--- OA_type: closed access _id: '20868' abstract: - lang: eng text: Residents of low-latitude megacities face growing vulnerability to humid-heat stress under urbanization and global warming, yet limited research has assessed the morbidity burden of mental and behavioral disorders (MBDs) linked to humid-heat exposures in these cities. Here we quantify the hospital admissions of MBDs in Shanghai, a megacity of over 25 million inhabitants, attributable to humid heat, and project future burdens under various greenhouse gas (GHG)-emission and population scenarios. Humid heat drives a higher morbidity burden than high temperature alone, especially in humid-heat nights. Without population change, the humid-heat-related morbidity burden of MBDs would increase by 68.2% (95% empirical confidence interval 56.7%–81.6%) under the highest-GHG-emission scenario by the 2090s, while 8,465 (95% empirical confidence interval 6,928–10,053) cases would be avoided by reducing emissions to the lowest pathway. With projected population decline, the attributable hospital admissions will decrease toward century’s end. These findings highlight the benefit of GHG mitigation in reducing the growing MBD risks posed by extreme humid heat. acknowledgement: 'This research was supported by the National Natural Science Foundation of China (grants 42288101 and 42175066) and Shanghai International Science and Technology Partnership Project (grant 21230780200). G.S. is supported by the China Brain Project (grant 2025ZD0215100), the National Natural Science Foundation of China (grant 82150710554), the Chinese National Key Project (grant 2023YFE0199700), the National Natural Science Foundation of China (grant W2541022) and the EC Horizon Europe: environMENTAL project.' article_processing_charge: No article_type: original author: - first_name: Chen full_name: Liang, Chen last_name: Liang - first_name: Jiacan full_name: Yuan, Jiacan last_name: Yuan - first_name: Renhe full_name: Zhang, Renhe last_name: Zhang - first_name: Xu full_name: Tang, Xu last_name: Tang - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Jean-Charles full_name: Roy, Jean-Charles last_name: Roy - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Ulrike-Helene full_name: Taron, Ulrike-Helene last_name: Taron - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Karina full_name: Janson, Karina last_name: Janson - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Dennis full_name: van der Meer, Dennis last_name: van der Meer - first_name: Sara full_name: Fernández-Cabello, Sara last_name: Fernández-Cabello - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Álvaro full_name: Pastor, Álvaro last_name: Pastor - first_name: Guillem full_name: Feixas, Guillem last_name: Feixas - first_name: Francisco José full_name: Eiroa-Orosa, Francisco José last_name: Eiroa-Orosa - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Carina full_name: Mathey, Carina last_name: Mathey - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Abigail full_name: Miller, Abigail last_name: Miller - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Anastasios-Polykarpos full_name: Athanasiadis, Anastasios-Polykarpos last_name: Athanasiadis - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Yuxiang full_name: Dai, Yuxiang last_name: Dai - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Yuzhu full_name: Li, Yuzhu last_name: Li - first_name: Yanqing full_name: Zhang, Yanqing last_name: Zhang - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Kofoworola full_name: Agunbiade, Kofoworola last_name: Agunbiade - first_name: Xinyang full_name: Yu, Xinyang last_name: Yu - first_name: Zuo full_name: Zhang, Zuo last_name: Zhang - first_name: Di full_name: Chen, Di last_name: Chen - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Vanessa full_name: Köhler, Vanessa last_name: Köhler - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: George full_name: Ogoh, George last_name: Ogoh - first_name: Tamara full_name: Schikowski, Tamara last_name: Schikowski - first_name: Ragnhild full_name: Brandlistuen, Ragnhild last_name: Brandlistuen citation: ama: Liang C, Yuan J, Zhang R, et al. Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai. Nature Mental Health. 2025;3(12):1532-1544. doi:10.1038/s44220-025-00519-y apa: Liang, C., Yuan, J., Zhang, R., Tang, X., Schumann, G., Hitchen, E., … Brandlistuen, R. (2025). Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-025-00519-y chicago: Liang, Chen, Jiacan Yuan, Renhe Zhang, Xu Tang, Gunter Schumann, Esther Hitchen, Elli Polemiti, et al. “Projecting the Morbidity Burden of Mental and Behavioral Disorders Associated with Increasing Humid Heat in Shanghai.” Nature Mental Health. Springer Nature, 2025. https://doi.org/10.1038/s44220-025-00519-y. ieee: C. Liang et al., “Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai,” Nature Mental Health, vol. 3, no. 12. Springer Nature, pp. 1532–1544, 2025. ista: Liang C, Yuan J, Zhang R, Tang X, Schumann G, Hitchen E, Polemiti E, Serin E, Kebir H, Lett TA, Vaidya N, Roy J-C, Walter H, Heinz A, Ralser M, Twardziok S, Eils R, Jentsch M, Taron U-H, Schütz T, Schepanski K, Banaschewski T, Neidhart M, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Christmann N, Janson K, Nees F, Neidhart M, Seefried B, Aden R, Andreassen OA, Westlye LT, van der Meer D, Fernández-Cabello S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Marquand A, Bernas A, Novarino G, Slater M, Gallego J, Pastor Á, Feixas G, Eiroa-Orosa FJ, Nöthen MM, Forstner AJ, Claus I, Mathey C, Heilmann-Heimbach S, Hoffmann P, Miller A, Sommer P, Schmitt K, Wilbertz J, Patraskaki M, Jirsa V, Petkoski S, Athanasiadis A-P, Spanlang B, Pearmund C, Hese S, Renner P, Jia T, Chang X, Dai Y, Xia Y, Li Y, Zhang Y, Calhoun V, Thompson P, Clinton N, Desrivières S, Agunbiade K, Yu X, Zhang Z, Chen D, Young AH, Schwalber A, Köhler V, Stahl B, Ogoh G, Schikowski T, Brandlistuen R. 2025. Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai. Nature Mental Health. 3(12), 1532–1544. mla: Liang, Chen, et al. “Projecting the Morbidity Burden of Mental and Behavioral Disorders Associated with Increasing Humid Heat in Shanghai.” Nature Mental Health, vol. 3, no. 12, Springer Nature, 2025, pp. 1532–44, doi:10.1038/s44220-025-00519-y. short: C. Liang, J. Yuan, R. Zhang, X. Tang, G. Schumann, E. Hitchen, E. Polemiti, E. Serin, H. Kebir, T.A. Lett, N. Vaidya, J.-C. Roy, H. Walter, A. Heinz, M. Ralser, S. Twardziok, R. Eils, M. Jentsch, U.-H. Taron, T. Schütz, K. Schepanski, T. Banaschewski, M. Neidhart, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, N. Christmann, K. Janson, F. Nees, M. Neidhart, B. Seefried, R. Aden, O.A. Andreassen, L.T. Westlye, D. van der Meer, S. Fernández-Cabello, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, A. Marquand, A. Bernas, G. Novarino, M. Slater, J. Gallego, Á. Pastor, G. Feixas, F.J. Eiroa-Orosa, M.M. Nöthen, A.J. Forstner, I. Claus, C. Mathey, S. Heilmann-Heimbach, P. Hoffmann, A. Miller, P. Sommer, K. Schmitt, J. Wilbertz, M. Patraskaki, V. Jirsa, S. Petkoski, A.-P. Athanasiadis, B. Spanlang, C. Pearmund, S. Hese, P. Renner, T. Jia, X. Chang, Y. Dai, Y. Xia, Y. Li, Y. Zhang, V. Calhoun, P. Thompson, N. Clinton, S. Desrivières, K. Agunbiade, X. Yu, Z. Zhang, D. Chen, A.H. Young, A. Schwalber, V. Köhler, B. Stahl, G. Ogoh, T. Schikowski, R. Brandlistuen, Nature Mental Health 3 (2025) 1532–1544. date_created: 2025-12-29T12:11:28Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-01-05T12:02:29Z day: '01' department: - _id: GaNo doi: 10.1038/s44220-025-00519-y intvolume: ' 3' issue: '12' language: - iso: eng month: '12' oa_version: None page: 1532-1544 project: - _id: 349d1832-11ca-11ed-8bc3-d79b574010e0 grant_number: '101057429' name: Reducing the impact of major environmental challenges on mental health publication: Nature Mental Health publication_identifier: issn: - 2731-6076 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '15016' abstract: - lang: eng text: Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: 'We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion, and support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru (Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination; our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC, and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.); FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund (FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.); EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Eliza C.B. full_name: Jaeger, Eliza C.B. last_name: Jaeger - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic - first_name: Astrid full_name: Deryckere, Astrid last_name: Deryckere - first_name: Nikol full_name: Zorin, Nikol last_name: Zorin - first_name: Akemi L. full_name: Nguyen, Akemi L. last_name: Nguyen - first_name: Georgiy full_name: Ivanian, Georgiy id: eaf2b366-cfd1-11ee-bbdf-c8790f800a05 last_name: Ivanian - first_name: Jamie full_name: Woych, Jamie last_name: Woych - first_name: Rebecca C full_name: Arnold, Rebecca C id: d6cce458-14c9-11ed-a755-c1c8fc6fde6f last_name: Arnold - first_name: Alonso full_name: Ortega Gurrola, Alonso last_name: Ortega Gurrola - first_name: Arik full_name: Shvartsman, Arik last_name: Shvartsman - first_name: Francesca full_name: Barbieri, Francesca id: a9492887-8972-11ed-ae7b-bfae10998254 last_name: Barbieri - first_name: Florina-Alexandra full_name: Toma, Florina-Alexandra id: 85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5 last_name: Toma - first_name: Gary J. full_name: Gorbsky, Gary J. last_name: Gorbsky - first_name: Marko E. full_name: Horb, Marko E. last_name: Horb - first_name: Hollis T. full_name: Cline, Hollis T. last_name: Cline - first_name: Timothy F. full_name: Shay, Timothy F. last_name: Shay - first_name: Darcy B. full_name: Kelley, Darcy B. last_name: Kelley - first_name: Ayako full_name: Yamaguchi, Ayako last_name: Yamaguchi - first_name: Mark full_name: Shein-Idelson, Mark last_name: Shein-Idelson - first_name: Maria Antonietta full_name: Tosches, Maria Antonietta last_name: Tosches - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 2025;60(5):794-812.e6. doi:10.1016/j.devcel.2024.10.025 apa: Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.10.025 chicago: Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” Developmental Cell. Elsevier, 2025. https://doi.org/10.1016/j.devcel.2024.10.025. ieee: E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” Developmental Cell, vol. 60, no. 5. Elsevier, p. 794–812.e6, 2025. ista: Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6. mla: Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” Developmental Cell, vol. 60, no. 5, Elsevier, 2025, p. 794–812.e6, doi:10.1016/j.devcel.2024.10.025. short: E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6. corr_author: '1' date_created: 2024-02-20T09:20:32Z date_published: 2025-03-10T00:00:00Z date_updated: 2025-09-30T10:00:55Z day: '10' ddc: - '570' department: - _id: LoSw - _id: MaDe - _id: GaNo doi: 10.1016/j.devcel.2024.10.025 external_id: isi: - '001444798600001' pmid: - '39603234' file: - access_level: open_access checksum: a83a4cb58f5941096d3ad91ca0172594 content_type: application/pdf creator: dernst date_created: 2025-06-04T05:43:27Z date_updated: 2025-06-04T05:43:27Z file_id: '19790' file_name: 2025_DevelopmentalCell_Jaeger.pdf file_size: 11936258 relation: main_file success: 1 file_date_updated: 2025-06-04T05:43:27Z has_accepted_license: '1' intvolume: ' 60' isi: 1 issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 794-812.e6 pmid: 1 project: - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e grant_number: F7814 name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity' publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Adeno-associated viral tools to trace neural development and connectivity across amphibians tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 60 year: '2025' ... --- OA_type: closed access _id: '19444' 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. 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. article_processing_charge: No article_type: original author: - first_name: Sergiu P. full_name: Pașca, Sergiu P. last_name: Pașca - first_name: Paola full_name: Arlotta, Paola last_name: Arlotta - first_name: Helen S. full_name: Bateup, Helen S. last_name: Bateup - first_name: J. Gray full_name: Camp, J. Gray last_name: Camp - first_name: Silvia full_name: Cappello, Silvia last_name: Cappello - first_name: Fred H. full_name: Gage, Fred H. last_name: Gage - first_name: Jürgen A. full_name: Knoblich, Jürgen A. last_name: Knoblich - first_name: Arnold R. full_name: Kriegstein, Arnold R. last_name: Kriegstein - first_name: Madeline A. full_name: Lancaster, Madeline A. last_name: Lancaster - first_name: Guo Li full_name: Ming, Guo Li last_name: Ming - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Hideyuki full_name: Okano, Hideyuki last_name: Okano - first_name: Malin full_name: Parmar, Malin last_name: Parmar - first_name: In Hyun full_name: Park, In Hyun last_name: Park - first_name: Orly full_name: Reiner, Orly last_name: Reiner - first_name: Hongjun full_name: Song, Hongjun last_name: Song - first_name: Lorenz full_name: Studer, Lorenz last_name: Studer - first_name: Jun full_name: Takahashi, Jun last_name: Takahashi - first_name: Sally full_name: Temple, Sally last_name: Temple - first_name: Giuseppe full_name: Testa, Giuseppe last_name: Testa - first_name: Barbara full_name: Treutlein, Barbara last_name: Treutlein - first_name: Flora M. full_name: Vaccarino, Flora M. last_name: Vaccarino - first_name: Pierre full_name: Vanderhaeghen, Pierre last_name: Vanderhaeghen - first_name: Tracy full_name: Young-Pearse, Tracy last_name: Young-Pearse citation: ama: Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids and transplantation studies. Nature. 2025;639(8054):315-320. doi:10.1038/s41586-024-08487-6 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. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-08487-6 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.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-024-08487-6. ieee: S. P. Pașca et al., “A framework for neural organoids, assembloids and transplantation studies,” Nature, vol. 639, no. 8054. Springer Nature, pp. 315–320, 2025. 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. mla: Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” Nature, vol. 639, no. 8054, Springer Nature, 2025, pp. 315–20, doi:10.1038/s41586-024-08487-6. 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. date_created: 2025-03-23T23:01:27Z date_published: 2025-03-13T00:00:00Z date_updated: 2025-09-30T11:13:47Z day: '13' department: - _id: GaNo doi: 10.1038/s41586-024-08487-6 external_id: isi: - '001437461900001' pmid: - '39653126' intvolume: ' 639' isi: 1 issue: '8054' language: - iso: eng month: '03' oa_version: None page: 315-320 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A framework for neural organoids, assembloids and transplantation studies type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 639 year: '2025' ... --- OA_place: publisher _id: '19557' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: ScienComp acknowledgement: "The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lena A full_name: Schwarz, Lena A id: 29A8453C-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz citation: ama: Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:10.15479/AT-ISTA-19557 apa: Schwarz, L. A. (2025). Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19557 chicago: Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19557. ieee: L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025. ista: Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria. mla: Schwarz, Lena A. Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19557. short: L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-14T06:59:06Z date_published: 2025-04-14T00:00:00Z date_updated: 2026-04-14T09:07:14Z day: '14' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/AT-ISTA-19557 file: - access_level: closed checksum: 50290a8604edb0a720387f01e9d59fe4 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lschwarz date_created: 2025-04-15T08:43:36Z date_updated: 2025-04-15T08:43:36Z file_id: '19561' file_name: Schwarz_Thesis_2025_FINAL.docx file_size: 21783427 relation: source_file - access_level: closed checksum: ed028488180ac4901e018ef1c330cf01 content_type: application/pdf creator: lschwarz date_created: 2025-04-15T08:43:42Z date_updated: 2026-03-27T13:15:08Z embargo: 2026-10-15 embargo_to: open_access file_id: '19562' file_name: Schwarz_Thesis_2025_FINALpdfa.pdf file_size: 11432175 relation: main_file file_date_updated: 2026-03-27T13:15:08Z has_accepted_license: '1' language: - iso: eng month: '04' oa_version: Published Version page: '124' project: - _id: 9B91375C-BA93-11EA-9121-9846C619BF3A grant_number: '707964' name: Critical windows and reversibility of ASD associated with mutations in chromatin remodelers - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public - id: '9429' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19704' abstract: - lang: eng text: The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: ScienComp - _id: PreCl - _id: M-Shop - _id: E-Lib acknowledgement: 'We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Michał full_name: Januszewski, Michał last_name: Januszewski - first_name: Vitali full_name: Vistunou, Vitali id: 7e146587-8972-11ed-ae7b-d7a32ea86a81 last_name: Vistunou - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Viren full_name: Jain, Viren last_name: Jain - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 2025;642:398-410. doi:10.1038/s41586-025-08985-1 apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08985-1 chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-08985-1. ieee: M. Tavakoli et al., “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” Nature, vol. 642. Springer Nature, pp. 398–410, 2025. ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410. mla: Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” Nature, vol. 642, Springer Nature, 2025, pp. 398–410, doi:10.1038/s41586-025-08985-1. short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410. corr_author: '1' date_created: 2025-05-18T22:02:51Z date_published: 2025-06-12T00:00:00Z date_updated: 2026-04-28T13:33:34Z day: '12' ddc: - '570' department: - _id: JoDa - _id: GradSch - _id: Bio - _id: GaNo doi: 10.1038/s41586-025-08985-1 ec_funded: 1 external_id: isi: - '001483477000001' pmid: - '40335689' file: - access_level: open_access checksum: ebc99d7108e728f46db0a009292675ef content_type: application/pdf creator: dernst date_created: 2025-07-03T06:55:20Z date_updated: 2025-07-03T06:55:20Z file_id: '19959' file_name: 2025_Nature_Tavakoli.pdf file_size: 133201290 relation: main_file success: 1 file_date_updated: 2025-07-03T06:55:20Z has_accepted_license: '1' intvolume: ' 642' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 398-410 pmid: 1 project: - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/ record: - id: '18677' relation: earlier_version status: public - id: '18697' relation: research_data status: public scopus_import: '1' status: public title: Light-microscopy-based connectomic reconstruction of mammalian brain tissue tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 642 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20662' abstract: - lang: eng text: Task-based functional magnetic resonance imaging (fMRI) reveals individual differences in neural correlates of cognition but faces scalability challenges due to cognitive demands, protocol variability, and limited task coverage in large datasets. Here, we propose DeepTaskGen, a deep-learning approach that synthesizes non-acquired task-based contrast maps from resting-state (rs-) fMRI. We validate this approach using the Human Connectome Project lifespan data, then generate 47 contrast maps from 7 different cognitive tasks for over 20,000 individuals from UK Biobank. DeepTaskGen outperforms several benchmarks in generating synthetic task-contrast maps, achieving superior reconstruction performance while retaining inter-individual variation essential for biomarker development. We further show comparable or superior predictive performance of synthetic maps relative to actual maps and rs-connectomes across diverse demographic, cognitive, and clinical variables. This approach facilitates the study of individual differences and the generation of task-related biomarkers by enabling the generation of arbitrary functional cognitive tasks from readily available rs-fMRI data. acknowledgement: 'Funded by the European Union (Grant agreement No 101057429). Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10131373 and 10038599) and the National Key R&D Program of Ministry of Science and Technology of China (MOST 2023YFE0199700). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA), UKRI or MOST. Neither the European Union nor HADEA nor UKRI nor MOST can be held responsible for them. This work has also been supported by a Grant from the German Research Foundation to the ENIGMA task-based fMRI Working Group (DFG ER 724/4–1, WA 1539/11–1). Data used in this study were provided in part by the Human Connectome Project, WU-Minn Consortium (principal investigators: D. Van Essen and K. Ugurbil; grant number 1U54MH091657), funded by the 16 National Institutes of Health (NIH) institutes and centers supporting the NIH Blueprint for Neuroscience Research, and by the McDonnell Center for Systems Neuroscience at Washington University. Additionally, this research utilized data obtained from UK Biobank, a large-scale biomedical database. Open Access funding enabled and organized by Projekt DEAL.' article_number: '1572' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Kerstin full_name: Ritter, Kerstin last_name: Ritter - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: George full_name: Ogoh, George last_name: Ogoh - first_name: Bernd Carsten full_name: Stahl, Bernd Carsten last_name: Stahl - first_name: Ragnhild full_name: Brandlistuen, Ragnhild last_name: Brandlistuen - first_name: Tamara full_name: Schikowski, Tamara last_name: Schikowski - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Yu full_name: Xinyang, Yu last_name: Xinyang - first_name: Zuo full_name: Zhang, Zuo last_name: Zhang - first_name: Kofoworola full_name: Agunbiade, Kofoworola last_name: Agunbiade - first_name: Di full_name: Chen, Di last_name: Chen - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Venessa full_name: Köhler, Venessa last_name: Köhler - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Vince D. full_name: Calhoun, Vince D. last_name: Calhoun - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Yanqing full_name: Zhang, Yanqing last_name: Zhang - first_name: Yuzhu full_name: Li, Yuzhu last_name: Li - first_name: Yuxiang full_name: Dai, Yuxiang last_name: Dai - first_name: Jiacan full_name: Yuan, Jiacan last_name: Yuan - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Johannes H. full_name: Wilbertz, Johannes H. last_name: Wilbertz - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Carina M. full_name: Mathey, Carina M. last_name: Mathey - first_name: Abigail J. full_name: Miller, Abigail J. last_name: Miller - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Reiya full_name: Itatani, Reiya last_name: Itatani - first_name: Francisco full_name: Eiroa-Orosa, Francisco last_name: Eiroa-Orosa - first_name: Guillem full_name: Feixas, Guillem last_name: Feixas - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Karina full_name: Janson, Karina last_name: Janson - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Jean Charles full_name: Roy, Jean Charles last_name: Roy - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann citation: ama: Serin E, Ritter K, Schumann G, et al. Generating synthetic task-based brain fingerprints for population neuroscience using deep learning. Communications Biology. 2025;8. doi:10.1038/s42003-025-09158-6 apa: Serin, E., Ritter, K., Schumann, G., Banaschewski, T., Marquand, A., Walter, H., … Schumann, G. (2025). Generating synthetic task-based brain fingerprints for population neuroscience using deep learning. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-025-09158-6 chicago: Serin, Emin, Kerstin Ritter, Gunter Schumann, Tobias Banaschewski, Andre Marquand, Henrik Walter, George Ogoh, et al. “Generating Synthetic Task-Based Brain Fingerprints for Population Neuroscience Using Deep Learning.” Communications Biology. Springer Nature, 2025. https://doi.org/10.1038/s42003-025-09158-6. ieee: E. Serin et al., “Generating synthetic task-based brain fingerprints for population neuroscience using deep learning,” Communications Biology, vol. 8. Springer Nature, 2025. ista: Serin E, Ritter K, Schumann G, Banaschewski T, Marquand A, Walter H, Ogoh G, Stahl BC, Brandlistuen R, Schikowski T, Young AH, Xinyang Y, Zhang Z, Agunbiade K, Chen D, Desrivières S, Clinton N, Thompson P, Köhler V, Schwalber A, Calhoun VD, Chang X, Zhang Y, Li Y, Dai Y, Yuan J, Xia Y, Jia T, Renner P, Hese S, Spanlang B, Pearmund C, Athanasiadis AP, Petkoski S, Jirsa V, Schmitt K, Wilbertz JH, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller AJ, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Itatani R, Eiroa-Orosa F, Feixas G, Slater M, Novarino G, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Janson K, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Schumann G. 2025. Generating synthetic task-based brain fingerprints for population neuroscience using deep learning. Communications Biology. 8, 1572. mla: Serin, Emin, et al. “Generating Synthetic Task-Based Brain Fingerprints for Population Neuroscience Using Deep Learning.” Communications Biology, vol. 8, 1572, Springer Nature, 2025, doi:10.1038/s42003-025-09158-6. short: E. Serin, K. Ritter, G. Schumann, T. Banaschewski, A. Marquand, H. Walter, G. Ogoh, B.C. Stahl, R. Brandlistuen, T. Schikowski, A.H. Young, Y. Xinyang, Z. Zhang, K. Agunbiade, D. Chen, S. Desrivières, N. Clinton, P. Thompson, V. Köhler, A. Schwalber, V.D. Calhoun, X. Chang, Y. Zhang, Y. Li, Y. Dai, J. Yuan, Y. Xia, T. Jia, P. Renner, S. Hese, B. Spanlang, C. Pearmund, A.P. Athanasiadis, S. Petkoski, V. Jirsa, K. Schmitt, J.H. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A.J. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, R. Itatani, F. Eiroa-Orosa, G. Feixas, M. Slater, G. Novarino, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Janson, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, G. Schumann, Communications Biology 8 (2025). date_created: 2025-11-23T23:01:38Z date_published: 2025-12-01T00:00:00Z date_updated: 2025-12-01T15:24:07Z day: '01' ddc: - '570' department: - _id: GaNo doi: 10.1038/s42003-025-09158-6 external_id: isi: - '001614464000001' pmid: - '41238730' file: - access_level: open_access checksum: b8b3c1abe7048a09b920082a37e786a5 content_type: application/pdf creator: dernst date_created: 2025-11-24T09:12:19Z date_updated: 2025-11-24T09:12:19Z file_id: '20675' file_name: 2025_CommunicationsBiology_Serin.pdf file_size: 1588155 relation: main_file success: 1 file_date_updated: 2025-11-24T09:12:19Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Communications Biology publication_identifier: eissn: - 2399-3642 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Generating synthetic task-based brain fingerprints for population neuroscience using deep learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20731' abstract: - lang: eng text: The adult human brain, under resting conditions, consumes approximately 20% of total body glucose, a demand that is even higher during the first decade of life. The brain metabolic landscape is intricately regulated throughout development, and each cell type exhibits distinct metabolic signatures at each specific stage. This picture becomes even more intricate when considering that metabolism is dynamically modulated to sustain critical biological processes, such as cell proliferation and differentiation and synaptic activity–dependent processes. The orchestration between metabolic regulation and the aforementioned physiological processes often relies on metabolism-dependent changes in the epigenetic landscape, which shape gene expression patterns to trigger selected downstream biological responses. Perturbations of brain metabolic pathways are frequently the cause of severe neurodevelopmental disorders. This review explores the latest insights into the regulation of brain metabolism in health and disease. acknowledgement: Funding provided by the European Union (grant 101057429) to G.N. article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Domenico full_name: Marano, Domenico id: 3b004c42-803f-11ed-ab7e-ecee8f08bd58 last_name: Marano - first_name: Vittoria full_name: Mariano, Vittoria id: ee829c33-edb3-11ed-b4fb-c020aaca4b01 last_name: Mariano - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Marano D, Mariano V, Novarino G. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 2025;59:415-434. doi:10.1146/annurev-genet-111523-102424' apa: 'Marano, D., Mariano, V., & Novarino, G. (2025). Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-111523-102424' chicago: 'Marano, Domenico, Vittoria Mariano, and Gaia Novarino. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review of Genetics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-genet-111523-102424.' ieee: 'D. Marano, V. Mariano, and G. Novarino, “Fueling the mind: Brain metabolism in health and neurodevelopmental disorders,” Annual Review of Genetics, vol. 59. Annual Reviews, pp. 415–434, 2025.' ista: 'Marano D, Mariano V, Novarino G. 2025. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 59, 415–434.' mla: 'Marano, Domenico, et al. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review of Genetics, vol. 59, Annual Reviews, 2025, pp. 415–34, doi:10.1146/annurev-genet-111523-102424.' short: D. Marano, V. Mariano, G. Novarino, Annual Review of Genetics 59 (2025) 415–434. corr_author: '1' date_created: 2025-12-07T23:02:01Z date_published: 2025-11-03T00:00:00Z date_updated: 2025-12-09T12:55:11Z day: '03' ddc: - '570' department: - _id: GaNo doi: 10.1146/annurev-genet-111523-102424 external_id: pmid: - '40902207' file: - access_level: open_access checksum: 1000228dc9aca3d48e92605607a99c41 content_type: application/pdf creator: dernst date_created: 2025-12-09T12:53:09Z date_updated: 2025-12-09T12:53:09Z file_id: '20745' file_name: 2025_AnnualRevGenetics_Marano.pdf file_size: 3629986 relation: main_file success: 1 file_date_updated: 2025-12-09T12:53:09Z has_accepted_license: '1' intvolume: ' 59' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 415-434 pmid: 1 project: - _id: 349d1832-11ca-11ed-8bc3-d79b574010e0 grant_number: '101057429' name: Reducing the impact of major environmental challenges on mental health publication: Annual Review of Genetics publication_identifier: eissn: - 1545-2948 issn: - 0066-4197 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: 'Fueling the mind: Brain metabolism in health and neurodevelopmental disorders' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 59 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '14257' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julia M full_name: Michalska, Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska orcid: 0000-0003-3862-1235 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Hana full_name: Korinkova, Hana id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed last_name: Korinkova - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Karl full_name: Roessler, Karl last_name: Roessler - first_name: Thomas full_name: Czech, Thomas last_name: Czech - first_name: Romana full_name: Höftberger, Romana last_name: Höftberger - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2024;42:1051-1064. doi:10.1038/s41587-023-01911-8 apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8 chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2024. https://doi.org/10.1038/s41587-023-01911-8. ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology, vol. 42. Springer Nature, pp. 1051–1064, 2024. ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064. mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:10.1038/s41587-023-01911-8. short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064. corr_author: '1' date_created: 2023-09-03T22:01:15Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-14T08:34:35Z day: '01' ddc: - '570' department: - _id: SaSi - _id: GaNo - _id: PeJo - _id: JoDa - _id: Bio - _id: RySh doi: 10.1038/s41587-023-01911-8 ec_funded: 1 external_id: isi: - '001065254200001' pmid: - '37653226' file: - access_level: open_access checksum: 57d5fafb16f02dcb9f7dddb1bd7e2a71 content_type: application/pdf creator: dernst date_created: 2025-01-09T07:48:01Z date_updated: 2025-01-09T07:48:01Z file_id: '18784' file_name: 2024_NatureBiotech_Michalska.pdf file_size: 26065165 relation: main_file success: 1 file_date_updated: 2025-01-09T07:48:01Z has_accepted_license: '1' intvolume: ' 42' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1051-1064 pmid: 1 project: - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: 23889792-32DE-11EA-91FC-C7463DDC885E grant_number: LS18-022 name: High content imaging to decode human immune cell interactions in health and allergic disease - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/danzllab/CATS record: - id: '18660' relation: dissertation_contains status: deleted - id: '13126' relation: research_data status: public - id: '18674' relation: dissertation_contains status: public scopus_import: '1' status: public title: Imaging brain tissue architecture across millimeter to nanometer scales tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2024' ... --- _id: '15385' abstract: - lang: eng text: "Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)" acknowledged_ssus: - _id: PreCl - _id: M-Shop - _id: LifeSc - _id: Bio acknowledgement: 'We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ' article_processing_charge: No author: - first_name: Laura full_name: Burnett, Laura id: 3B717F68-F248-11E8-B48F-1D18A9856A87 last_name: Burnett orcid: 0000-0002-8937-410X - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova orcid: 0000-0003-2012-9947 - first_name: Tomas full_name: Masson, Tomas id: 93ac43e8-8599-11eb-9b86-f6efb0a4c207 last_name: Masson orcid: 0000-0002-2634-6283 - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 citation: ama: Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:10.15479/AT:ISTA:15385 apa: Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:15385 chicago: Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:15385. ieee: L. Burnett et al., “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024. ista: Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, 10.15479/AT:ISTA:15385. mla: Burnett, Laura, et al. Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:15385. short: L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024). corr_author: '1' date_created: 2024-05-13T15:04:04Z date_published: 2024-05-15T00:00:00Z date_updated: 2025-09-08T07:57:11Z day: '15' ddc: - '570' department: - _id: MaJö - _id: PreCl - _id: SiHi - _id: RySh - _id: GaNo doi: 10.15479/AT:ISTA:15385 file: - access_level: open_access checksum: 9205eb0876f0f08552dbad80d6884b4b content_type: application/zip creator: mjoesch date_created: 2024-05-15T06:09:17Z date_updated: 2024-05-15T06:09:17Z file_id: '15396' file_name: PatchClamp.zip file_size: '1149617663' relation: main_file success: 1 - access_level: open_access content_type: application/zip creator: mjoesch date_created: 2024-05-15T06:09:12Z date_updated: 2024-05-15T06:09:12Z file_id: '15397' file_name: SiliconProbe.zip file_size: '564903112' relation: main_file success: 1 - access_level: open_access checksum: 49a807bbab06b5fada38f532e2176e2e content_type: application/zip creator: mjoesch date_created: 2024-05-15T06:09:14Z date_updated: 2024-05-15T06:09:14Z file_id: '15398' file_name: WesternBlot.zip file_size: '11685703' relation: main_file success: 1 - access_level: open_access checksum: beeeeaa43770090f3b291209ed6b0623 content_type: application/zip creator: mjoesch date_created: 2024-05-15T06:09:38Z date_updated: 2024-05-15T06:09:38Z file_id: '15399' file_name: Behaviour.zip file_size: '1335626779' relation: main_file success: 1 - access_level: open_access checksum: 8862ad7719388304d1d19f8e7db8bb00 content_type: text/plain creator: mjoesch date_created: 2024-05-16T09:08:20Z date_updated: 2024-05-16T09:08:20Z file_id: '15400' file_name: Readme_Data.txt file_size: 18841 relation: main_file success: 1 file_date_updated: 2024-05-16T09:08:20Z has_accepted_license: '1' keyword: - ASD - periaqueductal gray - perception - behavior - potassium channels month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '17142' relation: used_in_publication status: public status: public title: Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2024' ... --- _id: '17091' abstract: - lang: eng text: DNA sequences are connected to genes and functions in the developing and adult brain article_processing_charge: No article_type: letter_note author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Christoph full_name: Bock, Christoph last_name: Bock citation: ama: Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. Science. 2024;384(6698):860-861. doi:10.1126/science.adp4663 apa: Novarino, G., & Bock, C. (2024). Mapping the brain’s gene-regulatory maze. Science. AAAS. https://doi.org/10.1126/science.adp4663 chicago: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” Science. AAAS, 2024. https://doi.org/10.1126/science.adp4663. ieee: G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” Science, vol. 384, no. 6698. AAAS, pp. 860–861, 2024. ista: Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science. 384(6698), 860–861. mla: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” Science, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:10.1126/science.adp4663. short: G. Novarino, C. Bock, Science 384 (2024) 860–861. corr_author: '1' date_created: 2024-06-02T22:00:57Z date_published: 2024-05-24T00:00:00Z date_updated: 2025-09-08T07:40:10Z day: '24' department: - _id: GaNo doi: 10.1126/science.adp4663 external_id: isi: - '001230076500007' pmid: - '38781359' intvolume: ' 384' isi: 1 issue: '6698' language: - iso: eng month: '05' oa_version: None page: 860-861 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: Mapping the brain’s gene-regulatory maze type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 384 year: '2024' ... --- APC_amount: 6081,83 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17142' abstract: - lang: eng text: Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD. acknowledgement: 'This work was supported by a European Research Council Starting Grant 756502 (MJ). ' article_number: e3002668 article_processing_charge: Yes article_type: original author: - first_name: Laura full_name: Burnett, Laura id: 3B717F68-F248-11E8-B48F-1D18A9856A87 last_name: Burnett orcid: 0000-0002-8937-410X - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova orcid: 0000-0003-2012-9947 - first_name: Tomas full_name: Masson, Tomas id: 93ac43e8-8599-11eb-9b86-f6efb0a4c207 last_name: Masson orcid: 0000-0002-2634-6283 - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 citation: ama: Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 2024;22. doi:10.1371/journal.pbio.3002668 apa: Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002668 chicago: Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” PLoS Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pbio.3002668. ieee: L. Burnett et al., “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” PLoS Biology, vol. 22. Public Library of Science, 2024. ista: Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 22, e3002668. mla: Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” PLoS Biology, vol. 22, e3002668, Public Library of Science, 2024, doi:10.1371/journal.pbio.3002668. short: L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22 (2024). corr_author: '1' date_created: 2024-06-16T22:01:05Z date_published: 2024-06-10T00:00:00Z date_updated: 2025-09-08T07:57:11Z day: '10' ddc: - '570' department: - _id: RySh - _id: GaNo - _id: MaJö doi: 10.1371/journal.pbio.3002668 ec_funded: 1 external_id: isi: - '001246176800003' pmid: - '38857283' file: - access_level: open_access checksum: 496e1aa4fd5b92b7e4087ecc2c964133 content_type: application/pdf creator: dernst date_created: 2025-01-09T10:39:41Z date_updated: 2025-01-09T10:39:41Z file_id: '18805' file_name: 2024_PloS_Burnett.pdf file_size: 4016568 relation: main_file success: 1 file_date_updated: 2025-01-09T10:39:41Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention publication: PLoS Biology publication_identifier: eissn: - 1545-7885 issn: - 1544-9173 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://doi.org/10.5281/zenodo.11130587 record: - id: '15385' relation: research_data status: public scopus_import: '1' status: public title: Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 22 year: '2024' ... --- OA_place: repository _id: '18677' abstract: - lang: eng text: The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner. acknowledged_ssus: - _id: E-Lib - _id: M-Shop - _id: LifeSc - _id: Bio - _id: ScienComp acknowledgement: "We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n" article_processing_charge: No author: - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Michał full_name: Januszewski, Michał last_name: Januszewski - first_name: Vitali full_name: Vistunou, Vitali id: 7e146587-8972-11ed-ae7b-d7a32ea86a81 last_name: Vistunou - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Viren full_name: Jain, Viren last_name: Jain - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv. doi:10.1101/2024.03.01.582884 apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv. https://doi.org/10.1101/2024.03.01.582884 chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” BioRxiv, n.d. https://doi.org/10.1101/2024.03.01.582884. ieee: M. Tavakoli et al., “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” bioRxiv. . ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, 10.1101/2024.03.01.582884. mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” BioRxiv, doi:10.1101/2024.03.01.582884. short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.). corr_author: '1' date_created: 2024-12-18T14:48:24Z date_published: 2024-07-08T00:00:00Z date_updated: 2026-04-28T13:33:34Z day: '08' department: - _id: GaNo - _id: JoDa doi: 10.1101/2024.03.01.582884 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.03.01.582884 month: '07' oa: 1 oa_version: Preprint project: - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: bioRxiv publication_status: draft related_material: record: - id: '18681' relation: dissertation_contains status: public - id: '18674' relation: dissertation_contains status: public - id: '19704' relation: later_version status: public status: public title: Light-microscopy based dense connectomic reconstruction of mammalian brain tissue tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18779' abstract: - lang: eng text: Unsupervised segmentation in biological and non-biological images is only partially resolved. Segmentation either requires arbitrary thresholds or large teaching datasets. Here, we propose a spatial autocorrelation method based on Local Moran’s I coefficient to differentiate signal, background, and noise in any type of image. The method, originally described for geoinformatics, does not require a predefined intensity threshold or teaching algorithm for image segmentation and allows quantitative comparison of samples obtained in different conditions. It utilizes relative intensity as well as spatial information of neighboring elements to select spatially contiguous groups of pixels. We demonstrate that Moran’s method outperforms threshold-based method in both artificially generated as well as in natural images especially when background noise is substantial. This superior performance can be attributed to the exclusion of false positive pixels resulting from isolated, high intensity pixels in high noise conditions. To test the method’s power in real situation, we used high power confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3 (A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution of these clusters displayed strong correlation with large sensory axon terminals of subcortical origin. The unique association of the special presynaptic terminals and a postsynaptic voltage-gated ion channel cluster was confirmed with electron microscopy. These data demonstrate that Moran’s method is a rapid, simple image segmentation method optimal for variable and high noise conditions. acknowledgement: "This research was supported by the Wellcome Trust (ZN, LA). In addition, LA was supported by an ERC Advanced Grant (FRONTHAL, 742595) and the European Union project RRF-2.3.1-\r\n21-2022-00004 within the framework of the Artificial Intelligence National Laboratory and Lendület_2023_90. ZN is the recipient of a Hungarian Academy of Sciences Momentum Grant (Lendület, LP2012-29) and an ERC Advanced Grant (293681). We thank the Light Microscopy Center at Institute of Experimental Medicine for kindly providing microscopy support. Authors would like to express their deepest gratitude to Prof Luc Anselin (Center for Spatial Data Science, University of Chicago) and Dr Szabolcs Káli (Instiute of Experimental Medicine, Budapest) for the valuable discussion about analysis of spatial association, and to Krisztina Faddi for the excellent technical assistance. " article_number: '89361' article_processing_charge: Yes article_type: original author: - first_name: Csaba full_name: Dávid, Csaba last_name: Dávid - first_name: Kristóf full_name: Giber, Kristóf last_name: Giber - first_name: Margit Katalin full_name: Szigeti, Margit Katalin id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87 last_name: Szigeti orcid: 0000-0001-9500-8758 - first_name: Mihály full_name: Köllő, Mihály last_name: Köllő - first_name: Zoltan full_name: Nusser, Zoltan last_name: Nusser - first_name: Laszlo full_name: Acsady, Laszlo last_name: Acsady citation: ama: Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. eLife. 2024;12. doi:10.7554/elife.89361 apa: Dávid, C., Giber, K., Szigeti, M. K., Köllő, M., Nusser, Z., & Acsady, L. (2024). A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.89361 chicago: Dávid, Csaba, Kristóf Giber, Margit Katalin Szigeti, Mihály Köllő, Zoltan Nusser, and Laszlo Acsady. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.89361. ieee: C. Dávid, K. Giber, M. K. Szigeti, M. Köllő, Z. Nusser, and L. Acsady, “A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus,” eLife, vol. 12. eLife Sciences Publications, 2024. ista: Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. 2024. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. eLife. 12, 89361. mla: Dávid, Csaba, et al. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” ELife, vol. 12, 89361, eLife Sciences Publications, 2024, doi:10.7554/elife.89361. short: C. Dávid, K. Giber, M.K. Szigeti, M. Köllő, Z. Nusser, L. Acsady, ELife 12 (2024). date_created: 2025-01-08T13:25:45Z date_published: 2024-12-10T00:00:00Z date_updated: 2025-01-08T13:37:04Z day: '10' ddc: - '570' department: - _id: GaNo doi: 10.7554/elife.89361 file: - access_level: open_access checksum: 1d64265f62a3bf14550b4f5c684f1782 content_type: application/pdf creator: dernst date_created: 2025-01-08T13:33:05Z date_updated: 2025-01-08T13:33:05Z file_id: '18780' file_name: 2024_eLife_David.pdf file_size: 9992462 relation: main_file success: 1 file_date_updated: 2025-01-08T13:33:05Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2024' ... --- OA_type: closed access _id: '19446' abstract: - lang: eng text: This Comment explores new approaches to enrich large-scale population data, including incorporating macro-environmental and digital health measures. acknowledgement: Funded by the European Union. Complementary funding was received by the UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10041392 and 10038599). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA) or UKRI. The European Union, HADEA and UKRI cannot be held responsible for them. This work received also support from Chinese Ministry for Science and Technology (MOST), the Horizon 2020-funded European Research Council Advanced Grant ‘STRATIFY’ (695313), the German Research Foundation (COPE; 675346; NE 1383/15-1 (CoviDrug)) and the National Natural Science Foundation of China grant 82150710554. article_processing_charge: No article_type: letter_note author: - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Nathalie E. full_name: Holz, Nathalie E. last_name: Holz - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Sebastian full_name: Siehl, Sebastian last_name: Siehl - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Jean Charles full_name: Roy, Jean Charles last_name: Roy - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Jamie full_name: Banks, Jamie last_name: Banks - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Karina full_name: Jansone, Karina last_name: Jansone - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Lena full_name: Marr, Lena id: 4406F586-F248-11E8-B48F-1D18A9856A87 last_name: Marr - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Guillem Feixas full_name: Viapiana, Guillem Feixas last_name: Viapiana - first_name: Francisco Eiroa full_name: Orosa, Francisco Eiroa last_name: Orosa - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Abigail full_name: Miller, Abigail last_name: Miller - first_name: Carina M. full_name: Mathey, Carina M. last_name: Mathey - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Séverine full_name: Pitel, Séverine last_name: Pitel - first_name: Lisa full_name: Otten, Lisa last_name: Otten - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Elena full_name: Alvarez, Elena last_name: Alvarez - first_name: Mavi full_name: Sanchez, Mavi last_name: Sanchez - first_name: Arantxa full_name: Giner, Arantxa last_name: Giner - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Yanting full_name: Gong, Yanting last_name: Gong - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Jingyu full_name: Liu, Jingyu last_name: Liu - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: George full_name: Ogoh, George last_name: Ogoh citation: ama: Nees F, Renner P, Holz NE, et al. Large-scale population data enrichment in mental health research. Nature Mental Health. 2024;2(10):1124-1127. doi:10.1038/s44220-024-00316-z apa: Nees, F., Renner, P., Holz, N. E., Polemiti, E., Siehl, S., Hese, S., … Ogoh, G. (2024). Large-scale population data enrichment in mental health research. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00316-z chicago: Nees, Frauke, Paul Renner, Nathalie E. Holz, Elli Polemiti, Sebastian Siehl, Sören Hese, Kerstin Schepanski, et al. “Large-Scale Population Data Enrichment in Mental Health Research.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00316-z. ieee: F. Nees et al., “Large-scale population data enrichment in mental health research,” Nature Mental Health, vol. 2, no. 10. Springer Nature, pp. 1124–1127, 2024. ista: Nees F, Renner P, Holz NE, Polemiti E, Siehl S, Hese S, Schepanski K, Schumann G, Walter H, Heinz A, Ralser M, Twardziok S, Vaidya N, Bernas A, Serin E, Jentsch M, Hitchen E, Kebir H, Lett TA, Roy JC, Eils R, Taron UH, Schütz T, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Seefried B, Aden R, Andreassen OA, Westlye LT, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Marquand A, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J, Pastor A, Forstner AJ, Hoffmann P, Nöthen MM, Claus I, Miller A, Mathey CM, Heilmann-Heimbach S, Sommer P, Patraskaki M, Wilbertz J, Schmitt K, Jirsa V, Petkoski S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez M, Giner A, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J, Schwalber A, Thompson P, Clinton N, Desrivières S, Young AH, Stahl B, Ogoh G. 2024. Large-scale population data enrichment in mental health research. Nature Mental Health. 2(10), 1124–1127. mla: Nees, Frauke, et al. “Large-Scale Population Data Enrichment in Mental Health Research.” Nature Mental Health, vol. 2, no. 10, Springer Nature, 2024, pp. 1124–27, doi:10.1038/s44220-024-00316-z. short: F. Nees, P. Renner, N.E. Holz, E. Polemiti, S. Siehl, S. Hese, K. Schepanski, G. Schumann, H. Walter, A. Heinz, M. Ralser, S. Twardziok, N. Vaidya, A. Bernas, E. Serin, M. Jentsch, E. Hitchen, H. Kebir, T.A. Lett, J.C. Roy, R. Eils, U.H. Taron, T. Schütz, J. Banks, T. Banaschewski, K. Jansone, N. Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, M. Neidhart, B. Seefried, R. Aden, O.A. Andreassen, L.T. Westlye, D. Van Der Meer, S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, A. Marquand, G. Novarino, L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A.J. Forstner, P. Hoffmann, M.M. Nöthen, I. Claus, A. Miller, C.M. Mathey, S. Heilmann-Heimbach, P. Sommer, M. Patraskaki, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel, L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez, A. Giner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J. Liu, A. Schwalber, P. Thompson, N. Clinton, S. Desrivières, A.H. Young, B. Stahl, G. Ogoh, Nature Mental Health 2 (2024) 1124–1127. date_created: 2025-03-23T23:01:28Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-03-25T08:28:39Z day: '01' department: - _id: GaNo doi: 10.1038/s44220-024-00316-z intvolume: ' 2' issue: '10' language: - iso: eng month: '10' oa_version: None page: 1124-1127 publication: Nature Mental Health publication_identifier: eissn: - 2731-6076 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Large-scale population data enrichment in mental health research type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2024' ... --- OA_type: closed access _id: '20039' abstract: - lang: eng text: This Comment presents a high-level protocol for data harmonization within large cohorts, in which it postulates four main steps including (1) expert review, (2) pre-statistical harmonization, (3) statistical harmonization, and (4) validation. acknowledgement: Funded by the European Union. Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10041392 and 10038599). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA) or UKRI. The European Union, HADEA or UKRI cannot be held responsible for them. This work received support from the Chinese Ministry for Science and Technology (MOST), the Horizon 2020-funded European Research Council advanced grant ‘STRATIFY’ (695313); the German Research Foundation (COPE; 675346; NE 1383/15-1 and BA 2088/7-1 (CoviDrug)), the National Natural Science Foundation of China grant 82150710554, the Hector II foundation and the German Center for Mental Health (DZPG) (01EE2301A, 01EE2304A, 01EE2301D). article_processing_charge: No article_type: comment author: - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Karina full_name: Jansone, Karina last_name: Jansone - first_name: Barbora full_name: Rehák Bučková, Barbora last_name: Rehák Bučková - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Michael A. full_name: Rapp, Michael A. last_name: Rapp - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: George full_name: Ogoh, George last_name: Ogoh - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Jingyu full_name: Liu, Jingyu last_name: Liu - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Yanting full_name: Gong, Yanting last_name: Gong - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Arantxa full_name: Giner, Arantxa last_name: Giner - first_name: Mavi full_name: Sanchez, Mavi last_name: Sanchez - first_name: Elena full_name: Alvarez, Elena last_name: Alvarez - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Lisa full_name: Otten, Lisa last_name: Otten - first_name: Séverine full_name: Pitel, Séverine last_name: Pitel - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Carina M. full_name: Mathey, Carina M. last_name: Mathey - first_name: Abigail full_name: Miller, Abigail last_name: Miller - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Francisco Eiroa full_name: Orosa, Francisco Eiroa last_name: Orosa - first_name: Guillem Feixas full_name: Viapiana, Guillem Feixas last_name: Viapiana - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Lena full_name: Marr, Lena id: 4406F586-F248-11E8-B48F-1D18A9856A87 last_name: Marr - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Sebastian full_name: Siehl, Sebastian last_name: Siehl - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Jamie full_name: Banks, Jamie last_name: Banks - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Jean Charles full_name: Roy, Jean Charles last_name: Roy - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz citation: ama: Neidhart M, Kjelkenes R, Jansone K, et al. A protocol for data harmonization in large cohorts. Nature Mental Health. 2024;2(10):1134-1137. doi:10.1038/s44220-024-00315-0 apa: Neidhart, M., Kjelkenes, R., Jansone, K., Rehák Bučková, B., Holz, N., Nees, F., … Heinz, A. (2024). A protocol for data harmonization in large cohorts. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00315-0 chicago: Neidhart, Maja, Rikka Kjelkenes, Karina Jansone, Barbora Rehák Bučková, Nathalie Holz, Frauke Nees, Henrik Walter, et al. “A Protocol for Data Harmonization in Large Cohorts.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00315-0. ieee: M. Neidhart et al., “A protocol for data harmonization in large cohorts,” Nature Mental Health, vol. 2, no. 10. Springer Nature, pp. 1134–1137, 2024. ista: Neidhart M, Kjelkenes R, Jansone K, Rehák Bučková B, Holz N, Nees F, Walter H, Schumann G, Rapp MA, Banaschewski T, Schwarz E, Marquand A, Ogoh G, Stahl B, Young AH, Desrivières S, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller A, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Böttger SJ, Tschorn M, Rapp M, Ask H, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Stringaris A, Tost H, Meyer-Lindenberg A, Christmann N, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A. 2024. A protocol for data harmonization in large cohorts. Nature Mental Health. 