025:244-265. doi:<a href=\"https://doi.org/10.1007/978-981-96-2845-2_16\">10.1007/978-981-96-2845-2_16</a>"},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"ec_funded":1,"OA_type":"green","alternative_title":["LNCS"],"status":"public","day":"20"},{"_id":"19453","scopus_import":"1","type":"journal_article","acknowledgement":"We would like to thank Rebecca Morse for performing the recordings in one of the animals under the supervision of H.S.C.C., Jago Wallenschus for the technical support, especially with maze design, Wiktor Mlynarski for the advice and discussions and Andrea Cumpelik for suggestions during the writing. M.N. was supported by the Howard Hughes Medical Institute. H.S.C.C. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665385.","article_type":"original","intvolume":"       122","oa_version":"Published Version","department":[{"_id":"GaTk"},{"_id":"JoCs"}],"publisher":"National Academy of Sciences","date_updated":"2026-05-06T13:12:01Z","month":"03","language":[{"iso":"eng"}],"date_published":"2025-03-10T00:00:00Z","oa":1,"file_date_updated":"2025-03-25T07:49:04Z","isi":1,"day":"10","status":"public","OA_type":"hybrid","ec_funded":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"citation":{"ista":"Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. 2025. Learning reshapes the hippocampal representation hierarchy. Proceedings of the National Academy of Sciences. 122(11), e2417025122.","ama":"Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(11). doi:<a href=\"https://doi.org/10.1073/pnas.2417025122\">10.1073/pnas.2417025122</a>","short":"H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the National Academy of Sciences 122 (2025).","ieee":"H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes the hippocampal representation hierarchy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 11. National Academy of Sciences, 2025.","mla":"Chiossi, Heloisa S. C., et al. “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 11, e2417025122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2417025122\">10.1073/pnas.2417025122</a>.","chicago":"Chiossi, Heloisa S. C., Michele Nardin, Gašper Tkačik, and Jozsef L Csicsvari. “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2417025122\">https://doi.org/10.1073/pnas.2417025122</a>.","apa":"Chiossi, H. S. C., Nardin, M., Tkačik, G., &#38; Csicsvari, J. L. (2025). Learning reshapes the hippocampal representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2417025122\">https://doi.org/10.1073/pnas.2417025122</a>"},"related_material":{"link":[{"relation":"software","url":"https://github.com/hchiossi/hpc-hierarchy"}],"record":[{"status":"public","relation":"research_data","id":"18991"}]},"pmid":1,"OA_place":"publisher","volume":122,"author":[{"last_name":"Chiossi","first_name":"Heloisa","full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0004-2973-278X"},{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Learning reshapes the hippocampal representation hierarchy","abstract":[{"lang":"eng","text":"A key feature of biological and artificial neural networks is the progressive refinement of their neural representations with experience. In neuroscience, this fact has inspired several recent studies in sensory and motor systems. However, less is known about how higher associational cortical areas, such as the hippocampus, modify representations throughout the learning of complex tasks. Here, we focus on associative learning, a process that requires forming a connection between the representations of different variables for appropriate behavioral response. We trained rats in a space-context associative task and monitored hippocampal neural activity throughout the entire learning period, over several days. This allowed us to assess changes in the representations of context, movement direction, and position, as well as their relationship to behavior. We identified a hierarchical representational structure in the encoding of these three task variables that was preserved throughout learning. Nevertheless, we also observed changes at the lower levels of the hierarchy where context was encoded. These changes were local in neural activity space and restricted to physical positions where context identification was necessary for correct decision-making, supporting better context decoding and contextual code compression. Our results demonstrate that the hippocampal code not only accommodates hierarchical relationships between different variables but also enables efficient learning through minimal changes in neural activity space. Beyond the hippocampus, our work reveals a representation learning mechanism that might be implemented in other biological and artificial networks performing similar tasks."}],"external_id":{"pmid":["40063792"],"isi":["001459499500001"]},"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences","APC_amount":"3317,75 EUR","issue":"11","doi":"10.1073/pnas.2417025122","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_number":"e2417025122","year":"2025","date_created":"2025-03-25T07:38:35Z","ddc":["570"],"has_accepted_license":"1","file":[{"file_id":"19454","file_size":1553502,"date_updated":"2025-03-25T07:49:04Z","access_level":"open_access","checksum":"1217207c254553154faa065964990988","relation":"main_file","content_type":"application/pdf","file_name":"2025_PNAS_Chiossi.pdf","date_created":"2025-03-25T07:49:04Z","success":1,"creator":"dernst"}],"quality_controlled":"1","corr_author":"1"},{"quality_controlled":"1","corr_author":"1","article_number":"415","year":"2025","date_created":"2025-03-31T10:07:22Z","publication":"Nature Reviews Molecular Cell Biology","publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"doi":"10.1038/s41580-025-00844-1","external_id":{"pmid":["40155512"],"isi":["001455740100001"]},"publication_status":"published","article_processing_charge":"No","title":"Understanding the machinery that reads the genome","volume":26,"author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"citation":{"ama":"Bernecky C. Understanding the machinery that reads the genome. <i>Nature Reviews Molecular Cell Biology</i>. 2025;26. doi:<a href=\"https://doi.org/10.1038/s41580-025-00844-1\">10.1038/s41580-025-00844-1</a>","ista":"Bernecky C. 2025. Understanding the machinery that reads the genome. Nature Reviews Molecular Cell Biology. 26, 415.","short":"C. Bernecky, Nature Reviews Molecular Cell Biology 26 (2025).","ieee":"C. Bernecky, “Understanding the machinery that reads the genome,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 26. Springer Nature, 2025.","mla":"Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 26, 415, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41580-025-00844-1\">10.1038/s41580-025-00844-1</a>.","chicago":"Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41580-025-00844-1\">https://doi.org/10.1038/s41580-025-00844-1</a>.","apa":"Bernecky, C. (2025). Understanding the machinery that reads the genome. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-025-00844-1\">https://doi.org/10.1038/s41580-025-00844-1</a>"},"OA_type":"closed access","day":"01","status":"public","isi":1,"department":[{"_id":"CaBe"}],"publisher":"Springer Nature","date_updated":"2025-09-30T11:20:36Z","month":"06","language":[{"iso":"eng"}],"date_published":"2025-06-01T00:00:00Z","type":"journal_article","article_type":"letter_note","oa_version":"None","intvolume":"        26","_id":"19465","scopus_import":"1"},{"month":"05","language":[{"iso":"eng"}],"date_published":"2025-05-01T00:00:00Z","arxiv":1,"department":[{"_id":"VaKa"}],"publisher":"Springer Nature","date_updated":"2025-09-30T11:31:00Z","isi":1,"oa":1,"_id":"19496","scopus_import":"1","article_type":"original","intvolume":"       310","oa_version":"Preprint","type":"journal_article","citation":{"ama":"Helfter M. Scales. <i>Mathematische Zeitschrift</i>. 2025;310. doi:<a href=\"https://doi.org/10.1007/s00209-025-03719-5\">10.1007/s00209-025-03719-5</a>","ista":"Helfter M. 2025. Scales. Mathematische Zeitschrift. 310, 15.","ieee":"M. Helfter, “Scales,” <i>Mathematische Zeitschrift</i>, vol. 310. Springer Nature, 2025.","short":"M. Helfter, Mathematische Zeitschrift 310 (2025).","mla":"Helfter, Mathieu. “Scales.” <i>Mathematische Zeitschrift</i>, vol. 310, 15, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00209-025-03719-5\">10.1007/s00209-025-03719-5</a>.","apa":"Helfter, M. (2025). Scales. <i>Mathematische Zeitschrift</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00209-025-03719-5\">https://doi.org/10.1007/s00209-025-03719-5</a>","chicago":"Helfter, Mathieu. “Scales.” <i>Mathematische Zeitschrift</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00209-025-03719-5\">https://doi.org/10.1007/s00209-025-03719-5</a>."},"day":"01","status":"public","OA_type":"green","title":"Scales","article_processing_charge":"No","abstract":[{"text":"We introduce the notions of scale for sets and measures on metric space by generalizing the usual notions of dimension. Several versions of scales are introduced such as Hausdorff, packing, box, local and quantization. They are defined for different growth, allowing a refined study of infinite dimensional spaces. We prove general theorems comparing the different versions of scales. They are applied to describe geometries of ergodic decompositions, of the Wiener measure and from functional spaces. The first application solves a problem of Berger on the notions of emergence (2020); the second lies in the geometry of the Wiener measure and extends the work of Dereich–Lifshits (2005); the last refines Kolmogorov–Tikhomirov (1958) study on finitely differentiable functions.","lang":"eng"}],"external_id":{"arxiv":["2206.05231"],"isi":["001450830300001"]},"publication_status":"published","author":[{"first_name":"Mathieu","last_name":"Helfter","id":"7d296fbe-e2c6-11ee-84d3-d5c2945f9a57","full_name":"Helfter, Mathieu"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":310,"OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.05231"}],"corr_author":"1","quality_controlled":"1","doi":"10.1007/s00209-025-03719-5","publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"publication":"Mathematische Zeitschrift","year":"2025","date_created":"2025-04-06T22:01:32Z","article_number":"15"},{"title":"Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background?","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The stochastic gravitational wave (GW) background recently discovered by several pulsar timing array experiments is consistent with arising from a population of coalescing super-massive black hole binaries. The amplitude of the background is somewhat higher than expected in most previous population models or from the local mass density observations. Such binaries are expected to be produced in galaxy mergers, which are also thought to trigger bright quasar activity. Under the assumptions that (i) a fraction fbin∼1 of all quasars are associated with mergers, (ii) the typical quasar lifetime is tQ∼108 yr, and (iii) adopting Eddington ratios fEdd∼0.25 for the luminosity of quasars, we compute the GW background associated directly with the empirically measured quasar luminosity function. This approach bypasses the need to model the cosmological evolution of black holes or galaxy mergers from simulations or semi-analytical models. We find the amplitude matching the value measured by NANOGrav. Our results are consistent with most quasars being associated with black hole binaries and being the sources of the GW background, and imply a joint constraint on tQ, fEdd and the typical mass ratio q≡M2/M1. The signal in this case would be dominated by relatively distant ∼109M⊙ sources at z≈2−3, at the peak of quasar activity. Similarly to other models, our results remain in tension with the local super-massive black hole mass density."}],"publication_status":"published","external_id":{"isi":["001448904700001"],"arxiv":["2412.12726"]},"author":[{"last_name":"Kis-Tóth","first_name":"Ágnes","full_name":"Kis-Tóth, Ágnes"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","orcid":"0000-0003-3633-5403","full_name":"Haiman, Zoltán","last_name":"Haiman","first_name":"Zoltán"},{"full_name":"Frei, Zsolt","first_name":"Zsolt","last_name":"Frei"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","volume":42,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2412.12726"}],"quality_controlled":"1","issue":"7","doi":"10.1088/1361-6382/adbda6","publication_identifier":{"issn":["0264-9381"],"eissn":["1361-6382"]},"publication":"Classical and Quantum Gravity","year":"2025","date_created":"2025-04-06T22:01:32Z","article_number":"075007","month":"04","language":[{"iso":"eng"}],"date_published":"2025-04-04T00:00:00Z","publisher":"IOP Publishing","department":[{"_id":"ZoHa"}],"arxiv":1,"date_updated":"2025-09-30T11:30:11Z","isi":1,"oa":1,"_id":"19497","scopus_import":"1","article_type":"original","intvolume":"        42","oa_version":"Preprint","type":"journal_article","acknowledgement":"We thank Chengcheng Xin and Girish Kulkarni for useful discussions. ZH gratefully acknowledges the hospitality of Eötvös University during an extended sabbatical visit, where this work began. ZH acknowledges support from NSF Grant AST-2006176 and NASA Grants 80NSSC22K0822 and 80NSSC24K0440. ZF acknowledges support from the Hungarian National Research, Development and Innovation Office (NKFIH) through the Institutional Excellence Program No. TKP2021-NKTA-64.","citation":{"apa":"Kis-Tóth, Á., Haiman, Z., &#38; Frei, Z. (2025). Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background? <i>Classical and Quantum Gravity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6382/adbda6\">https://doi.org/10.1088/1361-6382/adbda6</a>","chicago":"Kis-Tóth, Ágnes, Zoltán Haiman, and Zsolt Frei. “Can Quasars, Triggered by Mergers, Account for NANOGrav’s Stochastic Gravitational Wave Background?” <i>Classical and Quantum Gravity</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-6382/adbda6\">https://doi.org/10.1088/1361-6382/adbda6</a>.","mla":"Kis-Tóth, Ágnes, et al. “Can Quasars, Triggered by Mergers, Account for NANOGrav’s Stochastic Gravitational Wave Background?” <i>Classical and Quantum Gravity</i>, vol. 42, no. 7, 075007, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-6382/adbda6\">10.1088/1361-6382/adbda6</a>.","short":"Á. Kis-Tóth, Z. Haiman, Z. Frei, Classical and Quantum Gravity 42 (2025).","ieee":"Á. Kis-Tóth, Z. Haiman, and Z. Frei, “Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background?,” <i>Classical and Quantum Gravity</i>, vol. 42, no. 7. IOP Publishing, 2025.","ama":"Kis-Tóth Á, Haiman Z, Frei Z. Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background? <i>Classical and Quantum Gravity</i>. 2025;42(7). doi:<a href=\"https://doi.org/10.1088/1361-6382/adbda6\">10.1088/1361-6382/adbda6</a>","ista":"Kis-Tóth Á, Haiman Z, Frei Z. 2025. Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational wave background? Classical and Quantum Gravity. 42(7), 075007."},"day":"04","status":"public","OA_type":"green"},{"corr_author":"1","file":[{"creator":"dernst","success":1,"date_created":"2025-04-07T11:42:22Z","content_type":"application/pdf","file_name":"2025_PNAS_Muroya.pdf","relation":"main_file","checksum":"83501b8a65ee5fdd3f5604fc28eddc22","access_level":"open_access","date_updated":"2025-04-07T11:42:22Z","file_size":6805668,"file_id":"19524"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["000"],"year":"2025","date_created":"2025-04-06T22:01:32Z","article_number":"e2419273122","issue":"12","doi":"10.1073/pnas.2419273122","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"Quantum hardware is inherently fragile and noisy. We find that the accuracy of traditional quantum error correction algorithms can be improved depending on the hardware. Given different hardware specifications, we automatically synthesize hardware-optimal algorithms for parity correction, qubit resetting, and GHZ (Greenberger–Horne–Zeilinger) state preparation. Using stochastic techniques from computer science, our method presents a computational tool to compute exact accuracy guarantees and synthesize optimal algorithms that are often different from traditional ones. We also show that improvements can be gained with respect to the Qiskit transpiler as we compute the hardware-optimal qubit mapping for the GHZ state-preparation problem."}],"publication_status":"published","external_id":{"pmid":["40106357"],"isi":["001459435600001"]},"title":"Hardware-optimal quantum algorithms","author":[{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei","first_name":"Stefanie"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":122,"OA_place":"publisher","related_material":{"link":[{"relation":"software","url":"https://github.com/smml1996/algorithm_synthesis"},{"url":"https://ista.ac.at/en/news/hardware-optimal-quantum-algorithms/","relation":"press_release","description":"News on ISTA website"}]},"pmid":1,"citation":{"mla":"Muroya Lei, Stefanie, et al. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 12, e2419273122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2419273122\">10.1073/pnas.2419273122</a>.","chicago":"Muroya Lei, Stefanie, Krishnendu Chatterjee, and Thomas A Henzinger. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2419273122\">https://doi.org/10.1073/pnas.2419273122</a>.","apa":"Muroya Lei, S., Chatterjee, K., &#38; Henzinger, T. A. (2025). Hardware-optimal quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2419273122\">https://doi.org/10.1073/pnas.2419273122</a>","ama":"Muroya Lei S, Chatterjee K, Henzinger TA. Hardware-optimal quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(12). doi:<a href=\"https://doi.org/10.1073/pnas.2419273122\">10.1073/pnas.2419273122</a>","ista":"Muroya Lei S, Chatterjee K, Henzinger TA. 2025. Hardware-optimal quantum algorithms. Proceedings of the National Academy of Sciences. 122(12), e2419273122.","short":"S. Muroya Lei, K. Chatterjee, T.A. Henzinger, Proceedings of the National Academy of Sciences 122 (2025).","ieee":"S. Muroya Lei, K. Chatterjee, and T. A. Henzinger, “Hardware-optimal quantum algorithms,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 12. National Academy of Sciences, 2025."},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"ec_funded":1,"OA_type":"hybrid","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","day":"25","isi":1,"oa":1,"file_date_updated":"2025-04-07T11:42:22Z","language":[{"iso":"eng"}],"month":"03","date_published":"2025-03-25T00:00:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"National Academy of Sciences","date_updated":"2026-04-28T13:41:14Z","article_type":"original","intvolume":"       122","oa_version":"Published Version","type":"journal_article","acknowledgement":"We thank the reviewers. In particular, they inspired us to analyze the reset and state-preparation problems, to compute optimal qubit mappings, and to apply our method to a quantum error correction scheme that includes both bitflip and phaseflip corrections. We also thank Raimundo Saona and Marek Chalupa for their time spent in insightful discussions. This research was partially supported by the European Research Council CoG 863818 (ForM-SMArt) grant.","_id":"19499","scopus_import":"1"},{"ddc":["510"],"has_accepted_license":"1","quality_controlled":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-04-07T11:21:13Z","file_name":"2025_DocumentaMathematica_Erdoes.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"97a02d18c05f2b9f2048747b140e7d43","file_size":1366865,"date_updated":"2025-04-07T11:21:13Z","file_id":"19523"}],"corr_author":"1","publication":"Documenta Mathematica","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"doi":"10.4171/DM/999","issue":"2","date_created":"2025-04-06T22:01:32Z","year":"2025","title":"Density of Brown measure of free circular Brownian motion","external_id":{"isi":["001450119900005"],"arxiv":["2307.08626"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We consider the Brown measure of the free circular Brownian motion,  a+t√x , with an arbitrary initial condition  a , i.e.  a  is a general non-normal operator and  x  is a circular element  ∗ -free from  a . We prove that, under a mild assumption on  a , the density of the Brown measure has one of the following two types of behavior around each point on the boundary of its support -- either (i) sharp cut, i.e. a jump discontinuity along the boundary, or (ii) quadratic decay at certain critical points on the boundary. Our result is in direct analogy with the previously known phenomenon for the spectral density of free semicircular Brownian motion, whose singularities are either a square-root edge or a cubic cusp. We also provide several examples and counterexamples, one of which shows that our assumption on  a  is necessary."}],"article_processing_charge":"Yes","page":"417-453","OA_place":"publisher","volume":30,"author":[{"last_name":"Erdös","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Ji, Hong Chang","last_name":"Ji","first_name":"Hong Chang"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"citation":{"mla":"Erdös, László, and Hong Chang Ji. “Density of Brown Measure of Free Circular Brownian Motion.” <i>Documenta Mathematica</i>, vol. 30, no. 2, EMS Press, 2025, pp. 417–53, doi:<a href=\"https://doi.org/10.4171/DM/999\">10.4171/DM/999</a>.","chicago":"Erdös, László, and Hong Chang Ji. “Density of Brown Measure of Free Circular Brownian Motion.” <i>Documenta Mathematica</i>. EMS Press, 2025. <a href=\"https://doi.org/10.4171/DM/999\">https://doi.org/10.4171/DM/999</a>.","apa":"Erdös, L., &#38; Ji, H. C. (2025). Density of Brown measure of free circular Brownian motion. <i>Documenta Mathematica</i>. EMS Press. <a href=\"https://doi.org/10.4171/DM/999\">https://doi.org/10.4171/DM/999</a>","ama":"Erdös L, Ji HC. Density of Brown measure of free circular Brownian motion. <i>Documenta Mathematica</i>. 2025;30(2):417-453. doi:<a href=\"https://doi.org/10.4171/DM/999\">10.4171/DM/999</a>","ista":"Erdös L, Ji HC. 2025. Density of Brown measure of free circular Brownian motion. Documenta Mathematica. 30(2), 417–453.","short":"L. Erdös, H.C. Ji, Documenta Mathematica 30 (2025) 417–453.","ieee":"L. Erdös and H. C. Ji, “Density of Brown measure of free circular Brownian motion,” <i>Documenta Mathematica</i>, vol. 30, no. 2. EMS Press, pp. 417–453, 2025."},"day":"20","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"OA_type":"gold","date_updated":"2025-09-30T11:28:02Z","arxiv":1,"publisher":"EMS Press","department":[{"_id":"LaEr"}],"date_published":"2025-03-20T00:00:00Z","language":[{"iso":"eng"}],"month":"03","DOAJ_listed":"1","file_date_updated":"2025-04-07T11:21:13Z","oa":1,"isi":1,"scopus_import":"1","_id":"19500","acknowledgement":"We thank Ping Zhong for pointing out references [15,19] and providing helpful comments. We also thank the anonymous referee for many valuable comments and proposals to streamline the presentation. This work was partially supported by ERC Advanced Grant “RMTBeyond” No. 10102033.","type":"journal_article","intvolume":"        30","oa_version":"Published Version","article_type":"original"},{"OA_place":"repository","volume":111,"author":[{"first_name":"Henrik H.","last_name":"Kristensen","full_name":"Kristensen, Henrik H."},{"full_name":"Kranabetter, Lorenz","last_name":"Kranabetter","first_name":"Lorenz"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","last_name":"Ghazaryan"},{"full_name":"Schouder, Constant A.","first_name":"Constant A.","last_name":"Schouder"},{"full_name":"Hansen, Emil","last_name":"Hansen","first_name":"Emil"},{"first_name":"Frank","last_name":"Jensen","full_name":"Jensen, Frank"},{"first_name":"Robert E.","last_name":"Zillich","full_name":"Zillich, Robert E."},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Nonadiabatic laser-induced alignment dynamics of alkali-metal dimers on the surface of a helium droplet","publication_status":"published","external_id":{"arxiv":["2502.14521"],"isi":["001459727400007"]},"abstract":[{"lang":"eng","text":"Alkali dimers, Ak2, located on the surface of a helium nanodroplet, are set into rotation through the polarizability interaction with a nonresonant 1-ps-long laser pulse. The time-dependent degree of alignment is recorded using femtosecond-probe-pulse-induced Coulomb explosion into a pair of Ak+ fragment ions. The results, obtained for Na2, K2, and Rb2 in both the ground state 11Σ+g and the lowest-lying triplet state 13Σ+u, exhibit distinct, periodic revivals with a gradually decreasing amplitude. The dynamics differ from that expected for dimers had they behaved as free rotors. Numerically, we solve the time-dependent rotational Schrödinger equation, including an effective mean-field potential to describe the interaction between the dimer and the droplet. The experimental and simulated alignment dynamics agree well and their comparison enables us to determine the effective rotational constants of the alkali dimers with the exception of Rb2(13Σ+u) that only exhibits a prompt alignment peak but no subsequent revivals. For Na2(13Σ+u), K2(11Σ+g), K2(13Σ+u) and Rb2(11Σ+g), the alignment dynamics are well-described by a 2D rotor model. We ascribe this to a significant confinement of the internuclear axis of these dimers, induced by the orientation-dependent droplet-dimer interaction, to the tangential plane of their residence point on the droplet."}],"article_processing_charge":"No","publication":"Physical Review A","doi":"10.1103/PhysRevA.111.033114","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"issue":"3","article_number":"033114","date_created":"2025-04-06T22:01:32Z","year":"2025","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2502.14521"}],"quality_controlled":"1","scopus_import":"1","_id":"19502","type":"journal_article","acknowledgement":"H.S. acknowledges support from the Villum Foundation through a Villum Investigator Grant No. 25886. We thank Jan Thøgersen for expert help with the optics and the laser system.","oa_version":"Preprint","intvolume":"       111","article_type":"original","date_updated":"2025-09-30T11:27:25Z","publisher":"American Physical Society","arxiv":1,"department":[{"_id":"MiLe"}],"date_published":"2025-03-21T00:00:00Z","month":"03","language":[{"iso":"eng"}],"oa":1,"isi":1,"status":"public","day":"21","OA_type":"green","citation":{"apa":"Kristensen, H. H., Kranabetter, L., Ghazaryan, A., Schouder, C. A., Hansen, E., Jensen, F., … Stapelfeldt, H. (2025). Nonadiabatic laser-induced alignment dynamics of alkali-metal dimers on the surface of a helium droplet. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.111.033114\">https://doi.org/10.1103/PhysRevA.111.033114</a>","chicago":"Kristensen, Henrik H., Lorenz Kranabetter, Areg Ghazaryan, Constant A. Schouder, Emil Hansen, Frank Jensen, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Nonadiabatic Laser-Induced Alignment Dynamics of Alkali-Metal Dimers on the Surface of a Helium Droplet.” <i>Physical Review A</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevA.111.033114\">https://doi.org/10.1103/PhysRevA.111.033114</a>.","mla":"Kristensen, Henrik H., et al. “Nonadiabatic Laser-Induced Alignment Dynamics of Alkali-Metal Dimers on the Surface of a Helium Droplet.” <i>Physical Review A</i>, vol. 111, no. 3, 033114, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.033114\">10.1103/PhysRevA.111.033114</a>.","ieee":"H. H. Kristensen <i>et al.</i>, “Nonadiabatic laser-induced alignment dynamics of alkali-metal dimers on the surface of a helium droplet,” <i>Physical Review A</i>, vol. 111, no. 3. American Physical Society, 2025.","short":"H.H. Kristensen, L. Kranabetter, A. Ghazaryan, C.A. Schouder, E. Hansen, F. Jensen, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review A 111 (2025).","ama":"Kristensen HH, Kranabetter L, Ghazaryan A, et al. Nonadiabatic laser-induced alignment dynamics of alkali-metal dimers on the surface of a helium droplet. <i>Physical Review A</i>. 2025;111(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.033114\">10.1103/PhysRevA.111.033114</a>","ista":"Kristensen HH, Kranabetter L, Ghazaryan A, Schouder CA, Hansen E, Jensen F, Zillich RE, Lemeshko M, Stapelfeldt H. 2025. Nonadiabatic laser-induced alignment dynamics of alkali-metal dimers on the surface of a helium droplet. Physical Review A. 111(3), 033114."}},{"acknowledgement":"Funded by SNSF Ambizione grant No. 216071. 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. Funded by SNSF grant CRSII5, 173721.","type":"journal_article","oa_version":"Published Version","intvolume":"        34","article_type":"original","scopus_import":"1","_id":"19503","file_date_updated":"2025-08-05T12:54:06Z","oa":1,"isi":1,"date_updated":"2025-09-30T11:26:00Z","arxiv":1,"department":[{"_id":"MaKw"}],"publisher":"Cambridge University Press","date_published":"2025-07-01T00:00:00Z","language":[{"iso":"eng"}],"month":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"OA_type":"hybrid","day":"01","status":"public","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"citation":{"mla":"Christoph, Micha, et al. “A Note on Digraph Splitting.” <i>Combinatorics Probability and Computing</i>, vol. 34, no. 4, Cambridge University Press, 2025, pp. 559–64, doi:<a href=\"https://doi.org/10.1017/S0963548325000045\">10.1017/S0963548325000045</a>.","apa":"Christoph, M., Petrova, K. H., &#38; Steiner, R. (2025). A note on digraph splitting. <i>Combinatorics Probability and Computing</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0963548325000045\">https://doi.org/10.1017/S0963548325000045</a>","chicago":"Christoph, Micha, Kalina H Petrova, and Raphael Steiner. “A Note on Digraph Splitting.” <i>Combinatorics Probability and Computing</i>. Cambridge University Press, 2025. <a href=\"https://doi.org/10.1017/S0963548325000045\">https://doi.org/10.1017/S0963548325000045</a>.","ista":"Christoph M, Petrova KH, Steiner R. 2025. A note on digraph splitting. Combinatorics Probability and Computing. 34(4), 559–564.","ama":"Christoph M, Petrova KH, Steiner R. A note on digraph splitting. <i>Combinatorics Probability and Computing</i>. 2025;34(4):559-564. doi:<a href=\"https://doi.org/10.1017/S0963548325000045\">10.1017/S0963548325000045</a>","ieee":"M. Christoph, K. H. Petrova, and R. Steiner, “A note on digraph splitting,” <i>Combinatorics Probability and Computing</i>, vol. 34, no. 4. Cambridge University Press, pp. 559–564, 2025.","short":"M. Christoph, K.H. Petrova, R. Steiner, Combinatorics Probability and Computing 34 (2025) 559–564."},"OA_place":"publisher","volume":34,"author":[{"first_name":"Micha","last_name":"Christoph","full_name":"Christoph, Micha"},{"full_name":"Petrova, Kalina H","id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","last_name":"Petrova","first_name":"Kalina H"},{"full_name":"Steiner, Raphael","first_name":"Raphael","last_name":"Steiner"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","external_id":{"isi":["001449245700001"],"arxiv":["2310.08449"]},"abstract":[{"lang":"eng","text":"A tantalizing open problem, posed independently by Stiebitz in 1995 and by Alon in 1996 and again in 2006, asks whether for every pair of integers  s,t≥1 there exists a finite number  F(s,t)\r\nsuch that the vertex set of every digraph of minimum out-degree at least  F(s,t) can be partitioned into non-empty parts  A  and  B  such that the subdigraphs induced on  A\r\n  and  B  have minimum out-degree at least  s  and  t , respectively.\r\nIn this short note, we prove that if  F(2,2)  exists, then all the numbers  F(s,t)  with  s,t≥1\r\n  exist and satisfy  F(s,t)=Θ(s+t) . In consequence, the problem of Alon and Stiebitz reduces to the case  s=t=2 . Moreover, the numbers  F(s,t)  with  s,t≥2  either all exist and grow linearly, or all of them do not exist."}],"article_processing_charge":"Yes (in subscription journal)","page":"559-564","title":"A note on digraph splitting","date_created":"2025-04-06T22:01:32Z","year":"2025","publication":"Combinatorics Probability and Computing","doi":"10.1017/S0963548325000045","publication_identifier":{"issn":["0963-5483"],"eissn":["1469-2163"]},"issue":"4","file":[{"date_created":"2025-08-05T12:54:06Z","file_name":"2025_CombProbComputing_Christoph.pdf","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"20135","access_level":"open_access","checksum":"98491e59b4f0d05d69f608bbd5706f1a","relation":"main_file","date_updated":"2025-08-05T12:54:06Z","file_size":188818}],"quality_controlled":"1","ddc":["510"],"has_accepted_license":"1"},{"article_processing_charge":"No","page":"710-719","external_id":{"isi":["001447477100001"],"pmid":["40417329"],"arxiv":["2409.17956"]},"publication_status":"published","abstract":[{"text":"Observational studies have shown that galaxy disks were already in place in the first few billion years of the Universe. The early disks detected so far, with typical half-light radii of 3 kpc at stellar masses around 1011 M⊙ for redshift z ≈ 3, are significantly smaller than today’s disks with similar masses, which is in agreement with expectations from current galaxy models. Here we report observations of a giant disk at z = 3.25, when the Universe was only two billion years old, with a half-light radius of 9.6 kpc and stellar mass of (math formular). This galaxy is larger than any other kinematically confirmed disks at similar epochs and is surprisingly similar to today’s largest disks with regard to size and mass. James Webb Space Telescope imaging and spectroscopy reveal its spiral morphology and a rotational velocity consistent with a local Tully–Fisher relationship. Multiwavelength observations show that it lies in an exceptionally dense environment, where the galaxy number density is more than ten times higher than the cosmic average and mergers are frequent. The discovery of such a giant disk suggests the presence of favourable physical conditions for large-disk formation in dense environments in the early Universe, which may include efficient accretion of gas carrying coherent angular momentum and non-destructive mergers between exceptionally gas-rich progenitor galaxies.","lang":"eng"}],"title":"A giant disk galaxy two billion years after the Big Bang","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Wang","first_name":"Weichen","full_name":"Wang, Weichen"},{"full_name":"Cantalupo, Sebastiano","first_name":"Sebastiano","last_name":"Cantalupo"},{"first_name":"Antonio","last_name":"Pensabene","full_name":"Pensabene, Antonio"},{"first_name":"Marta","last_name":"Galbiati","full_name":"Galbiati, Marta"},{"first_name":"Andrea","last_name":"Travascio","full_name":"Travascio, Andrea"},{"full_name":"Steidel, Charles C.","last_name":"Steidel","first_name":"Charles C."},{"full_name":"Maseda, Michael V.","first_name":"Michael V.","last_name":"Maseda"},{"full_name":"Pezzulli, Gabriele","last_name":"Pezzulli","first_name":"Gabriele"},{"first_name":"Stephanie","last_name":"De Beer","full_name":"De Beer, Stephanie"},{"first_name":"Matteo","last_name":"Fossati","full_name":"Fossati, Matteo"},{"full_name":"Fumagalli, Michele","last_name":"Fumagalli","first_name":"Michele"},{"full_name":"Gallego, Sofia G.","first_name":"Sofia G.","last_name":"Gallego"},{"first_name":"Titouan","last_name":"Lazeyras","full_name":"Lazeyras, Titouan"},{"last_name":"Mackenzie","first_name":"Ruari","full_name":"Mackenzie, Ruari"},{"first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Nanayakkara, Themiya","first_name":"Themiya","last_name":"Nanayakkara"},{"full_name":"Quadri, Giada","last_name":"Quadri","first_name":"Giada"}],"volume":9,"OA_place":"publisher","pmid":1,"quality_controlled":"1","file":[{"file_id":"20134","file_size":4912850,"date_updated":"2025-08-05T12:49:36Z","checksum":"a0e65fe3374bd755b18ba03fd5e42a3f","relation":"main_file","access_level":"open_access","file_name":"2025_NatureAstronomy_Wang.pdf","content_type":"application/pdf","date_created":"2025-08-05T12:49:36Z","creator":"dernst","success":1}],"has_accepted_license":"1","ddc":["520"],"date_created":"2025-04-06T22:01:32Z","year":"2025","publication_identifier":{"eissn":["2397-3366"]},"doi":"10.1038/s41550-025-02500-2","publication":"Nature Astronomy","isi":1,"file_date_updated":"2025-08-05T12:49:36Z","oa":1,"date_published":"2025-03-17T00:00:00Z","month":"03","language":[{"iso":"eng"}],"date_updated":"2025-09-30T11:25:14Z","arxiv":1,"publisher":"Springer Nature","department":[{"_id":"JoMa"}],"intvolume":"         9","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We thank B. Wang, P. Madau, M. Dotti, A. de la Vega, Y. Guo, C. Bacchini, Z. Cai, C. Conselice, A. Dekel, S. Faber, F. Fraternali, L. Ho, F. Jiang, S. Kassin, D. Koo, N. Mandelker, S. Mao and D. Xu for the valuable and insightful discussions regarding the research topics relevant to this paper. This project was supported by the European Research Council (ERC) Consolidator Grant no. 864361 (CosmicWeb). A.P. acknowledges the support from Fondazione Cariplo grant no. 2020-0902. M.V.M. acknowledges funding from NASA by means of HST-GO-17065. T.N. acknowledges support from Australian Research Council Laureate Fellowship FL180100060. This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programme no. 1835. Support for programme no. 1835 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. This research is based on observations made with the NASA/ESA Hubble Space Telescope obtained from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with programme 17065. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The scientific results reported in this article are based in part on observations made by the Chandra X-ray Observatory. This work is also based on observations collected at the European Southern Observatory under ESO programme 110.23ZX.","scopus_import":"1","_id":"19504","citation":{"ieee":"W. Wang <i>et al.</i>, “A giant disk galaxy two billion years after the Big Bang,” <i>Nature Astronomy</i>, vol. 9. Springer Nature, pp. 710–719, 2025.","short":"W. Wang, S. Cantalupo, A. Pensabene, M. Galbiati, A. Travascio, C.C. Steidel, M.V. Maseda, G. Pezzulli, S. De Beer, M. Fossati, M. Fumagalli, S.G. Gallego, T. Lazeyras, R. Mackenzie, J.J. Matthee, T. Nanayakkara, G. Quadri, Nature Astronomy 9 (2025) 710–719.","ista":"Wang W, Cantalupo S, Pensabene A, Galbiati M, Travascio A, Steidel CC, Maseda MV, Pezzulli G, De Beer S, Fossati M, Fumagalli M, Gallego SG, Lazeyras T, Mackenzie R, Matthee JJ, Nanayakkara T, Quadri G. 2025. A giant disk galaxy two billion years after the Big Bang. Nature Astronomy. 9, 710–719.","ama":"Wang W, Cantalupo S, Pensabene A, et al. A giant disk galaxy two billion years after the Big Bang. <i>Nature Astronomy</i>. 2025;9:710-719. doi:<a href=\"https://doi.org/10.1038/s41550-025-02500-2\">10.1038/s41550-025-02500-2</a>","chicago":"Wang, Weichen, Sebastiano Cantalupo, Antonio Pensabene, Marta Galbiati, Andrea Travascio, Charles C. Steidel, Michael V. Maseda, et al. “A Giant Disk Galaxy Two Billion Years after the Big Bang.” <i>Nature Astronomy</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41550-025-02500-2\">https://doi.org/10.1038/s41550-025-02500-2</a>.","apa":"Wang, W., Cantalupo, S., Pensabene, A., Galbiati, M., Travascio, A., Steidel, C. C., … Quadri, G. (2025). A giant disk galaxy two billion years after the Big Bang. <i>Nature Astronomy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41550-025-02500-2\">https://doi.org/10.1038/s41550-025-02500-2</a>","mla":"Wang, Weichen, et al. “A Giant Disk Galaxy Two Billion Years after the Big Bang.” <i>Nature Astronomy</i>, vol. 9, Springer Nature, 2025, pp. 710–19, doi:<a href=\"https://doi.org/10.1038/s41550-025-02500-2\">10.1038/s41550-025-02500-2</a>."},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"OA_type":"hybrid","day":"17","status":"public"},{"external_id":{"isi":["001434322900016"],"arxiv":["2210.05973"]},"publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we introduce and study the primitive equations with non-isothermal turbulent pressure and transport noise. They are derived from the Navier–Stokes equations by employing stochastic versions of the Boussinesq and the hydrostatic approximations. The temperature dependence of the turbulent pressure can be seen as a consequence of an additive noise acting on the small vertical dynamics. For such a model we prove global well-posedness in H^1 where the noise is considered in both the Itô and Stratonovich formulations. Compared to previous variants of the primitive equations, the one considered here presents a more intricate coupling between the velocity field and the temperature. The corresponding analysis is seriously more involved than in the deterministic setting. Finally, the continuous dependence on the initial data and the energy estimates proven here are new, even in the case of isothermal turbulent pressure."}],"article_processing_charge":"No","page":"635-700","title":"The stochastic primitive equations with nonisothermal turbulent pressure","volume":35,"OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Agresti","first_name":"Antonio","orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio"},{"last_name":"Hieber","first_name":"Matthias","full_name":"Hieber, Matthias"},{"last_name":"Hussein","first_name":"Amru","full_name":"Hussein, Amru"},{"full_name":"Saal, Martin","last_name":"Saal","first_name":"Martin"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.05973"}],"date_created":"2025-04-06T22:01:32Z","year":"2025","publication":"Annals of Applied Probability","doi":"10.1214/24-AAP2124","publication_identifier":{"issn":["1050-5164"]},"issue":"1","oa":1,"isi":1,"date_updated":"2025-09-30T11:23:58Z","department":[{"_id":"JuFi"}],"arxiv":1,"publisher":"Institute of Mathematical Statistics","date_published":"2025-02-01T00:00:00Z","month":"02","language":[{"iso":"eng"}],"type":"journal_article","acknowledgement":"The first author thanks Umberto Pappalettera for helpful suggestions on Section 2 and for bringing to his attention the reference [56]. The first author is grateful to Marco Romito for helpful comments related to Remarks 2.1 and 2.2. Finally, the first author thanks Caterina Balzotti for her support in creating the picture.\r\nAntonio Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819). Antonio Agresti is a member of GNAMPA (INδAM).\r\nMatthias Hieber gratefully acknowledges the support by the Deutsche Forschungsgemeinschaft (DFG) through the Research Unit 5528—project number 500072446.\r\nAmru Hussein has been supported by Deutsche Forschungsgemeinschaft (DFG)—project\r\nnumber 508634462 and by MathApp—Mathematics Applied to Real-World Problems—part\r\nof the Research Initiative of the Federal State of Rhineland-Palatinate, Germany.\r\nMartin Saal has been supported by Deutsche Forschungsgemeinschaft (DFG)—project\r\nnumber 429483464.","intvolume":"        35","oa_version":"Preprint","article_type":"original","scopus_import":"1","_id":"19505","project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"citation":{"short":"A. Agresti, M. Hieber, A. Hussein, M. Saal, Annals of Applied Probability 35 (2025) 635–700.","ieee":"A. Agresti, M. Hieber, A. Hussein, and M. Saal, “The stochastic primitive equations with nonisothermal turbulent pressure,” <i>Annals of Applied Probability</i>, vol. 35, no. 1. Institute of Mathematical Statistics, pp. 635–700, 2025.","ama":"Agresti A, Hieber M, Hussein A, Saal M. The stochastic primitive equations with nonisothermal turbulent pressure. <i>Annals of Applied Probability</i>. 2025;35(1):635-700. doi:<a href=\"https://doi.org/10.1214/24-AAP2124\">10.1214/24-AAP2124</a>","ista":"Agresti A, Hieber M, Hussein A, Saal M. 2025. The stochastic primitive equations with nonisothermal turbulent pressure. Annals of Applied Probability. 35(1), 635–700.","apa":"Agresti, A., Hieber, M., Hussein, A., &#38; Saal, M. (2025). The stochastic primitive equations with nonisothermal turbulent pressure. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/24-AAP2124\">https://doi.org/10.1214/24-AAP2124</a>","chicago":"Agresti, Antonio, Matthias Hieber, Amru Hussein, and Martin Saal. “The Stochastic Primitive Equations with Nonisothermal Turbulent Pressure.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/24-AAP2124\">https://doi.org/10.1214/24-AAP2124</a>.","mla":"Agresti, Antonio, et al. “The Stochastic Primitive Equations with Nonisothermal Turbulent Pressure.” <i>Annals of Applied Probability</i>, vol. 35, no. 1, Institute of Mathematical Statistics, 2025, pp. 635–700, doi:<a href=\"https://doi.org/10.1214/24-AAP2124\">10.1214/24-AAP2124</a>."},"ec_funded":1,"OA_type":"green","status":"public","day":"01"},{"article_type":"original","intvolume":"       113","oa_version":"Published Version","acknowledgement":"We thank Andrea Cumpelik, Lisa Genzel, and Freya Ólafsdóttir for comments on an earlier version of the manuscript. This work was supported by the European Research Council (281511) and Austrian Science Fund (FWF I3713).","type":"journal_article","_id":"19506","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2025-08-05T12:43:44Z","language":[{"iso":"eng"}],"month":"05","date_published":"2025-05-07T00:00:00Z","department":[{"_id":"JoCs"}],"publisher":"Elsevier","date_updated":"2026-04-28T13:39:22Z","OA_type":"hybrid","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"07","status":"public","PlanS_conform":"1","citation":{"mla":"Bollmann, Lars, et al. “Sleep Stages Antagonistically Modulate Reactivation Drift.” <i>Neuron</i>, vol. 113, no. 9, Elsevier, 2025, p. 1446–1459.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">10.1016/j.neuron.2025.02.025</a>.","chicago":"Bollmann, Lars, Peter Baracskay, Federico Stella, and Jozsef L Csicsvari. “Sleep Stages Antagonistically Modulate Reactivation Drift.” <i>Neuron</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">https://doi.org/10.1016/j.neuron.2025.02.025</a>.","apa":"Bollmann, L., Baracskay, P., Stella, F., &#38; Csicsvari, J. L. (2025). Sleep stages antagonistically modulate reactivation drift. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">https://doi.org/10.1016/j.neuron.2025.02.025</a>","ista":"Bollmann L, Baracskay P, Stella F, Csicsvari JL. 2025. Sleep stages antagonistically modulate reactivation drift. Neuron. 113(9), 1446–1459.e6.","ama":"Bollmann L, Baracskay P, Stella F, Csicsvari JL. Sleep stages antagonistically modulate reactivation drift. <i>Neuron</i>. 2025;113(9):1446-1459.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2025.02.025\">10.1016/j.neuron.2025.02.025</a>","short":"L. Bollmann, P. Baracskay, F. Stella, J.L. Csicsvari, Neuron 113 (2025) 1446–1459.e6.","ieee":"L. Bollmann, P. Baracskay, F. Stella, and J. L. Csicsvari, “Sleep stages antagonistically modulate reactivation drift,” <i>Neuron</i>, vol. 113, no. 9. Elsevier, p. 1446–1459.e6, 2025."},"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Interneuro plasticity during spatial learning","_id":"2654F984-B435-11E9-9278-68D0E5697425","grant_number":"I 3713-B27"}],"author":[{"first_name":"Lars","last_name":"Bollmann","full_name":"Bollmann, Lars","id":"47AD3038-F248-11E8-B48F-1D18A9856A87"},{"id":"361CC00E-F248-11E8-B48F-1D18A9856A87","full_name":"Baracskay, Peter","last_name":"Baracskay","first_name":"Peter"},{"full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico","last_name":"Stella"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":113,"OA_place":"publisher","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/how-sleep-keeps-our-memories-fresh/"}]},"pmid":1,"page":"1446-1459.e6","article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Hippocampal reactivation of waking neuronal assemblies in sleep is a key initial step of systems consolidation. Nevertheless, it is unclear whether reactivated assemblies are static or whether they reorganize gradually over prolonged sleep. We tracked reactivated CA1 assembly patterns over ∼20 h of sleep/rest periods and related them to assemblies seen before or after in a spatial learning paradigm using rats. We found that reactivated assembly patterns were gradually transformed and started to resemble those seen in the subsequent recall session. Periods of rapid eye movement (REM) sleep and non-REM (NREM) had antagonistic roles: whereas NREM accelerated the assembly drift, REM countered it. Moreover, only a subset of rate-changing pyramidal cells contributed to the drift, whereas stable-firing-rate cells maintained unaltered reactivation patterns. Our data suggest that prolonged sleep promotes the spontaneous reorganization of spatial assemblies, which can contribute to daily cognitive map changes or encoding new learning situations.","lang":"eng"}],"external_id":{"pmid":["40132588"],"isi":["001510440400001"]},"publication_status":"published","title":"Sleep stages antagonistically modulate reactivation drift","year":"2025","date_created":"2025-04-06T22:01:32Z","issue":"9","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2025.02.025","publication":"Neuron","corr_author":"1","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2025_Neuron_Bollmann.pdf","date_created":"2025-08-05T12:43:44Z","success":1,"creator":"dernst","file_id":"20133","file_size":27047730,"date_updated":"2025-08-05T12:43:44Z","access_level":"open_access","checksum":"5e57852a45a78a751dd3a5e807bf015f","relation":"main_file"}],"has_accepted_license":"1","ddc":["570"]},{"OA_type":"hybrid","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"01","status":"public","citation":{"mla":"Andersen, Marianne S., et al. “Spatiotemporal Switches in Progenitor Cell Fate Govern Upper Hair Follicle Growth and Maintenance.” <i>Journal of Investigative Dermatology</i>, vol. 145, no. 9, Elsevier, 2025, p. 2191–2202.e5, doi:<a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">10.1016/j.jid.2025.01.034</a>.","chicago":"Andersen, Marianne S., Svetlana Ulyanchenko, Pawel J. Schweiger, Edouard B Hannezo, Benjamin D. Simons, and Kim B. Jensen. “Spatiotemporal Switches in Progenitor Cell Fate Govern Upper Hair Follicle Growth and Maintenance.” <i>Journal of Investigative Dermatology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">https://doi.org/10.1016/j.jid.2025.01.034</a>.","apa":"Andersen, M. S., Ulyanchenko, S., Schweiger, P. J., Hannezo, E. B., Simons, B. D., &#38; Jensen, K. B. (2025). Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance. <i>Journal of Investigative Dermatology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">https://doi.org/10.1016/j.jid.2025.01.034</a>","ama":"Andersen MS, Ulyanchenko S, Schweiger PJ, Hannezo EB, Simons BD, Jensen KB. Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance. <i>Journal of Investigative Dermatology</i>. 2025;145(9):2191-2202.e5. doi:<a href=\"https://doi.org/10.1016/j.jid.2025.01.034\">10.1016/j.jid.2025.01.034</a>","ista":"Andersen MS, Ulyanchenko S, Schweiger PJ, Hannezo EB, Simons BD, Jensen KB. 2025. Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance. Journal of Investigative Dermatology. 145(9), 2191–2202.e5.","ieee":"M. S. Andersen, S. Ulyanchenko, P. J. Schweiger, E. B. Hannezo, B. D. Simons, and K. B. Jensen, “Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance,” <i>Journal of Investigative Dermatology</i>, vol. 145, no. 9. Elsevier, p. 2191–2202.e5, 2025.","short":"M.S. Andersen, S. Ulyanchenko, P.J. Schweiger, E.B. Hannezo, B.D. Simons, K.B. Jensen, Journal of Investigative Dermatology 145 (2025) 2191–2202.e5."},"type":"journal_article","acknowledgement":"We thank the members of the Jensen Laboratory for experimental and technical advice, the imaging facilities at reNEW, and animal caretakers for expert assistance. This work was supported by the Lundbeck Foundation (R105-A9755 to KBJ) and the Leo Pharma Foundation (LF-OC-20-000169). The Novo Nordisk Foundation Center for Stem Cell Medicine was supported by a Novo Nordisk Foundation grant (NNF21CC0073729). B.D.S. was supported by the Wellcome Trust (219478/Z/19/Z) and a Royal Society EP Abraham Research Professorship (RP/R1/180165 and RP\\R\\231004). Figure elements were adapted from Bio-Render. KBJ is the lead contact and guarantor of this study.","article_type":"original","oa_version":"Published Version","intvolume":"       145","_id":"19507","scopus_import":"1","oa":1,"file_date_updated":"2025-12-29T14:13:01Z","isi":1,"publisher":"Elsevier","department":[{"_id":"EdHa"}],"date_updated":"2025-12-29T14:13:43Z","month":"09","language":[{"iso":"eng"}],"date_published":"2025-09-01T00:00:00Z","year":"2025","date_created":"2025-04-06T22:01:32Z","publication":"Journal of Investigative Dermatology","issue":"9","doi":"10.1016/j.jid.2025.01.034","publication_identifier":{"eissn":["1523-1747"],"issn":["0022-202X"]},"quality_controlled":"1","file":[{"date_created":"2025-12-29T14:13:01Z","file_name":"2025_JourInvestigativeDerma_Andersen.pdf","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"20874","access_level":"open_access","checksum":"a2b313de3cacb53f20f2b91c42612ad9","relation":"main_file","date_updated":"2025-12-29T14:13:01Z","file_size":7301679}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","OA_place":"publisher","volume":145,"author":[{"first_name":"Marianne S.","last_name":"Andersen","full_name":"Andersen, Marianne S."},{"first_name":"Svetlana","last_name":"Ulyanchenko","full_name":"Ulyanchenko, Svetlana"},{"last_name":"Schweiger","first_name":"Pawel J.","full_name":"Schweiger, Pawel J."},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"full_name":"Jensen, Kim B.","last_name":"Jensen","first_name":"Kim B."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"abstract":[{"lang":"eng","text":"The epidermis provides a protective barrier against hostile environments. However, our knowledge of how this barrier forms during development and is subsequently maintained remains incomplete. The infundibulum is a cylindrical epidermal tissue compartment that serves as an outlet for hair follicles protruding from the skin and the excretion of the sebaceous glands that are essential for proper skin function. In this study, we applied quantitative fate mapping to address how infundibulum are maintained during adulthood. We demonstrate that progenitors build and maintain tissues through stochastic cell fate choices. Long-term analysis identified a preferential transient contribution from cells initially located at the bottom of the structure to the maintenance of the tissue, with bursts of local progenitor expansion associated with the phases of hair growth. Beyond providing compartment-wide insights into progenitor cell dynamics in infundibulum, these findings demonstrate how spatiotemporal regulation controls transient progenitor dominance."}],"external_id":{"pmid":["40010488"],"isi":["001604396400001"]},"publication_status":"published","page":"2191-2202.e5","article_processing_charge":"No","title":"Spatiotemporal switches in progenitor cell fate govern upper hair follicle growth and maintenance"},{"oa_version":"Published Version","intvolume":"        15","article_type":"original","acknowledgement":"The authors would like to thank the Ministry of National Education of Republic of Türkiye within the scope of the YLSY scholarship program for funding (AO). This article is based upon work from COST Action CA20121, supported by COST (European Cooperation in Science and Technology) (www.cost.eu) (https://benbedphar.org/about-benbedphar/). The molecular dynamics simulations reported in this paper were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). The authors thank Dr Sharad Mistry for his support in acquiring and processing the MS data.","type":"journal_article","scopus_import":"1","_id":"19529","isi":1,"DOAJ_listed":"1","file_date_updated":"2025-04-10T06:21:11Z","oa":1,"date_published":"2025-03-14T00:00:00Z","language":[{"iso":"eng"}],"month":"03","date_updated":"2025-09-30T11:33:37Z","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","day":"14","status":"public","citation":{"ama":"Ozleyen A, Duran GN, Dönmez S, Ozbil M, Doveston RG, Tumer TB. Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches. <i>Scientific Reports</i>. 2025;15. doi:<a href=\"https://doi.org/10.1038/s41598-025-89342-0\">10.1038/s41598-025-89342-0</a>","ista":"Ozleyen A, Duran GN, Dönmez S, Ozbil M, Doveston RG, Tumer TB. 2025. Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches. Scientific Reports. 15, 8907.","short":"A. Ozleyen, G.N. Duran, S. Dönmez, M. Ozbil, R.G. Doveston, T.B. Tumer, Scientific Reports 15 (2025).","ieee":"A. Ozleyen, G. N. Duran, S. Dönmez, M. Ozbil, R. G. Doveston, and T. B. Tumer, “Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches,” <i>Scientific Reports</i>, vol. 15. Springer Nature, 2025.","mla":"Ozleyen, Adem, et al. “Identification and Inhibition of PIN1-NRF2 Protein–Protein Interactions through Computational and Biophysical Approaches.” <i>Scientific Reports</i>, vol. 15, 8907, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41598-025-89342-0\">10.1038/s41598-025-89342-0</a>.","chicago":"Ozleyen, Adem, Gizem Nur Duran, Serhat Dönmez, Mehmet Ozbil, Richard G. Doveston, and Tugba Boyunegmez Tumer. “Identification and Inhibition of PIN1-NRF2 Protein–Protein Interactions through Computational and Biophysical Approaches.” <i>Scientific Reports</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41598-025-89342-0\">https://doi.org/10.1038/s41598-025-89342-0</a>.","apa":"Ozleyen, A., Duran, G. N., Dönmez, S., Ozbil, M., Doveston, R. G., &#38; Tumer, T. B. (2025). Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-025-89342-0\">https://doi.org/10.1038/s41598-025-89342-0</a>"},"author":[{"full_name":"Ozleyen, Adem","first_name":"Adem","last_name":"Ozleyen"},{"full_name":"Duran, Gizem Nur","first_name":"Gizem Nur","last_name":"Duran"},{"first_name":"Serhat","last_name":"Dönmez","full_name":"Dönmez, Serhat","id":"7c624079-3200-11ee-973b-9fcc8a575580"},{"full_name":"Ozbil, Mehmet","first_name":"Mehmet","last_name":"Ozbil"},{"last_name":"Doveston","first_name":"Richard G.","full_name":"Doveston, Richard G."},{"full_name":"Tumer, Tugba Boyunegmez","first_name":"Tugba Boyunegmez","last_name":"Tumer"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":15,"OA_place":"publisher","pmid":1,"article_processing_charge":"Yes","publication_status":"published","external_id":{"pmid":["40087364"],"isi":["001445507400002"]},"abstract":[{"lang":"eng","text":"NRF2 is a transcription factor responsible for coordinating the expression of over a thousand cytoprotective genes. Although NRF2 is constitutively expressed, its stability is modulated by the redox-sensitive protein KEAP1 and other conditional binding partner regulators. The new era of NRF2 research has highlighted the cooperation between NRF2 and PIN1 in modifying its cytoprotective effect. Despite numerous studies, the understanding of the PIN1-NRF2 interaction remains limited. Herein, we described the binding interaction of PIN1 and three different 14-mer long phospho-peptides mimicking NRF2 protein using computer-based, biophysical, and biochemical approaches. According to our computational analyses, the residues positioned in the WW domain of PIN1 (Ser16, Arg17, Ser18, Tyr23, Ser32, Gln33, and Trp34) were found to be crucial for PIN1-NRF2 interactions. Biophysical FP assays were used to verify the computational prediction. The data demonstrated that Pintide, a peptide predominantly interacting with the PIN1 WW-domain, led to a significant reduction in the binding affinity of the NRF2 mimicking peptides. Moreover, we evaluated the impact of known PIN1 inhibitors (juglone, KPT-6566, and EGCG) on the PIN1-NRF2 interaction. Among the inhibitors, KPT-6566 showed the most potent inhibitory effect on PIN1-NRF2 interaction within an IC<jats:sub>50</jats:sub> range of 0.3–1.4 µM. Furthermore, our mass spectrometry analyses showed that KPT-6566 appeared to covalently modify PIN1 via conjugate addition, rather than disulfide exchange of the sulfonyl-acetate moiety. Altogether, such inhibitors would also be highly valuable molecular probes for further investigation of PIN1 regulation of NRF2 in the cellular context and potentially pave the way for drug molecules that specifically inhibit the cytoprotective effects of NRF2 in cancer."}],"title":"Identification and inhibition of PIN1-NRF2 protein–protein interactions through computational and biophysical approaches","date_created":"2025-04-08T11:12:20Z","year":"2025","article_number":"8907","doi":"10.1038/s41598-025-89342-0","publication_identifier":{"eissn":["2045-2322"]},"publication":"Scientific Reports","quality_controlled":"1","file":[{"file_size":5333058,"date_updated":"2025-04-10T06:21:11Z","access_level":"open_access","relation":"main_file","checksum":"6124a10402a67b66364cfa9350d35b4b","file_id":"19537","success":1,"creator":"dernst","file_name":"2025_ScientificReports_Ozleyen.pdf","content_type":"application/pdf","date_created":"2025-04-10T06:21:11Z"}],"has_accepted_license":"1","ddc":["570"]},{"month":"04","language":[{"iso":"eng"}],"date_published":"2025-04-04T00:00:00Z","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"date_updated":"2026-05-06T13:06:08Z","isi":1,"oa":1,"file_date_updated":"2025-04-10T06:12:49Z","DOAJ_listed":"1","_id":"19531","scopus_import":"1","article_type":"original","intvolume":"        10","oa_version":"Published Version","type":"journal_article","citation":{"mla":"Shiva Kumar, Abhishek, et al. “Massive Dirac-Pauli Physics in Lead-Halide Perovskites.” <i>Npj Quantum Materials</i>, vol. 10, 37, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41535-025-00754-7\">10.1038/s41535-025-00754-7</a>.","apa":"Shiva Kumar, A., Maslov, M., Lemeshko, M., Volosniev, A., &#38; Alpichshev, Z. (2025). Massive Dirac-Pauli physics in lead-halide perovskites. <i>Npj Quantum Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41535-025-00754-7\">https://doi.org/10.1038/s41535-025-00754-7</a>","chicago":"Shiva Kumar, Abhishek, Mikhail Maslov, Mikhail Lemeshko, Artem Volosniev, and Zhanybek Alpichshev. “Massive Dirac-Pauli Physics in Lead-Halide Perovskites.” <i>Npj Quantum Materials</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41535-025-00754-7\">https://doi.org/10.1038/s41535-025-00754-7</a>.","ama":"Shiva Kumar A, Maslov M, Lemeshko M, Volosniev A, Alpichshev Z. Massive Dirac-Pauli physics in lead-halide perovskites. <i>npj Quantum Materials</i>. 2025;10. doi:<a href=\"https://doi.org/10.1038/s41535-025-00754-7\">10.1038/s41535-025-00754-7</a>","ista":"Shiva Kumar A, Maslov M, Lemeshko M, Volosniev A, Alpichshev Z. 2025. Massive Dirac-Pauli physics in lead-halide perovskites. npj Quantum Materials. 10, 37.","ieee":"A. Shiva Kumar, M. Maslov, M. Lemeshko, A. Volosniev, and Z. Alpichshev, “Massive Dirac-Pauli physics in lead-halide perovskites,” <i>npj Quantum Materials</i>, vol. 10. Springer Nature, 2025.","short":"A. Shiva Kumar, M. Maslov, M. Lemeshko, A. Volosniev, Z. Alpichshev, Npj Quantum Materials 10 (2025)."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"day":"04","status":"public","OA_type":"gold","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"title":"Massive Dirac-Pauli physics in lead-halide perovskites","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"In standard quantum electrodynamics (QED), the so-called non-minimal (Pauli) coupling is suppressed for elementary particles and has no physical implications. Here, we show that the Pauli term naturally appears in a known family of Dirac materials—the lead-halide perovskites, suggesting a novel playground for the study of analog QED effects. We outline measurable manifestations of the Pauli term in the phenomena pertaining to (i) relativistic corrections to bound states (ii) the Klein paradox, and (iii) spin effects in scattering. In particular, we demonstrate that (a) the binding energy of an electron in the vicinity of a positively charged defect is noticeably decreased due to the polarizability of lead ions and the appearance of a Darwin-like term, (b) strong spin-orbit coupling due to the Pauli term affects the exciton states, and (c) scattering of an electron off an energy barrier with broken mirror symmetry produces spin polarization in the outgoing current. Our study adds to the understanding of quantum phenomena in lead-halide perovskites and paves the way for tabletop simulations of analog Dirac-Pauli equations."}],"external_id":{"isi":["001459830100002"]},"publication_status":"published","related_material":{"link":[{"url":"https://git.ista.ac.at/mmaslov/dirac_pauli_LHP","relation":"software"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Abhishek","last_name":"Shiva Kumar","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","full_name":"Shiva Kumar, Abhishek"},{"orcid":"0000-0003-4074-2570","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","full_name":"Maslov, Mikhail","last_name":"Maslov","first_name":"Mikhail"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev"},{"last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek"}],"OA_place":"publisher","volume":10,"has_accepted_license":"1","ddc":["530"],"corr_author":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-04-10T06:12:49Z","file_name":"2025_njpQuantumMaterials_Kumar.pdf","content_type":"application/pdf","access_level":"open_access","checksum":"08b1a94b362bb65482887e50020810e5","relation":"main_file","date_updated":"2025-04-10T06:12:49Z","file_size":592092,"file_id":"19536"}],"quality_controlled":"1","doi":"10.1038/s41535-025-00754-7","publication_identifier":{"eissn":["2397-4648"]},"publication":"npj Quantum Materials","APC_amount":"3054 EUR","year":"2025","date_created":"2025-04-08T18:13:06Z","article_number":"37"},{"OA_place":"publisher","volume":111,"author":[{"full_name":"Glasgow, Margalit","last_name":"Glasgow","first_name":"Margalit"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"last_name":"Sah","first_name":"Ashwin","full_name":"Sah, Ashwin"},{"first_name":"Mehtaab","last_name":"Sawhney","full_name":"Sawhney, Mehtaab"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A central limit theorem for the matching number of a sparse random graph","abstract":[{"lang":"eng","text":"In 1981, Karp and Sipser proved a law of large numbers for the matching number of a sparse Erdős–Rényi random graph, in an influential paper pioneering the so-called differential equation method for analysis of random graph processes. Strengthening this classical result, and answering a question of Aronson, Frieze and Pittel, we prove a central limit theorem in the same setting: the fluctuations in the matching number of a sparse random graph are asymptotically Gaussian. Our new contribution is to prove this central limit theorem in the subcritical and critical regimes, according to a celebrated algorithmic phase transition first observed by Karp and Sipser. Indeed, in the supercritical regime, a central limit theorem has recently been proved in the PhD thesis of Kreačić, using a stochastic generalisation of the differential equation method (comparing the so-called Karp–Sipser process to a system of stochastic differential equations). Our proof builds on these methods, and introduces new techniques to handle certain degeneracies present in the subcritical and critical cases. Curiously, our new techniques lead to a non-constructive result: we are able to characterise the fluctuations of the matching number around its mean, despite these fluctuations being much smaller than the error terms in our best estimates of the mean. We also prove a central limit theorem for the rank of the adjacency matrix of a sparse random graph."}],"publication_status":"published","external_id":{"arxiv":["2402.05851"],"isi":["001473087200024"]},"article_processing_charge":"Yes (via OA deal)","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication":"Journal of the London Mathematical Society","issue":"4","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"doi":"10.1112/jlms.70101","article_number":"e70101","year":"2025","date_created":"2025-04-13T22:01:19Z","ddc":["510"],"has_accepted_license":"1","file":[{"date_updated":"2025-04-15T13:18:43Z","file_size":392208,"relation":"main_file","checksum":"69ce9feaf64e776b99f3afd1041b1b11","access_level":"open_access","file_id":"19564","creator":"dernst","success":1,"content_type":"application/pdf","file_name":"2025_JourLondMathSoc_Glasgow.pdf","date_created":"2025-04-15T13:18:43Z"}],"quality_controlled":"1","corr_author":"1","_id":"19554","scopus_import":"1","acknowledgement":"We would like to thank Christina Goldschmidt and Eleonora Kreačić for insightful discussions and clarifications about their work in the thesis [26]. Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777. Ashwin Sah and Mehtaab Sawhney were supported by NSF Graduate Research Fellowship Program DGE-2141064. Ashwin Sah was supported by the PD Soros Fellowship.\r\nOpen access funding provided by Institute of Science and Technology Austria/KEMÖ.","type":"journal_article","article_type":"original","intvolume":"       111","oa_version":"Published Version","arxiv":1,"department":[{"_id":"MaKw"}],"publisher":"Wiley","date_updated":"2025-09-30T11:35:55Z","language":[{"iso":"eng"}],"month":"04","date_published":"2025-04-01T00:00:00Z","oa":1,"file_date_updated":"2025-04-15T13:18:43Z","isi":1,"day":"01","status":"public","OA_type":"hybrid","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"project":[{"_id":"bd95085b-d553-11ed-ba76-e55d3349be45","grant_number":"101076777","name":"Randomness and structure in combinatorics"}],"citation":{"mla":"Glasgow, Margalit, et al. “A Central Limit Theorem for the Matching Number of a Sparse Random Graph.” <i>Journal of the London Mathematical Society</i>, vol. 111, no. 4, e70101, Wiley, 2025, doi:<a href=\"https://doi.org/10.1112/jlms.70101\">10.1112/jlms.70101</a>.","chicago":"Glasgow, Margalit, Matthew Alan Kwan, Ashwin Sah, and Mehtaab Sawhney. “A Central Limit Theorem for the Matching Number of a Sparse Random Graph.” <i>Journal of the London Mathematical Society</i>. Wiley, 2025. <a href=\"https://doi.org/10.1112/jlms.70101\">https://doi.org/10.1112/jlms.70101</a>.","apa":"Glasgow, M., Kwan, M. A., Sah, A., &#38; Sawhney, M. (2025). A central limit theorem for the matching number of a sparse random graph. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.70101\">https://doi.org/10.1112/jlms.70101</a>","ama":"Glasgow M, Kwan MA, Sah A, Sawhney M. A central limit theorem for the matching number of a sparse random graph. <i>Journal of the London Mathematical Society</i>. 2025;111(4). doi:<a href=\"https://doi.org/10.1112/jlms.70101\">10.1112/jlms.70101</a>","ista":"Glasgow M, Kwan MA, Sah A, Sawhney M. 2025. A central limit theorem for the matching number of a sparse random graph. Journal of the London Mathematical Society. 111(4), e70101.","ieee":"M. Glasgow, M. A. Kwan, A. Sah, and M. Sawhney, “A central limit theorem for the matching number of a sparse random graph,” <i>Journal of the London Mathematical Society</i>, vol. 111, no. 4. Wiley, 2025.","short":"M. Glasgow, M.A. Kwan, A. Sah, M. Sawhney, Journal of the London Mathematical Society 111 (2025)."}}]