2(10), 1134–1137. mla: Neidhart, Maja, et al. “A Protocol for Data Harmonization in Large Cohorts.” Nature Mental Health, vol. 2, no. 10, Springer Nature, 2024, pp. 1134–37, doi:10.1038/s44220-024-00315-0. short: M. Neidhart, R. Kjelkenes, K. Jansone, B. Rehák Bučková, N. Holz, F. Nees, H. Walter, G. Schumann, M.A. Rapp, T. Banaschewski, E. Schwarz, A. Marquand, G. Ogoh, B. Stahl, A.H. Young, S. Desrivières, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, A. Stringaris, H. Tost, A. Meyer-Lindenberg, N. Christmann, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, Nature Mental Health 2 (2024) 1134–1137. date_created: 2025-07-20T22:02:04Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-07-22T08:59:10Z day: '01' department: - _id: GaNo doi: 10.1038/s44220-024-00315-0 intvolume: ' 2' issue: '10' language: - iso: eng month: '10' oa_version: None page: 1134-1137 publication: Nature Mental Health publication_identifier: eissn: - 2731-6076 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A protocol for data harmonization in large cohorts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2024' ... --- OA_type: closed access _id: '20156' abstract: - lang: eng text: Integrative analyses that incorporate different levels of ‘-omics’ data represent a powerful tool for deciphering the biological mechanisms that underlie environmental influences on mental health and disease. This Comment highlights various aspects of such multi-omics approaches, using the example of the EU-funded environMENTAL project. acknowledgement: 'This work was supported by the Horizon 2021 (grant 101057429) and UK Research and Innovation (grants 10038599 and 10041392)-funded project environMENTAL. Other funding included the Medical Research Council and Medical Research Foundation (MR/R00465X/, MRF-058-0004-RG-DESRI, ‘ESTRA’- Neurobiological underpinning of eating disorders: integrative biopsychosocial longitudinal analyses in adolescents; and MR/S020306/1, MRF-058-0009-RG-DESR-C0759 ‘ESTRA’-Establishing causal relationships between biopsychosocial predictors and correlates of eating disorders and their mediation by neural pathways), the EU-funded FP6 Integrated Project IMAGEN (reinforcement-related behavior in normal brain function and psychopathology; LSHM-CT- 2007-037286), the Horizon 2020-funded European Research Council advanced grant for STRATIFY (brain network-based stratification of reinforcement-related disorders; 695313) and the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. This paper represents independent research, partly funded by the NIHR Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. The authors thank C. Schmäl for proofreading the manuscript.' article_processing_charge: No article_type: comment author: - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Abigail full_name: Miller, Abigail last_name: Miller - first_name: Carina M. full_name: Mathey, Carina M. last_name: Mathey - first_name: Xinyang full_name: Yu, Xinyang last_name: Yu - first_name: Di full_name: Chen, Di last_name: Chen - first_name: Kofoworola full_name: Agunbiade, Kofoworola last_name: Agunbiade - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: George full_name: Ogoh, George last_name: Ogoh - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Jingyu full_name: Liu, Jingyu last_name: Liu - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Yanting full_name: Gong, Yanting last_name: Gong - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Arantxa full_name: Giner, Arantxa last_name: Giner - first_name: Mavi full_name: Sanchez, Mavi last_name: Sanchez - first_name: Elena full_name: Alvarez, Elena last_name: Alvarez - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Lisa full_name: Otten, Lisa last_name: Otten - first_name: Séverine full_name: Pitel, Séverine last_name: Pitel - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Francisco Eiroa full_name: Orosa, Francisco Eiroa last_name: Orosa - first_name: Guillem Feixas full_name: Viapiana, Guillem Feixas last_name: Viapiana - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Lena full_name: Marr, Lena id: 4406F586-F248-11E8-B48F-1D18A9856A87 last_name: Marr - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Sebastian full_name: Siehl, Sebastian last_name: Siehl - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Karina full_name: Jansone, Karina last_name: Jansone - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Jamie full_name: Banks, Jamie last_name: Banks - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Jean Charles full_name: Roy, Jean Charles last_name: Roy - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Henrik full_name: Walter, Henrik last_name: Walter citation: ama: Desrivières S, Miller A, Mathey CM, et al. Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. 2024;2(10):1131-1133. doi:10.1038/s44220-024-00317-y apa: Desrivières, S., Miller, A., Mathey, C. M., Yu, X., Chen, D., Agunbiade, K., … Walter, H. (2024). Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00317-y chicago: Desrivières, Sylvane, Abigail Miller, Carina M. Mathey, Xinyang Yu, Di Chen, Kofoworola Agunbiade, Stefanie Heilmann-Heimbach, et al. “Multi-Omics Analyses of the EnvironMENTAL Project Provide Insights into Mental Health and Disease.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00317-y. ieee: S. Desrivières et al., “Multi-omics analyses of the environMENTAL project provide insights into mental health and disease,” Nature Mental Health, vol. 2, no. 10. Springer Nature, pp. 1131–1133, 2024. ista: Desrivières S, Miller A, Mathey CM, Yu X, Chen D, Agunbiade K, Heilmann-Heimbach S, Forstner AJ, Schumann G, Hoffmann P, Nöthen MM, Ogoh G, Stahl B, Young AH, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Claus I, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Marquand A, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Jansone K, Banaschewski T, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Walter H. 2024. Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. 2(10), 1131–1133. mla: Desrivières, Sylvane, et al. “Multi-Omics Analyses of the EnvironMENTAL Project Provide Insights into Mental Health and Disease.” Nature Mental Health, vol. 2, no. 10, Springer Nature, 2024, pp. 1131–33, doi:10.1038/s44220-024-00317-y. short: S. Desrivières, A. Miller, C.M. Mathey, X. Yu, D. Chen, K. Agunbiade, S. Heilmann-Heimbach, A.J. Forstner, G. Schumann, P. Hoffmann, M.M. Nöthen, G. Ogoh, B. Stahl, A.H. Young, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, I. Claus, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, A. Marquand, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Jansone, T. Banaschewski, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, H. Walter, Nature Mental Health 2 (2024) 1131–1133. date_created: 2025-08-10T22:01:30Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-08-11T06:44:03Z day: '01' department: - _id: GaNo doi: 10.1038/s44220-024-00317-y intvolume: ' 2' issue: '10' language: - iso: eng month: '10' oa_version: None page: 1131-1133 publication: Nature Mental Health publication_identifier: eissn: - 2731-6076 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Multi-omics analyses of the environMENTAL project provide insights into mental health and disease type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2024' ... --- OA_type: closed access _id: '20157' abstract: - lang: eng text: The focus of much of contemporary research ethics is on compliance with established protocols. However, large data-driven neuroscience research raises new ethical concerns that have no agreed-upon solution. Here we reflect on these challenges and propose better integration of public and patient involvement in this evolving landscape. acknowledgement: Funded provided by the European Union. Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10131373and 10038599) and Ministry of Science and Technology of China (MOST) National Key Project of ‘Inter-governmental International Scientific and Technological Innovation Cooperation’ (2023YFE0199700). article_number: 1128-1130 article_processing_charge: No article_type: comment author: - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: George full_name: Ogoh, George last_name: Ogoh - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Jingyu full_name: Liu, Jingyu last_name: Liu - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Yanting full_name: Gong, Yanting last_name: Gong - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Arantxa full_name: Giner, Arantxa last_name: Giner - first_name: Mavi full_name: Sanchez, Mavi last_name: Sanchez - first_name: Elena full_name: Alvarez, Elena last_name: Alvarez - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Lisa full_name: Otten, Lisa last_name: Otten - first_name: Séverine full_name: Pitel, Séverine last_name: Pitel - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Carina M. full_name: Mathey, Carina M. last_name: Mathey - first_name: Abigail full_name: Miller, Abigail last_name: Miller - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Francisco Eiroa full_name: Orosa, Francisco Eiroa last_name: Orosa - first_name: Guillem Feixas full_name: Viapiana, Guillem Feixas last_name: Viapiana - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Lena full_name: Marr, Lena id: 4406F586-F248-11E8-B48F-1D18A9856A87 last_name: Marr - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Sebastian full_name: Siehl, Sebastian last_name: Siehl - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Karina full_name: Jansone, Karina last_name: Jansone - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Jamie full_name: Banks, Jamie last_name: Banks - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Jean Charles full_name: Roy, Jean Charles last_name: Roy - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Henrik full_name: Walter, Henrik last_name: Walter citation: ama: Stahl B, Ogoh G, Schumann G, et al. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. 2024;2(10). doi:10.1038/s44220-024-00320-3 apa: Stahl, B., Ogoh, G., Schumann, G., Walter, H., Stahl, B., Young, A. H., … Walter, H. (2024). Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00320-3 chicago: Stahl, Bernd, George Ogoh, Gunter Schumann, Henrik Walter, Bernd Stahl, Allan H. Young, Sylvane Desrivières, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00320-3. ieee: B. Stahl et al., “Rethinking ethics in interdisciplinary and big data-driven neuroscience projects,” Nature Mental Health, vol. 2, no. 10. Springer Nature, 2024. ista: Stahl B, Ogoh G, Schumann G, Walter H, Stahl B, Young AH, Desrivières S, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller A, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Marquand A, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Jansone K, Banaschewski T, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Walter H. 2024. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. 2(10), 1128–1130. mla: Stahl, Bernd, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” Nature Mental Health, vol. 2, no. 10, 1128–1130, Springer Nature, 2024, doi:10.1038/s44220-024-00320-3. short: B. Stahl, G. Ogoh, G. Schumann, H. Walter, B. Stahl, A.H. Young, S. Desrivières, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, A. Marquand, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Jansone, T. Banaschewski, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, H. Walter, Nature Mental Health 2 (2024). date_created: 2025-08-10T22:01:30Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-08-11T06:53:55Z day: '01' department: - _id: GaNo doi: 10.1038/s44220-024-00320-3 intvolume: ' 2' issue: '10' language: - iso: eng month: '10' oa_version: None publication: Nature Mental Health publication_identifier: eissn: - 2731-6076 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Rethinking ethics in interdisciplinary and big data-driven neuroscience projects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2024' ... --- OA_place: repository OA_type: green _id: '17331' abstract: - lang: eng text: Amyloidosis are a group of diseases in which soluble proteins aggregate and deposit in fibrillar conformation extracellularly in tissues. The effectiveness of therapeutic strategies depends on the specific protein involved, being crucial to accurately determine its nature. Moreover, following the diagnosis, the search for the mutation within relatives allows the clinical advice. Here we report the precise diagnosis and explored the possible reasons of the structural pathogenicity for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome sequencing and GATK calling pipeline were leveraged to characterize the protein variant present in a patient with kidney failure. Bioinformatics strategies were applied to suggest potential explanations of the variants aggregation. Our pipeline allowed the identification of a single-point variant of fibrinogen Aα-chain, which opened the possibility of curative transplantation. In silico structural analysis suggested that the pathogenicity of the variant may be attributed to a heightened susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet structure. Exploiting the comprehensive coverage of whole-genome sequencing, we managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and to stimulate the advancement in biomedicine. acknowledgement: The authors acknowledge Rosana del Cid for her help with English corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP 11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592), Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct these studies. article_processing_charge: No article_type: original author: - first_name: Elizabeth R full_name: Cattaneo, Elizabeth R last_name: Cattaneo - first_name: Romina A full_name: Gisonno, Romina A id: a9e08d76-6a98-11ec-8f7b-c777fe5ca519 last_name: Gisonno - first_name: Martín C full_name: Abba, Martín C last_name: Abba - first_name: Marianela full_name: Santana, Marianela last_name: Santana - first_name: Silvana A full_name: Rosú, Silvana A last_name: Rosú - first_name: Elsa full_name: Nucifora, Elsa last_name: Nucifora - first_name: María A full_name: Aguirre, María A last_name: Aguirre - first_name: María C full_name: Giordani, María C last_name: Giordani - first_name: M. Alejandra full_name: Tricerri, M. Alejandra last_name: Tricerri - first_name: Nahuel A full_name: Ramella, Nahuel A last_name: Ramella citation: ama: 'Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. 2024;92(12):1366-1374. doi:10.1002/prot.26732' apa: 'Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora, E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. Wiley. https://doi.org/10.1002/prot.26732' chicago: 'Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana, Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” Proteins: Structure, Function and Bioinformatics. Wiley, 2024. https://doi.org/10.1002/prot.26732.' ieee: 'E. R. Cattaneo et al., “Hereditary amyloidosis: Insights into a fibrinogen A variant protein,” Proteins: Structure, Function and Bioinformatics, vol. 92, no. 12. Wiley, pp. 1366–1374, 2024.' ista: 'Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. 92(12), 1366–1374.' mla: 'Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” Proteins: Structure, Function and Bioinformatics, vol. 92, no. 12, Wiley, 2024, pp. 1366–74, doi:10.1002/prot.26732.' short: 'E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora, M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure, Function and Bioinformatics 92 (2024) 1366–1374.' date_created: 2024-07-28T22:01:10Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-09-08T08:33:53Z day: '01' department: - _id: GaNo doi: 10.1002/prot.26732 external_id: isi: - '001272128100001' pmid: - '39031927' intvolume: ' 92' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.22541/au.171804763.37967262/v1 month: '12' oa: 1 oa_version: Preprint page: 1366-1374 pmid: 1 publication: 'Proteins: Structure, Function and Bioinformatics' publication_identifier: eissn: - 1097-0134 issn: - 0887-3585 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Hereditary amyloidosis: Insights into a fibrinogen A variant protein' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 92 year: '2024' ... --- _id: '12802' abstract: - lang: eng text: Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction. acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: Bio - _id: LifeSc acknowledgement: We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Daniel full_name: Malzl, Daniel last_name: Malzl - first_name: Maria full_name: Gerykova Bujalkova, Maria last_name: Gerykova Bujalkova - first_name: Mateja full_name: Smogavec, Mateja last_name: Smogavec - first_name: Lena A. full_name: Schwarz, Lena A. last_name: Schwarz - first_name: Sarah full_name: Gorkiewicz, Sarah id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f last_name: Gorkiewicz - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Christian full_name: Knittl-Frank, Christian last_name: Knittl-Frank - first_name: Marianna full_name: Tassinari, Marianna id: 7af593f1-d44a-11ed-bf94-a3646a6bb35e last_name: Tassinari - first_name: Nuno full_name: Maulide, Nuno last_name: Maulide - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Jörg full_name: Menche, Jörg last_name: Menche - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037 apa: Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037 chicago: Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier, 2023. https://doi.org/10.1016/j.cell.2023.02.037. ieee: L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023. ista: Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25. mla: Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:10.1016/j.cell.2023.02.037. short: L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25. corr_author: '1' date_created: 2023-04-05T08:15:40Z date_published: 2023-04-27T00:00:00Z date_updated: 2026-04-14T08:34:36Z day: '27' ddc: - '570' department: - _id: SiHi - _id: GaNo doi: 10.1016/j.cell.2023.02.037 ec_funded: 1 external_id: isi: - '000991468700001' pmid: - '36996814' file: - access_level: open_access checksum: 47e94fbe19e86505b429cb7a5b503ce6 content_type: application/pdf creator: dernst date_created: 2023-05-02T09:26:21Z date_updated: 2023-05-02T09:26:21Z file_id: '12889' file_name: 2023_Cell_Knaus.pdf file_size: 15712841 relation: main_file success: 1 file_date_updated: 2023-05-02T09:26:21Z has_accepted_license: '1' intvolume: ' 186' isi: 1 issue: '9' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1950-1967.e25 pmid: 1 project: - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/feed-them-or-lose-them/ record: - id: '19557' relation: dissertation_contains status: public - id: '13107' relation: dissertation_contains status: public scopus_import: '1' status: public title: Large neutral amino acid levels tune perinatal neuronal excitability and survival tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 186 year: '2023' ... --- OA_place: publisher _id: '13107' abstract: - lang: eng text: "Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus citation: ama: 'Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107' apa: 'Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107' chicago: 'Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.' ieee: 'L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.' ista: 'Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.' mla: 'Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.' short: 'L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.' corr_author: '1' date_created: 2023-06-01T09:05:24Z date_published: 2023-05-31T00:00:00Z date_updated: 2026-04-14T08:34:36Z day: '31' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/at:ista:13107 ec_funded: 1 file: - access_level: closed checksum: 4b69a4ac0bbf4163d59c0b58dcb4f2c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lknaus date_created: 2023-06-01T13:48:41Z date_updated: 2023-06-01T13:48:41Z file_id: '13112' file_name: Thesis_Lisa Knaus_approved_final.docx file_size: 12991551 relation: source_file - access_level: open_access checksum: 6903d152aa01181d87a696085af31c83 content_type: application/pdf creator: lknaus date_created: 2023-06-02T09:47:29Z date_updated: 2023-06-07T08:41:49Z file_id: '13114' file_name: Thesis_Lisa Knaus_approved_final_pdfa2b.pdf file_size: 9309015 relation: main_file file_date_updated: 2023-06-07T08:41:49Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: 'The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ...