[{"license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"Yes","date_created":"2024-06-03T08:54:50Z","year":"2024","isi":1,"_id":"17103","intvolume":"        15","language":[{"iso":"eng"}],"day":"23","file":[{"checksum":"80cb2f2c538e81064f4836b54bc313ca","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":8013695,"date_created":"2024-06-03T12:05:10Z","date_updated":"2024-06-03T12:05:10Z","file_id":"17110","creator":"dernst","success":1,"file_name":"2024_NatureComm_Jiang.pdf"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2024-06-03T12:05:10Z","publication_status":"published","acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for his generous support with the sakuranetin measurement. We thank International Rice Research Institute (IRRI) for provision of the rice NILs. We thank Professor Zhongkai Zhang (Yunnan Academy of Agricultural Sciences) for his generous support with subcellular structure observation of rice roots. We thank Professor Barbara Valent (Kansas State University) for her generously provision of the plasmid containing the PWL2 gene. We thank Professor Zuhua He (Chinese Academy of Sciences) for the gift of the transgenic rice line expressing the Pigm gene, OsNPR1-RNAi mutant line and ROD1-overexpression rice line. We thank Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. We thank Professor Muyuan Zhu (Zhejiang University) for provision of the transgenic plants overexpressing miR393a. We thank Professor Zhengge Zhu (Hebei Normal University) for provision of the rice line overexpressing OsPIN3t-GFP. We thank Professor Yanhua Qi (Zhejiang University) for provision of the arf12 mutant line. Thanks also go to Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the fungus M. oryzae strain Guy11 (AvrCo39-mRFP). This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31760500 and 31901870), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005). The project was also sponsored by SRF for ROCS, SEM (Grant No. [2013] 1792), the Key Projects of Applied Basic Research Plan of Yunnan Province (Grant No. 2017FA018, 202301AS070082), the Major Science and Technology Project in Yunnan Province (202102AE090042, 202202AE090036 and 202102AE090017), the Young and Middle-Aged Academic and Technical Leaders Reserve Talent Program in Yunnan Province (202205AC160076), the China Postdoctoral Science Foundation (2019M653849XB) and the National Key Research and Development Program of China (2023YFE0107500).","has_accepted_license":"1","DOAJ_listed":"1","quality_controlled":"1","month":"04","publication":"Nature Communications","date_updated":"2025-09-08T07:46:24Z","volume":15,"abstract":[{"lang":"eng","text":"Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription."}],"type":"journal_article","department":[{"_id":"JiFr"}],"ddc":["580"],"article_type":"original","external_id":{"isi":["001207290500013"],"pmid":["38653755"]},"article_number":"3437","date_published":"2024-04-23T00:00:00Z","title":"Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast","status":"public","doi":"10.1038/s41467-024-47746-y","pmid":1,"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Jiang L, Zhang X, Zhao Y, et al. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47746-y\">10.1038/s41467-024-47746-y</a>","apa":"Jiang, L., Zhang, X., Zhao, Y., Zhu, H., Fu, Q., Lu, X., … Du, Y. (2024). Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47746-y\">https://doi.org/10.1038/s41467-024-47746-y</a>","ista":"Jiang L, Zhang X, Zhao Y, Zhu H, Fu Q, Lu X, Huang W, Yang X, Zhou X, Wu L, Yang A, He X, Dong M, Peng Z, Yang J, Guo L, Wen J, Huang H, Xie Y, Zhu S, Li C, He X, Zhu Y, Friml J, Du Y. 2024. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. 15, 3437.","ieee":"L. Jiang <i>et al.</i>, “Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Jiang, Lihui, Xiaoyan Zhang, Yiting Zhao, Haiyan Zhu, Qijing Fu, Xinqi Lu, Wuying Huang, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47746-y\">https://doi.org/10.1038/s41467-024-47746-y</a>.","mla":"Jiang, Lihui, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” <i>Nature Communications</i>, vol. 15, 3437, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47746-y\">10.1038/s41467-024-47746-y</a>.","short":"L. Jiang, X. Zhang, Y. Zhao, H. Zhu, Q. Fu, X. Lu, W. Huang, X. Yang, X. Zhou, L. Wu, A. Yang, X. He, M. Dong, Z. Peng, J. Yang, L. Guo, J. Wen, H. Huang, Y. Xie, S. Zhu, C. Li, X. He, Y. Zhu, J. Friml, Y. Du, Nature Communications 15 (2024)."},"publisher":"Springer Nature","author":[{"last_name":"Jiang","first_name":"Lihui","full_name":"Jiang, Lihui"},{"last_name":"Zhang","full_name":"Zhang, Xiaoyan","first_name":"Xiaoyan"},{"full_name":"Zhao, Yiting","first_name":"Yiting","last_name":"Zhao"},{"last_name":"Zhu","first_name":"Haiyan","full_name":"Zhu, Haiyan"},{"last_name":"Fu","first_name":"Qijing","full_name":"Fu, Qijing"},{"first_name":"Xinqi","full_name":"Lu, Xinqi","last_name":"Lu"},{"last_name":"Huang","first_name":"Wuying","full_name":"Huang, Wuying"},{"full_name":"Yang, Xinyue","first_name":"Xinyue","last_name":"Yang"},{"last_name":"Zhou","first_name":"Xuan","full_name":"Zhou, Xuan"},{"first_name":"Lixia","full_name":"Wu, Lixia","last_name":"Wu"},{"last_name":"Yang","first_name":"Ao","full_name":"Yang, Ao"},{"last_name":"He","first_name":"Xie","full_name":"He, Xie"},{"full_name":"Dong, Man","first_name":"Man","last_name":"Dong"},{"full_name":"Peng, Ziai","first_name":"Ziai","last_name":"Peng"},{"last_name":"Yang","first_name":"Jing","full_name":"Yang, Jing"},{"first_name":"Liwei","full_name":"Guo, Liwei","last_name":"Guo"},{"first_name":"Jiancheng","full_name":"Wen, Jiancheng","last_name":"Wen"},{"full_name":"Huang, Huichuan","first_name":"Huichuan","last_name":"Huang"},{"full_name":"Xie, Yong","first_name":"Yong","last_name":"Xie"},{"full_name":"Zhu, Shusheng","first_name":"Shusheng","last_name":"Zhu"},{"last_name":"Li","first_name":"Chengyun","full_name":"Li, Chengyun"},{"first_name":"Xiahong","full_name":"He, Xiahong","last_name":"He"},{"first_name":"Youyong","full_name":"Zhu, Youyong","last_name":"Zhu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"Yunlong","full_name":"Du, Yunlong","last_name":"Du"}]},{"publication":"SciPost Physics","month":"04","quality_controlled":"1","arxiv":1,"volume":16,"date_updated":"2025-09-08T07:45:40Z","publication_status":"published","file_date_updated":"2024-06-03T11:18:51Z","oa":1,"acknowledgement":"JE and JK gratefully acknowledge financial support from the Initiative and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed with computing resources granted by RWTH Aachen University under project ‘rwth0475’.","has_accepted_license":"1","status":"public","article_number":"097","title":"Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells","date_published":"2024-04-08T00:00:00Z","external_id":{"isi":["001202370200001"],"arxiv":["2310.04272"]},"author":[{"first_name":"Johannes C.","full_name":"Krämer, Johannes C.","last_name":"Krämer"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Gerhard","full_name":"Gompper, Gerhard","last_name":"Gompper"},{"first_name":"Jens","full_name":"Elgeti, Jens","last_name":"Elgeti"}],"citation":{"mla":"Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>.","short":"J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).","chicago":"Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>.","ieee":"J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” <i>SciPost Physics</i>, vol. 16, no. 4. SciPost Foundation, 2024.","apa":"Krämer, J. C., Hannezo, E. B., Gompper, G., &#38; Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>","ista":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 16(4), 097.","ama":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. 2024;16(4). doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>"},"publisher":"SciPost Foundation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","doi":"10.21468/scipostphys.16.4.097","ddc":["530"],"department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth, the regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue steady-state are still poorly understood. Here, we develop a computational model that incorporates basic assumptions of stem cell renewal into distinct populations and mechanical interactions between cells. We find that the model generates unexpected dynamic features: stem cells repel each other in the bulk tissue and are thus found rather isolated, as in a number of in vivo contexts. By mapping the system onto a gas of passive Brownian particles with effective repulsive interactions, that arise from the generated flows of differentiated cells, we show that we can quantitatively describe such stem cell distribution in tissues. The interaction potential between a pair of stem cells decays exponentially with a characteristic length that spans several cell sizes, corresponding to the volume of cells generated per stem cell division. Our findings may help understanding the dynamics of normal and cancerous epithelial tissues."}],"type":"journal_article","article_type":"original","article_processing_charge":"No","publication_identifier":{"issn":["2542-4653"]},"issue":"4","scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"6fdeecd21c166db8dedb927ecc2e6025","relation":"main_file","file_size":4973291,"date_created":"2024-06-03T11:18:51Z","date_updated":"2024-06-03T11:18:51Z","file_id":"17109","success":1,"creator":"dernst","file_name":"2024_SciPostPhys_Kraemer.pdf"}],"day":"08","_id":"17104","language":[{"iso":"eng"}],"intvolume":"        16","date_created":"2024-06-03T08:58:44Z","year":"2024","isi":1},{"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"scopus_import":"1","issue":"23","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","checksum":"7ecb0892051f6ed8f6a6f25baa47543a","access_level":"open_access","relation":"main_file","date_created":"2024-06-03T10:33:17Z","file_size":2363206,"date_updated":"2024-06-03T10:33:17Z","creator":"dernst","file_id":"17107","success":1,"file_name":"2024_AngChemieInt_Sheng.pdf"}],"intvolume":"        63","_id":"17105","language":[{"iso":"eng"}],"day":"26","date_created":"2024-06-03T09:00:01Z","year":"2024","publication":"Angewandte Chemie International Edition","month":"03","quality_controlled":"1","volume":63,"date_updated":"2025-04-23T07:48:28Z","publication_status":"published","oa":1,"file_date_updated":"2024-06-03T10:33:17Z","acknowledgement":"This work was supported from the following sources: China Scholarship Council (CSC PhD Fellowship No. 201808330459 to J.S.), the Ministry of Education, Culture and Science of the Netherlands (Gravitation Program No. 024.001.035 to BLF), Financial support from The Netherlands Organization for Scientific Research (NWO-CW), the European Research Council (ERC; advanced Grant No. 694345 to B.L.F.). PRIN (SHERPA 2020 No. H45F21003430001) and PRIN (HySTAR 2022 No. H53D23004720006) and Lombardy Region for “Enhancing Photosynthesis” grant (2021-2023 No. H45F21002830007). W.D. is grateful for financial support from Marie Skłodowska-Curie Actions (Individual Fellowship No. 101027639). P.C. is grateful for the financial support provided by the PRELUDIUM grant from the National Science Center Poland (Reg. No: 2023/49/N/ST5/01864).","has_accepted_license":"1","status":"public","external_id":{"pmid":["38530132"]},"article_number":"e202404878","date_published":"2024-03-26T00:00:00Z","title":"Orthogonal photoswitching in a porous organic framework","publisher":"Wiley","citation":{"mla":"Sheng, Jinyu, et al. “Orthogonal Photoswitching in a Porous Organic Framework.” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 23, e202404878, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202404878\">10.1002/anie.202404878</a>.","short":"J. Sheng, J. Perego, S. Bracco, P. Cieciórski, W. Danowski, A. Comotti, B.L. Feringa, Angewandte Chemie International Edition 63 (2024).","chicago":"Sheng, Jinyu, Jacopo Perego, Silvia Bracco, Piotr Cieciórski, Wojciech Danowski, Angiolina Comotti, and Ben L. Feringa. “Orthogonal Photoswitching in a Porous Organic Framework.” <i>Angewandte Chemie International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202404878\">https://doi.org/10.1002/anie.202404878</a>.","ieee":"J. Sheng <i>et al.</i>, “Orthogonal photoswitching in a porous organic framework,” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 23. Wiley, 2024.","ista":"Sheng J, Perego J, Bracco S, Cieciórski P, Danowski W, Comotti A, Feringa BL. 2024. Orthogonal photoswitching in a porous organic framework. Angewandte Chemie International Edition. 63(23), e202404878.","apa":"Sheng, J., Perego, J., Bracco, S., Cieciórski, P., Danowski, W., Comotti, A., &#38; Feringa, B. L. (2024). Orthogonal photoswitching in a porous organic framework. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202404878\">https://doi.org/10.1002/anie.202404878</a>","ama":"Sheng J, Perego J, Bracco S, et al. Orthogonal photoswitching in a porous organic framework. <i>Angewandte Chemie International Edition</i>. 2024;63(23). doi:<a href=\"https://doi.org/10.1002/anie.202404878\">10.1002/anie.202404878</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Sheng, Jinyu","first_name":"Jinyu","last_name":"Sheng","id":"639f0526-27c9-11ee-95a6-966cd7f102d8"},{"last_name":"Perego","full_name":"Perego, Jacopo","first_name":"Jacopo"},{"last_name":"Bracco","full_name":"Bracco, Silvia","first_name":"Silvia"},{"last_name":"Cieciórski","full_name":"Cieciórski, Piotr","first_name":"Piotr"},{"last_name":"Danowski","first_name":"Wojciech","full_name":"Danowski, Wojciech"},{"last_name":"Comotti","full_name":"Comotti, Angiolina","first_name":"Angiolina"},{"full_name":"Feringa, Ben L.","first_name":"Ben L.","last_name":"Feringa"}],"pmid":1,"doi":"10.1002/anie.202404878","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The development of photoresponsive systems with non-invasive orthogonal control by distinct wavelengths of light is still in its infancy. In particular, the design of photochemically triggered-orthogonal systems integrated into solid materials that enable multiple dynamic control over their properties remains a longstanding challenge. Here, we report the orthogonal and reversible control of two types of photoswitches in an integrated solid porous framework, that is, visible-light responsive o-fluoroazobenzene and nitro-spiropyran motifs. The properties of the constructed material can be selectively controlled by different wavelengths of light thus generating four distinct states providing a basis for dynamic multifunctional materials. Solid-state NMR spectroscopy demonstrated the selective transformation of the azobenzene switch in the bulk, which in turn modulates N2 and CO2 adsorption.","lang":"eng"}],"ddc":["540"],"department":[{"_id":"RaKl"}],"article_type":"original"},{"publication_status":"published","date_updated":"2025-01-13T11:03:41Z","volume":123,"quality_controlled":"1","month":"06","publication":"Biophysical Journal","article_type":"original","page":"1494-1507","abstract":[{"text":"Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.","lang":"eng"}],"type":"journal_article","oa_version":"None","doi":"10.1016/j.bpj.2024.03.015","pmid":1,"author":[{"last_name":"Kamatar","first_name":"Advika","full_name":"Kamatar, Advika"},{"last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly"},{"first_name":"Feng","full_name":"Yuan, Feng","last_name":"Yuan"},{"last_name":"Wang","full_name":"Wang, Liping","first_name":"Liping"},{"full_name":"Lafer, Eileen M.","first_name":"Eileen M.","last_name":"Lafer"},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."},{"full_name":"Stachowiak, Jeanne C.","first_name":"Jeanne C.","last_name":"Stachowiak"},{"first_name":"Sapun H.","full_name":"Parekh, Sapun H.","last_name":"Parekh"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kamatar, Advika, Jack Peter Kelly Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, and Sapun H. Parekh. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>.","short":"A. Kamatar, J.P.K. Bravo, F. Yuan, L. Wang, E.M. Lafer, D.W. Taylor, J.C. Stachowiak, S.H. Parekh, Biophysical Journal 123 (2024) 1494–1507.","mla":"Kamatar, Advika, et al. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>, vol. 123, no. 11, Elsevier, 2024, pp. 1494–507, doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>.","ama":"Kamatar A, Bravo JPK, Yuan F, et al. Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. 2024;123(11):1494-1507. doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>","apa":"Kamatar, A., Bravo, J. P. K., Yuan, F., Wang, L., Lafer, E. M., Taylor, D. W., … Parekh, S. H. (2024). Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>","ista":"Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC, Parekh SH. 2024. Lipid droplets as substrates for protein phase separation. Biophysical Journal. 123(11), 1494–1507.","ieee":"A. Kamatar <i>et al.</i>, “Lipid droplets as substrates for protein phase separation,” <i>Biophysical Journal</i>, vol. 123, no. 11. Elsevier, pp. 1494–1507, 2024."},"date_published":"2024-06-04T00:00:00Z","title":"Lipid droplets as substrates for protein phase separation","external_id":{"pmid":["38462838"]},"status":"public","issue":"11","scopus_import":"1","publication_identifier":{"issn":["0006-3495"]},"article_processing_charge":"No","extern":"1","date_created":"2024-06-04T06:41:03Z","year":"2024","day":"04","_id":"17111","intvolume":"       123","language":[{"iso":"eng"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.06.23.546230"}],"date_created":"2024-06-04T06:41:26Z","year":"2024","language":[{"iso":"eng"}],"_id":"17112","intvolume":"       383","day":"01","scopus_import":"1","issue":"6682","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_processing_charge":"No","extern":"1","OA_type":"green","page":"512-519","article_type":"original","type":"journal_article","abstract":[{"lang":"eng","text":"The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities."}],"doi":"10.1126/science.adk0378","pmid":1,"oa_version":"Preprint","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","citation":{"apa":"Steens, J. A., Bravo, J. P. K., Salazar, C. R. P., Yildiz, C., Amieiro, A. M., Köstlbacher, S., … Staals, R. H. J. (2024). Type III-B CRISPR-Cas cascade of proteolytic cleavages. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adk0378\">https://doi.org/10.1126/science.adk0378</a>","ista":"Steens JA, Bravo JPK, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen SHP, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJG, van der Oost J, Taylor DW, Staals RHJ. 2024. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science. 383(6682), 512–519.","ieee":"J. A. Steens <i>et al.</i>, “Type III-B CRISPR-Cas cascade of proteolytic cleavages,” <i>Science</i>, vol. 383, no. 6682. American Association for the Advancement of Science, pp. 512–519, 2024.","ama":"Steens JA, Bravo JPK, Salazar CRP, et al. Type III-B CRISPR-Cas cascade of proteolytic cleavages. <i>Science</i>. 2024;383(6682):512-519. doi:<a href=\"https://doi.org/10.1126/science.adk0378\">10.1126/science.adk0378</a>","mla":"Steens, Jurre A., et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” <i>Science</i>, vol. 383, no. 6682, American Association for the Advancement of Science, 2024, pp. 512–19, doi:<a href=\"https://doi.org/10.1126/science.adk0378\">10.1126/science.adk0378</a>.","short":"J.A. Steens, J.P.K. Bravo, C.R.P. Salazar, C. Yildiz, A.M. Amieiro, S. Köstlbacher, S.H.P. Prinsen, C. Patinios, A. Bardis, A. Barendregt, R.A. Scheltema, T.J.G. Ettema, J. van der Oost, D.W. Taylor, R.H.J. Staals, Science 383 (2024) 512–519.","chicago":"Steens, Jurre A., Jack Peter Kelly Bravo, Carl Raymund P. Salazar, Caglar Yildiz, Afonso M. Amieiro, Stephan Köstlbacher, Stijn H.P. Prinsen, et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adk0378\">https://doi.org/10.1126/science.adk0378</a>."},"author":[{"first_name":"Jurre A.","full_name":"Steens, Jurre A.","last_name":"Steens"},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly"},{"last_name":"Salazar","first_name":"Carl Raymund P.","full_name":"Salazar, Carl Raymund P."},{"last_name":"Yildiz","full_name":"Yildiz, Caglar","first_name":"Caglar"},{"last_name":"Amieiro","first_name":"Afonso M.","full_name":"Amieiro, Afonso M."},{"last_name":"Köstlbacher","full_name":"Köstlbacher, Stephan","first_name":"Stephan"},{"full_name":"Prinsen, Stijn H.P.","first_name":"Stijn H.P.","last_name":"Prinsen"},{"last_name":"Patinios","first_name":"Constantinos","full_name":"Patinios, Constantinos"},{"last_name":"Bardis","full_name":"Bardis, Andreas","first_name":"Andreas"},{"last_name":"Barendregt","full_name":"Barendregt, Arjan","first_name":"Arjan"},{"full_name":"Scheltema, Richard A.","first_name":"Richard A.","last_name":"Scheltema"},{"full_name":"Ettema, Thijs J.G.","first_name":"Thijs J.G.","last_name":"Ettema"},{"last_name":"van der Oost","first_name":"John","full_name":"van der Oost, John"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"},{"full_name":"Staals, Raymond H.J.","first_name":"Raymond H.J.","last_name":"Staals"}],"external_id":{"pmid":["38301007"]},"title":"Type III-B CRISPR-Cas cascade of proteolytic cleavages","date_published":"2024-02-01T00:00:00Z","status":"public","acknowledgement":"We thank R. Fregoso Ocampo for assistance with negative-stain EM imaging. This work was funded by Dutch Research Council (NWO) VIDI grant VI.Vidi.203.074 (R.H.J.S.), NWO Spinoza grant SPI 93-537 (J.v.d.O.), European Research Council (ERC) Advanced grant ERC-AdG-834279 (J.v.d.O.), ERC CoG grant 817834 (T.J.G.E.), NWO VICI grant VI.C.192.016 (T.J.G.E.), Volkswagen Foundation grant 96725 (T.J.G.E.), National Institute of General Medical Sciences of the National Institutes of Health grant R35GM138348 (D.W.T.), Welch Foundation research grant F-1938 (D.W.T.), a Robert J. Kleberg, Jr. And Helen C. Kleberg Foundation medical research grant (D.W.T.), and American Cancer Society Research Scholar grant RSG-21-050-01-DMC (D.W.T.).","oa":1,"publication_status":"published","date_updated":"2025-09-24T08:31:45Z","volume":383,"month":"02","quality_controlled":"1","publication":"Science"},{"status":"public","external_id":{"pmid":["38688943"]},"date_published":"2024-04-30T00:00:00Z","article_number":"3663","title":"Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9","citation":{"short":"G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J. Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).","mla":"Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>, vol. 15, 3663, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>.","chicago":"Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>.","ieee":"G. N. Hibshman <i>et al.</i>, “Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang, H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47830-3\">https://doi.org/10.1038/s41467-024-47830-3</a>","ista":"Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nature Communications. 15, 3663.","ama":"Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47830-3\">10.1038/s41467-024-47830-3</a>"},"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hibshman","first_name":"Grace N.","full_name":"Hibshman, Grace N."},{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"last_name":"Hooper","first_name":"Matthew M.","full_name":"Hooper, Matthew M."},{"full_name":"Dangerfield, Tyler L.","first_name":"Tyler L.","last_name":"Dangerfield"},{"last_name":"Zhang","first_name":"Hongshan","full_name":"Zhang, Hongshan"},{"first_name":"Ilya J.","full_name":"Finkelstein, Ilya J.","last_name":"Finkelstein"},{"last_name":"Johnson","first_name":"Kenneth A.","full_name":"Johnson, Kenneth A."},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"doi":"10.1038/s41467-024-47830-3","pmid":1,"oa_version":"Published Version","abstract":[{"text":"CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for <jats:italic>Streptococcus pyogenes</jats:italic> Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.","lang":"eng"}],"type":"journal_article","article_type":"original","publication":"Nature Communications","month":"04","quality_controlled":"1","volume":15,"date_updated":"2024-10-14T12:34:26Z","publication_status":"published","oa":1,"intvolume":"        15","_id":"17113","language":[{"iso":"eng"}],"day":"30","date_created":"2024-06-04T06:42:07Z","year":"2024","main_file_link":[{"url":"https://doi.org/10.1038/s41467-024-47830-3","open_access":"1"}],"extern":"1","article_processing_charge":"Yes","publication_identifier":{"issn":["2041-1723"]},"scopus_import":"1"},{"publication_status":"published","oa":1,"publication":"Nature Communications","month":"04","quality_controlled":"1","volume":15,"date_updated":"2024-06-04T07:05:26Z","type":"journal_article","abstract":[{"text":"CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction<jats:sup>1–5</jats:sup>. Target RNA cleavage at regular intervals is characteristic of type III effector complexes<jats:sup>6–8</jats:sup>. Here, we determine the structures of the <jats:italic>Synechocystis</jats:italic> type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors<jats:sup>9,10</jats:sup>, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.","lang":"eng"}],"article_type":"original","status":"public","external_id":{"pmid":["38637512"]},"article_number":"3324","date_published":"2024-04-18T00:00:00Z","title":"RNA targeting and cleavage by the type III-Dv CRISPR effector complex","citation":{"ista":"Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 15, 3324.","apa":"Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>","ieee":"E. A. Schwartz <i>et al.</i>, “RNA targeting and cleavage by the type III-Dv CRISPR effector complex,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Schwartz EA, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>","mla":"Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>, vol. 15, 3324, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-47506-y\">10.1038/s41467-024-47506-y</a>.","short":"E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, Nature Communications 15 (2024).","chicago":"Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR Effector Complex.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-47506-y\">https://doi.org/10.1038/s41467-024-47506-y</a>."},"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Schwartz, Evan A.","first_name":"Evan A.","last_name":"Schwartz"},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"},{"last_name":"Ahsan","first_name":"Mohd","full_name":"Ahsan, Mohd"},{"last_name":"Macias","first_name":"Luis A.","full_name":"Macias, Luis A."},{"last_name":"McCafferty","full_name":"McCafferty, Caitlyn L.","first_name":"Caitlyn L."},{"last_name":"Dangerfield","full_name":"Dangerfield, Tyler L.","first_name":"Tyler L."},{"full_name":"Walker, Jada N.","first_name":"Jada N.","last_name":"Walker"},{"last_name":"Brodbelt","full_name":"Brodbelt, Jennifer S.","first_name":"Jennifer S."},{"last_name":"Palermo","full_name":"Palermo, Giulia","first_name":"Giulia"},{"last_name":"Fineran","full_name":"Fineran, Peter C.","first_name":"Peter C."},{"full_name":"Fagerlund, Robert D.","first_name":"Robert D.","last_name":"Fagerlund"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"}],"pmid":1,"doi":"10.1038/s41467-024-47506-y","oa_version":"Published Version","publication_identifier":{"issn":["2041-1723"]},"scopus_import":"1","extern":"1","article_processing_charge":"Yes","date_created":"2024-06-04T06:43:02Z","year":"2024","main_file_link":[{"url":"https://doi.org/10.1038/s41467-024-47506-y","open_access":"1"}],"language":[{"iso":"eng"}],"_id":"17114","intvolume":"        15","day":"18"},{"month":"05","quality_controlled":"1","publication":"BMC Psychiatry","date_updated":"2025-04-23T07:51:51Z","volume":24,"oa":1,"file_date_updated":"2024-06-10T10:44:26Z","publication_status":"published","has_accepted_license":"1","acknowledgement":"This work was supported by the project ‘Fellows Ride’ of the Thomas Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’ (to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL.","external_id":{"pmid":["38811916"]},"date_published":"2024-05-29T00:00:00Z","title":"The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study","article_number":"401","status":"public","doi":"10.1186/s12888-024-05849-2","pmid":1,"oa_version":"Published Version","citation":{"ista":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. BMC Psychiatry. 24, 401.","apa":"Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., &#38; Kittel-Schneider, S. (2024). The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>","ieee":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study,” <i>BMC Psychiatry</i>, vol. 24. Springer Nature, 2024.","ama":"Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association between maximal muscle strength, disease severity and psychopharmacotherapy among young to middle-aged inpatients with affective disorders – a prospective pilot study. <i>BMC Psychiatry</i>. 2024;24. doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>","mla":"Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>, vol. 24, 401, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s12888-024-05849-2\">10.1186/s12888-024-05849-2</a>.","short":"H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC Psychiatry 24 (2024).","chicago":"Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s12888-024-05849-2\">https://doi.org/10.1186/s12888-024-05849-2</a>."},"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ramming","full_name":"Ramming, Hannah","first_name":"Hannah"},{"last_name":"Theuerkauf","full_name":"Theuerkauf, Linda","first_name":"Linda"},{"last_name":"Hoos","full_name":"Hoos, Olaf","first_name":"Olaf"},{"full_name":"Lichter, Katharina","first_name":"Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","last_name":"Lichter","orcid":"0000-0002-1485-0351"},{"first_name":"Sarah","full_name":"Kittel-Schneider, Sarah","last_name":"Kittel-Schneider"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Background: Motor alterations and lowered physical activity are common in affective disorders. Previous research has indicated a link between depressive symptoms and declining muscle strength primarily focusing on the elderly but not younger individuals. Thus, we aimed to evaluate the relationship between mood and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy. The study was carried out as a prospective observational study at a German psychiatric university hospital between September 2021 and March 2022.\r\nMethods: Employing a standardized strength circuit consisting of computerized strength training devices, we measured the maximal muscle strength (Fmax) using three repetitions maximum across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3) over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood lipid profiling in a clinical setting. For analysis of psychopharmacotherapy, medication was split into activating (AM) and inhibiting (IM) medication and dosages were normalized by the respective WHO defined daily dose.\r\nResults: While we observed a significant decrease of the MADRS score and increase of the relative total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001), we did not reveal a significant bivariate correlation between disease severity (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with longer disease history displayed reduced rTFmax (p = .048). IM was significantly associated with decreased rTFmax (p = .032). Regression models provide a more substantial effect of gender, age, and IM on muscle strength than the depressive episode itself (p < .001).\r\nConclusions: The results of the study indicate that disease severity and muscle strength are not associated in young to middle-aged inpatients with affective disorders using a strength circuit as observational measurement. Future research will be needed to differentiate the effect of medication, gender, and age on muscle strength and to develop interventions for prevention of muscle weakness, especially in younger patients with chronic affective illnesses."}],"department":[{"_id":"PeJo"}],"ddc":["570"],"article_type":"original","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","publication_identifier":{"eissn":["1471-244X"]},"intvolume":"        24","_id":"17122","language":[{"iso":"eng"}],"day":"29","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"2024_BMCPsychiatry_Ramming.pdf","creator":"dernst","success":1,"file_id":"17131","date_updated":"2024-06-10T10:44:26Z","file_size":2320147,"date_created":"2024-06-10T10:44:26Z","relation":"main_file","checksum":"5df60d3c9388955c5b682ea34748d59d","content_type":"application/pdf","access_level":"open_access"}],"date_created":"2024-06-09T22:01:01Z","year":"2024"},{"file":[{"file_name":"2024_PNAS_Brueckner.pdf","date_updated":"2024-06-10T10:27:37Z","success":1,"file_id":"17130","creator":"dernst","relation":"main_file","date_created":"2024-06-10T10:27:37Z","file_size":12329234,"access_level":"open_access","content_type":"application/pdf","checksum":"59797a75db7beb3721ed7a4d14c241f9"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"corr_author":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/dbrueckner/SelforgInformation"},{"url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/","description":"News on the ISTA website","relation":"press_release"}]},"day":"04","_id":"17123","language":[{"iso":"eng"}],"intvolume":"       121","isi":1,"year":"2024","date_created":"2024-06-09T22:01:02Z","APC_amount":"2570,79 EUR","article_processing_charge":"Yes (in subscription journal)","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"23","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","author":[{"first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"publisher":"National Academy of Sciences","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>.","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024.","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>"},"oa_version":"Published Version","OA_place":"publisher","doi":"10.1073/pnas.2322326121","pmid":1,"status":"public","date_published":"2024-06-04T00:00:00Z","title":"Information content and optimization of self-organized developmental systems","article_number":"e2322326121","external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"article_type":"original","OA_type":"hybrid","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"ddc":["570"],"abstract":[{"text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes.","lang":"eng"}],"type":"journal_article","volume":121,"date_updated":"2025-09-08T07:51:01Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","month":"06","has_accepted_license":"1","acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","publication_status":"published","file_date_updated":"2024-06-10T10:27:37Z","oa":1},{"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"scopus_import":"1","issue":"23","article_processing_charge":"No","isi":1,"date_created":"2024-06-09T22:01:02Z","year":"2024","language":[{"iso":"eng"}],"_id":"17125","intvolume":"        18","day":"30","acknowledgement":"This research was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958 to the Kavli Institute for Theoretical Physics. The biophysics part of this paper was supported in part by the Gordon and Betty Moore Foundation Grant No. 2919.02. CLB acknowledges the sponsorship of the Alexander von Humboldt Foundation through the Humboldt Research Fellowship for postdoctoral researchers, and the support of the Emerging Talents Initiative (ETI) and the EAM Starting Grant (EAM-SG23-1) of the Competence Center Engineering of Advanced Materials of the Friedrich-Alexander-Universität Erlangen-Nürnberg. CLB and ME acknowledge the support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Project-ID 416229255-SFB 1411. The research of AT was supported by the U.S. Department of Energy (U.S. DOE), Office of Basic Energy Sciences, Division of Materials Sciences and Engineering. Iowa State University operates Ames National Laboratory for the U.S. DOE under Contract DE-AC02-07CH11358.","publication_status":"published","volume":18,"date_updated":"2025-09-08T07:52:37Z","publication":"ACS Nano","quality_controlled":"1","month":"05","page":"14791-14840","OA_type":"closed access","article_type":"review","abstract":[{"text":"We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.","lang":"eng"}],"type":"journal_article","department":[{"_id":"MaIb"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Chemical Society","citation":{"ama":"Bassani CL, Van Anders G, Banin U, et al. Nanocrystal assemblies: Current advances and open problems. <i>ACS Nano</i>. 2024;18(23):14791-14840. doi:<a href=\"https://doi.org/10.1021/acsnano.3c10201\">10.1021/acsnano.3c10201</a>","ieee":"C. L. Bassani <i>et al.</i>, “Nanocrystal assemblies: Current advances and open problems,” <i>ACS Nano</i>, vol. 18, no. 23. American Chemical Society, pp. 14791–14840, 2024.","apa":"Bassani, C. L., Van Anders, G., Banin, U., Baranov, D., Chen, Q., Dijkstra, M., … Travesset, A. (2024). Nanocrystal assemblies: Current advances and open problems. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c10201\">https://doi.org/10.1021/acsnano.3c10201</a>","ista":"Bassani CL, Van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. 2024. Nanocrystal assemblies: Current advances and open problems. ACS Nano. 18(23), 14791–14840.","chicago":"Bassani, Carlos L., Greg Van Anders, Uri Banin, Dmitry Baranov, Qian Chen, Marjolein Dijkstra, Michael S. Dimitriyev, et al. “Nanocrystal Assemblies: Current Advances and Open Problems.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.3c10201\">https://doi.org/10.1021/acsnano.3c10201</a>.","short":"C.L. Bassani, G. Van Anders, U. Banin, D. Baranov, Q. Chen, M. Dijkstra, M.S. Dimitriyev, E. Efrati, J. Faraudo, O. Gang, N. Gaston, R. Golestanian, G.I. Guerrero-Garcia, M. Gruenwald, A. Haji-Akbari, M. Ibáñez, M. Karg, T. Kraus, B. Lee, R.C. Van Lehn, R.J. Macfarlane, B.M. Mognetti, A. Nikoubashman, S. Osat, O.V. Prezhdo, G.M. Rotskoff, L. Saiz, A.C. Shi, S. Skrabalak, I.I. Smalyukh, M. Tagliazucchi, D.V. Talapin, A.V. Tkachenko, S. Tretiak, D. Vaknin, A. Widmer-Cooper, G.C.L. Wong, X. Ye, S. Zhou, E. Rabani, M. Engel, A. Travesset, ACS Nano 18 (2024) 14791–14840.","mla":"Bassani, Carlos L., et al. “Nanocrystal Assemblies: Current Advances and Open Problems.” <i>ACS Nano</i>, vol. 18, no. 23, American Chemical Society, 2024, pp. 14791–840, doi:<a href=\"https://doi.org/10.1021/acsnano.3c10201\">10.1021/acsnano.3c10201</a>."},"author":[{"last_name":"Bassani","full_name":"Bassani, Carlos L.","first_name":"Carlos L."},{"last_name":"Van Anders","full_name":"Van Anders, Greg","first_name":"Greg"},{"last_name":"Banin","first_name":"Uri","full_name":"Banin, Uri"},{"last_name":"Baranov","first_name":"Dmitry","full_name":"Baranov, Dmitry"},{"full_name":"Chen, Qian","first_name":"Qian","last_name":"Chen"},{"last_name":"Dijkstra","first_name":"Marjolein","full_name":"Dijkstra, Marjolein"},{"first_name":"Michael S.","full_name":"Dimitriyev, Michael S.","last_name":"Dimitriyev"},{"last_name":"Efrati","full_name":"Efrati, Efi","first_name":"Efi"},{"full_name":"Faraudo, Jordi","first_name":"Jordi","last_name":"Faraudo"},{"last_name":"Gang","first_name":"Oleg","full_name":"Gang, Oleg"},{"first_name":"Nicola","full_name":"Gaston, Nicola","last_name":"Gaston"},{"last_name":"Golestanian","full_name":"Golestanian, Ramin","first_name":"Ramin"},{"full_name":"Guerrero-Garcia, G. Ivan","first_name":"G. Ivan","last_name":"Guerrero-Garcia"},{"last_name":"Gruenwald","first_name":"Michael","full_name":"Gruenwald, Michael"},{"last_name":"Haji-Akbari","full_name":"Haji-Akbari, Amir","first_name":"Amir"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria"},{"last_name":"Karg","first_name":"Matthias","full_name":"Karg, Matthias"},{"last_name":"Kraus","first_name":"Tobias","full_name":"Kraus, Tobias"},{"last_name":"Lee","first_name":"Byeongdu","full_name":"Lee, Byeongdu"},{"full_name":"Van Lehn, Reid C.","first_name":"Reid C.","last_name":"Van Lehn"},{"first_name":"Robert J.","full_name":"Macfarlane, Robert J.","last_name":"Macfarlane"},{"first_name":"Bortolo M.","full_name":"Mognetti, Bortolo M.","last_name":"Mognetti"},{"first_name":"Arash","full_name":"Nikoubashman, Arash","last_name":"Nikoubashman"},{"last_name":"Osat","first_name":"Saeed","full_name":"Osat, Saeed"},{"full_name":"Prezhdo, Oleg V.","first_name":"Oleg V.","last_name":"Prezhdo"},{"first_name":"Grant M.","full_name":"Rotskoff, Grant M.","last_name":"Rotskoff"},{"last_name":"Saiz","first_name":"Leonor","full_name":"Saiz, Leonor"},{"last_name":"Shi","first_name":"An Chang","full_name":"Shi, An Chang"},{"last_name":"Skrabalak","first_name":"Sara","full_name":"Skrabalak, Sara"},{"full_name":"Smalyukh, Ivan I.","first_name":"Ivan I.","last_name":"Smalyukh"},{"full_name":"Tagliazucchi, Mario","first_name":"Mario","last_name":"Tagliazucchi"},{"last_name":"Talapin","first_name":"Dmitri V.","full_name":"Talapin, Dmitri V."},{"full_name":"Tkachenko, Alexei V.","first_name":"Alexei V.","last_name":"Tkachenko"},{"first_name":"Sergei","full_name":"Tretiak, Sergei","last_name":"Tretiak"},{"full_name":"Vaknin, David","first_name":"David","last_name":"Vaknin"},{"first_name":"Asaph","full_name":"Widmer-Cooper, Asaph","last_name":"Widmer-Cooper"},{"last_name":"Wong","first_name":"Gerard C.L.","full_name":"Wong, Gerard C.L."},{"last_name":"Ye","full_name":"Ye, Xingchen","first_name":"Xingchen"},{"last_name":"Zhou","first_name":"Shan","full_name":"Zhou, Shan"},{"first_name":"Eran","full_name":"Rabani, Eran","last_name":"Rabani"},{"first_name":"Michael","full_name":"Engel, Michael","last_name":"Engel"},{"last_name":"Travesset","full_name":"Travesset, Alex","first_name":"Alex"}],"pmid":1,"doi":"10.1021/acsnano.3c10201","oa_version":"None","status":"public","external_id":{"isi":["001236199900001"],"pmid":["38814908"]},"date_published":"2024-05-30T00:00:00Z","title":"Nanocrystal assemblies: Current advances and open problems"},{"year":"2024","date_created":"2024-06-09T22:01:03Z","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2024-05-26","location":"Zurich, Switzerland","end_date":"2024-05-30"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/719.pdf"}],"isi":1,"language":[{"iso":"eng"}],"_id":"17126","intvolume":"     14652","day":"08","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031587221"],"issn":["0302-9743"]},"scopus_import":"1","alternative_title":["LNCS"],"article_processing_charge":"No","abstract":[{"text":"Functional encryption (FE) is a primitive where the holder of a master secret key can control which functions a user can evaluate on encrypted data. It is a powerful primitive that even implies indistinguishability obfuscation (iO), given sufficiently compact ciphertexts (Ananth-Jain, CRYPTO’15 and Bitansky-Vaikuntanathan, FOCS’15). However, despite being extensively studied, there are FE schemes, such as function-hiding inner-product FE (Bishop-Jain-Kowalczyk, AC’15, Abdalla-Catalano-Fiore-Gay-Ursu, CRYPTO’18) and compact quadratic FE (Baltico-Catalano-Fiore-Gay, Lin, CRYPTO’17), that can be only realized using pairings. This raises the question if there are some mathematical barriers that hinder us from realizing these FE schemes from other assumptions.\r\n\r\nIn this paper, we study the difficulty of constructing lattice-based compact FE. We generalize the impossibility results of Ünal (EC’20) for lattice-based function-hiding FE, and extend it to the case of compact FE. Concretely, we prove lower bounds for lattice-based compact FE schemes which meet some (natural) algebraic restrictions at encryption and decryption, and have ciphertexts of linear size and secret keys of minimal degree. We see our results as important indications of why it is hard to construct lattice-based FE schemes for new functionalities, and which mathematical barriers have to be overcome.","lang":"eng"}],"type":"conference","department":[{"_id":"KrPi"}],"page":"249-279","status":"public","external_id":{"isi":["001278247600009"]},"date_published":"2024-05-08T00:00:00Z","title":"Lower bounds for lattice-based compact functional encryption","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Tairi E, Ünal A. Lower bounds for lattice-based compact functional encryption. In: <i>Advances in Cryptology – EUROCRYPT 2024</i>. Vol 14652. Springer Nature; 2024:249-279. doi:<a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">10.1007/978-3-031-58723-8_9</a>","ista":"Tairi E, Ünal A. 2024. Lower bounds for lattice-based compact functional encryption. Advances in Cryptology – EUROCRYPT 2024. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 14652, 249–279.","apa":"Tairi, E., &#38; Ünal, A. (2024). Lower bounds for lattice-based compact functional encryption. In <i>Advances in Cryptology – EUROCRYPT 2024</i> (Vol. 14652, pp. 249–279). Zurich, Switzerland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">https://doi.org/10.1007/978-3-031-58723-8_9</a>","ieee":"E. Tairi and A. Ünal, “Lower bounds for lattice-based compact functional encryption,” in <i>Advances in Cryptology – EUROCRYPT 2024</i>, Zurich, Switzerland, 2024, vol. 14652, pp. 249–279.","chicago":"Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional Encryption.” In <i>Advances in Cryptology – EUROCRYPT 2024</i>, 14652:249–79. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">https://doi.org/10.1007/978-3-031-58723-8_9</a>.","short":"E. Tairi, A. Ünal, in:, Advances in Cryptology – EUROCRYPT 2024, Springer Nature, 2024, pp. 249–279.","mla":"Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional Encryption.” <i>Advances in Cryptology – EUROCRYPT 2024</i>, vol. 14652, Springer Nature, 2024, pp. 249–79, doi:<a href=\"https://doi.org/10.1007/978-3-031-58723-8_9\">10.1007/978-3-031-58723-8_9</a>."},"publisher":"Springer Nature","author":[{"first_name":"Erkan","full_name":"Tairi, Erkan","last_name":"Tairi"},{"orcid":"0000-0002-8929-0221","last_name":"Ünal","id":"f6b56fb6-dc63-11ee-9dbf-f6780863a85a","full_name":"Ünal, Akin","first_name":"Akin"}],"doi":"10.1007/978-3-031-58723-8_9","oa_version":"Submitted Version","publication_status":"published","oa":1,"acknowledgement":"We want to thank the anonymous reviewers of TCC and Eurocrypt for their very helpful comments and suggestions. This work has received funding from the Austrian Science Fund (FWF) and netidee SCIENCE via grant P31621-N38 (PROFET).","publication":"Advances in Cryptology – EUROCRYPT 2024","month":"05","quality_controlled":"1","volume":14652,"date_updated":"2025-09-08T07:48:18Z"},{"acknowledgement":"We gratefully acknowledge the assistance of J. M. Lopez with DNSs at an early stage of this work. This work was partially supported by two grants from the Simons Foundation (grant nos. 662985 (N.G.) and 662960 (B.H.)) and by Ministry of Science and Technology, Taiwan (grant nos. MOST 109-2112-M-001-017-MY3 and MOST 111-2112-M-001-027-MY3 (H.-Y.S.)). Part of this work was performed using computing resources of CRIANN (Normandy, France).","publication_status":"published","date_updated":"2025-09-08T07:50:20Z","volume":20,"month":"08","quality_controlled":"1","publication":"Nature Physics","article_type":"original","page":"1339-1345","department":[{"_id":"BjHo"}],"type":"journal_article","abstract":[{"text":"The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.","lang":"eng"}],"oa_version":"None","doi":"10.1038/s41567-024-02513-0","author":[{"first_name":"Grégoire M","full_name":"Lemoult, Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","last_name":"Lemoult"},{"last_name":"Vasudevan","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","full_name":"Vasudevan, Mukund","first_name":"Mukund"},{"first_name":"Hong Yan","full_name":"Shih, Hong Yan","last_name":"Shih"},{"last_name":"Linga","first_name":"Gaute","full_name":"Linga, Gaute"},{"full_name":"Mathiesen, Joachim","first_name":"Joachim","last_name":"Mathiesen"},{"last_name":"Goldenfeld","full_name":"Goldenfeld, Nigel","first_name":"Nigel"},{"full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Lemoult, Grégoire M., et al. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1339–45, doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>.","short":"G.M. Lemoult, M. Vasudevan, H.Y. Shih, G. Linga, J. Mathiesen, N. Goldenfeld, B. Hof, Nature Physics 20 (2024) 1339–1345.","chicago":"Lemoult, Grégoire M, Mukund Vasudevan, Hong Yan Shih, Gaute Linga, Joachim Mathiesen, Nigel Goldenfeld, and Björn Hof. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>.","ieee":"G. M. Lemoult <i>et al.</i>, “Directed percolation and puff jamming near the transition to pipe turbulence,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1339–1345, 2024.","apa":"Lemoult, G. M., Vasudevan, M., Shih, H. Y., Linga, G., Mathiesen, J., Goldenfeld, N., &#38; Hof, B. (2024). Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>","ista":"Lemoult GM, Vasudevan M, Shih HY, Linga G, Mathiesen J, Goldenfeld N, Hof B. 2024. Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. 20, 1339–1345.","ama":"Lemoult GM, Vasudevan M, Shih HY, et al. Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. 2024;20:1339-1345. doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>"},"publisher":"Springer Nature","title":"Directed percolation and puff jamming near the transition to pipe turbulence","date_published":"2024-08-01T00:00:00Z","external_id":{"isi":["001232300600001"]},"status":"public","scopus_import":"1","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"article_processing_charge":"No","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"}],"isi":1,"year":"2024","date_created":"2024-06-09T22:01:03Z","day":"01","_id":"17128","language":[{"iso":"eng"}],"intvolume":"        20","corr_author":"1"},{"has_accepted_license":"1","oa":1,"file_date_updated":"2024-06-20T11:52:22Z","degree_awarded":"PhD","publication_status":"published","date_updated":"2026-04-15T06:43:02Z","month":"06","page":"161","supervisor":[{"first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","abstract":[{"lang":"eng","text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing."}],"ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"doi":"10.15479/at:ista:17133","oa_version":"Published Version","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","citation":{"ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>."},"author":[{"orcid":"0000-0001-6937-5773","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","full_name":"Hassani, Farid"}],"title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","date_published":"2024-06-11T00:00:00Z","status":"public","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"article_processing_charge":"No","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_created":"2024-06-11T18:20:05Z","year":"2024","_id":"17133","language":[{"iso":"eng"}],"keyword":["Quantum information","Qubits","Superconducting devices"],"day":"11","corr_author":"1","related_material":{"record":[{"id":"13227","relation":"part_of_dissertation","status":"public"},{"id":"9928","relation":"part_of_dissertation","status":"public"},{"id":"8755","relation":"part_of_dissertation","status":"public"}]},"file":[{"relation":"main_file","file_size":28370759,"date_created":"2024-06-12T07:53:19Z","checksum":"258c353d47fa37ea63ea43b1e10a34a0","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_main_final.pdf","date_updated":"2024-06-20T11:52:22Z","creator":"fhassani","file_id":"17137"},{"checksum":"deffa5d0db88093f74812fa71520d5e1","content_type":"text/x-tex","access_level":"closed","date_created":"2024-06-12T07:54:27Z","file_size":445735,"relation":"source_file","creator":"fhassani","file_id":"17138","date_updated":"2024-06-12T07:54:27Z","file_name":"Thesis_main.tex"}],"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"}},{"external_id":{"arxiv":["2406.07026"]},"date_published":"2024-06-11T00:00:00Z","title":"Majority dynamics and internal partitions of random regular graphs: Experimental results","article_number":"2406.07026","status":"public","doi":"10.48550/arXiv.2406.07026","_id":"17136","language":[{"iso":"eng"}],"day":"11","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>","ista":"Arkhipov P. Majority dynamics and internal partitions of random regular graphs: Experimental results. arXiv, 2406.07026.","apa":"Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular graphs: Experimental results. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>","ieee":"P. Arkhipov, “Majority dynamics and internal partitions of random regular graphs: Experimental results,” <i>arXiv</i>. .","chicago":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2406.07026\">https://doi.org/10.48550/arXiv.2406.07026</a>.","mla":"Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular Graphs: Experimental Results.” <i>ArXiv</i>, 2406.07026, doi:<a href=\"https://doi.org/10.48550/arXiv.2406.07026\">10.48550/arXiv.2406.07026</a>.","short":"P. Arkhipov, ArXiv (n.d.)."},"author":[{"first_name":"Pavel","full_name":"Arkhipov, Pavel","last_name":"Arkhipov","id":"b25f2ab2-1fed-11ee-8599-fe02d211784f"}],"type":"preprint","abstract":[{"lang":"eng","text":"This paper focuses on Majority Dynamics in sparse graphs, in particular, as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates with\r\nperiod two. The empirical evidence acquired by simulations suggests that for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating with high probability. We notice a local symmetry between\r\noscillating and non-oscillating vertices, that potentially can explain why the\r\nfraction of the oscillating vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe that the parts of random odd-regular graph under\r\nMajority Dynamics with high probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep, and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist in odd-regular graphs almost surely. However, we\r\nsuggest a modification of Majority Dynamics, that yields parts with desired\r\ncores with high probability."}],"date_created":"2024-06-12T07:01:52Z","department":[{"_id":"GradSch"}],"year":"2024","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.07026"}],"arxiv":1,"month":"06","publication":"arXiv","date_updated":"2024-06-17T10:45:32Z","article_processing_charge":"No","oa":1,"publication_status":"submitted","acknowledgement":"I am grateful to Matthew Kwan for setting the problem, providing useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement and support."},{"article_processing_charge":"No","publication_identifier":{"isbn":["9783200096455"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"f7d3dded6df2dcdb4818904cf2e1c183","file_size":206746,"date_created":"2024-06-17T09:36:51Z","relation":"main_file","file_id":"17153","creator":"dernst","success":1,"date_updated":"2024-06-17T09:36:51Z","file_name":"2024_ASHPC_Schloegl.pdf"}],"language":[{"iso":"eng"}],"_id":"17139","day":"13","conference":{"start_date":"2024-06-10","name":"ASHPC: Austrian-Slovenian HPC Meeting","end_date":"2024-06-13","location":"Grundlsee, Austria"},"date_created":"2024-06-14T09:06:36Z","year":"2024","date_updated":"2024-06-17T09:40:37Z","publication":"ASHPC24 - Austrian-Slovenian HPC Meeting 2024","quality_controlled":"1","month":"06","has_accepted_license":"1","publication_status":"published","oa":1,"file_date_updated":"2024-06-17T09:36:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer. “How Much Memory per CPU Core Is Requested?” In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, 46. EuroCC Austria, 2024. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>.","short":"A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46.","mla":"Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, EuroCC Austria, 2024, p. 46, doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>.","ama":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core is requested? In: <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>. EuroCC Austria; 2024:46. doi:<a href=\"https://doi.org/10.25365/phaidra.463\">10.25365/phaidra.463</a>","ieee":"A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per CPU core is requested?,” in <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>, Grundlsee, Austria, 2024, p. 46.","ista":"Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian HPC Meeting, 46.","apa":"Schlögl, A., Khalid, W., Elefante, S., &#38; Stadlbauer, S. (2024). How much memory per CPU core is requested? In <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i> (p. 46). Grundlsee, Austria: EuroCC Austria. <a href=\"https://doi.org/10.25365/phaidra.463\">https://doi.org/10.25365/phaidra.463</a>"},"publisher":"EuroCC Austria","author":[{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois"},{"first_name":"Waleed","full_name":"Khalid, Waleed","last_name":"Khalid","id":"097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1"},{"first_name":"Stefano","full_name":"Elefante, Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephan","full_name":"Stadlbauer, Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","last_name":"Stadlbauer"}],"doi":"10.25365/phaidra.463","oa_version":"Published Version","status":"public","date_published":"2024-06-13T00:00:00Z","title":"How much memory per CPU core is requested?","page":"46","type":"conference_abstract","ddc":["000"],"department":[{"_id":"ScienComp"}]},{"article_type":"original","OA_type":"hybrid","ddc":["580"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"type":"journal_article","abstract":[{"text":"The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted to (de)active transcriptional regulation, thus controlling auxin-associated developmental processes. However, the theme of a rapid auxin response has emerged since the 2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling components have been identified to mediate both slow and rapid auxin responses, which unveils the complexity of auxin signaling.","lang":"eng"}],"OA_place":"publisher","oa_version":"Published Version","doi":"10.1093/jxb/erae246","pmid":1,"author":[{"last_name":"Zhang","full_name":"Zhang, Zilin","first_name":"Zilin"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"full_name":"Peng, Shuaiying","first_name":"Shuaiying","last_name":"Peng"},{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Oxford University Press","citation":{"ama":"Zhang Z, Chen H, Peng S, Han H. Slow and rapid auxin responses in Arabidopsis. <i>Journal of Experimental Botany</i>. 2024;75(18). doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>","ieee":"Z. Zhang, H. Chen, S. Peng, and H. Han, “Slow and rapid auxin responses in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 75, no. 18. Oxford University Press, 2024.","ista":"Zhang Z, Chen H, Peng S, Han H. 2024. Slow and rapid auxin responses in Arabidopsis. Journal of Experimental Botany. 75(18), erae246.","apa":"Zhang, Z., Chen, H., Peng, S., &#38; Han, H. (2024). Slow and rapid auxin responses in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>","chicago":"Zhang, Zilin, Huihuang Chen, Shuaiying Peng, and Huibin Han. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>.","mla":"Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 75, no. 18, erae246, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>.","short":"Z. Zhang, H. Chen, S. Peng, H. Han, Journal of Experimental Botany 75 (2024)."},"date_published":"2024-09-27T00:00:00Z","title":"Slow and rapid auxin responses in Arabidopsis","article_number":"erae246","external_id":{"isi":["001270051200001"],"pmid":["38794966"]},"status":"public","acknowledgement":"We thank other lab members for their critical comments on this manuscript. We also thank the editor and reviewers for their constructive comments to improve our manuscript. We apologize to authors whose important work we could not include due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural University (9232308314) and the Science and Technology Department of Jiangxi Province (20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province (20202ACB215002) to SYP.","has_accepted_license":"1","file_date_updated":"2025-01-02T10:26:22Z","oa":1,"publication_status":"published","date_updated":"2025-09-08T07:57:50Z","volume":75,"quality_controlled":"1","month":"09","publication":"Journal of Experimental Botany","isi":1,"date_created":"2024-06-15T19:50:15Z","year":"2024","day":"27","_id":"17141","intvolume":"        75","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_updated":"2025-01-02T10:26:22Z","success":1,"file_id":"18720","creator":"dernst","file_name":"2024_JourExperimentalBotany_Zhang.pdf","checksum":"91b9435ed0f6640809c7588df19abf2f","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2025-01-02T10:26:22Z","file_size":763097}],"issue":"18","scopus_import":"1","publication_identifier":{"issn":["0022-0957"]},"article_processing_charge":"No"},{"publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"scopus_import":"1","ec_funded":1,"APC_amount":"6081,83 EUR","article_processing_charge":"Yes","project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2024","date_created":"2024-06-16T22:01:05Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"2024_PloS_Burnett.pdf","creator":"dernst","success":1,"file_id":"18805","date_updated":"2025-01-09T10:39:41Z","date_created":"2025-01-09T10:39:41Z","file_size":4016568,"relation":"main_file","access_level":"open_access","checksum":"496e1aa4fd5b92b7e4087ecc2c964133","content_type":"application/pdf"}],"corr_author":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"15385"}],"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.11130587"}]},"day":"10","intvolume":"        22","_id":"17142","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by a European Research Council Starting Grant 756502 (MJ). ","has_accepted_license":"1","publication_status":"published","file_date_updated":"2025-01-09T10:39:41Z","oa":1,"volume":22,"date_updated":"2025-09-08T07:57:11Z","publication":"PLoS Biology","quality_controlled":"1","month":"06","DOAJ_listed":"1","article_type":"original","OA_type":"gold","department":[{"_id":"RySh"},{"_id":"GaNo"},{"_id":"MaJö"}],"ddc":["570"],"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."}],"type":"journal_article","author":[{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura","first_name":"Laura"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner"},{"first_name":"Olga","full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947"},{"full_name":"Masson, Tomas","first_name":"Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson","orcid":"0000-0002-2634-6283"},{"full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga"},{"full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Public Library of Science","citation":{"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.","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. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” <i>PLoS Biology</i>, vol. 22. Public Library of Science, 2024.","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. <i>PLoS Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>","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.” <i>PLoS Biology</i>, vol. 22, e3002668, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>.","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).","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.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","OA_place":"publisher","doi":"10.1371/journal.pbio.3002668","pmid":1,"status":"public","date_published":"2024-06-10T00:00:00Z","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","article_number":"e3002668","external_id":{"isi":["001246176800003"],"pmid":["38857283"]}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Mathematical Society","citation":{"short":"L. Dello Schiavo, J. Maas, F. Pedrotti, Transactions of the American Mathematical Society 377 (2024) 3779–3804.","mla":"Dello Schiavo, Lorenzo, et al. “Local Conditions for Global Convergence of Gradient Flows and Proximal Point Sequences in Metric Spaces.” <i>Transactions of the American Mathematical Society</i>, vol. 377, no. 6, American Mathematical Society, 2024, pp. 3779–804, doi:<a href=\"https://doi.org/10.1090/tran/9156\">10.1090/tran/9156</a>.","chicago":"Dello Schiavo, Lorenzo, Jan Maas, and Francesco Pedrotti. “Local Conditions for Global Convergence of Gradient Flows and Proximal Point Sequences in Metric Spaces.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2024. <a href=\"https://doi.org/10.1090/tran/9156\">https://doi.org/10.1090/tran/9156</a>.","ieee":"L. Dello Schiavo, J. Maas, and F. Pedrotti, “Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces,” <i>Transactions of the American Mathematical Society</i>, vol. 377, no. 6. American Mathematical Society, pp. 3779–3804, 2024.","apa":"Dello Schiavo, L., Maas, J., &#38; Pedrotti, F. (2024). Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/9156\">https://doi.org/10.1090/tran/9156</a>","ista":"Dello Schiavo L, Maas J, Pedrotti F. 2024. Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces. Transactions of the American Mathematical Society. 377(6), 3779–3804.","ama":"Dello Schiavo L, Maas J, Pedrotti F. Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces. <i>Transactions of the American Mathematical Society</i>. 2024;377(6):3779-3804. doi:<a href=\"https://doi.org/10.1090/tran/9156\">10.1090/tran/9156</a>"},"author":[{"full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870"},{"orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan"},{"id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","full_name":"Pedrotti, Francesco","first_name":"Francesco"}],"doi":"10.1090/tran/9156","oa_version":"Preprint","status":"public","external_id":{"arxiv":["2304.05239"],"isi":["001203273300001"]},"date_published":"2024-06-01T00:00:00Z","title":"Local conditions for global convergence of gradient flows and proximal point sequences in metric spaces","page":"3779-3804","article_type":"original","abstract":[{"text":"This paper deals with local criteria for the convergence to a global minimiser for gradient flow trajectories and their discretisations. To obtain quantitative estimates on the speed of convergence, we consider variations on the classical Kurdyka–Łojasiewicz inequality for a large class of parameter functions. Our assumptions are given in terms of the initial data, without any reference to an equilibrium point. The main results are convergence statements for gradient flow curves and proximal point sequences to a global minimiser, together with sharp quantitative estimates on the speed of convergence. These convergence results apply in the general setting of lower semicontinuous functionals on complete metric spaces, generalising recent results for smooth functionals on Rn. While the non-smooth setting covers very general spaces, it is also useful for (non)-smooth functionals on Rn.\r\n.","lang":"eng"}],"type":"journal_article","department":[{"_id":"JaMa"}],"volume":377,"date_updated":"2026-04-07T13:00:02Z","publication":"Transactions of the American Mathematical Society","arxiv":1,"month":"06","quality_controlled":"1","acknowledgement":"The authors gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 716117). This research was funded in part by the Austrian Science Fund (FWF) project 10.55776/ESP208. This research was funded in part by the Austrian Science Fund (FWF) project 10.55776/F65","publication_status":"published","oa":1,"related_material":{"record":[{"id":"17336","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"_id":"17143","intvolume":"       377","day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.05239"}],"isi":1,"year":"2024","date_created":"2024-06-16T22:01:06Z","article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208"}],"publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"scopus_import":"1","issue":"6","ec_funded":1},{"volume":293,"date_updated":"2025-04-15T07:16:58Z","publication":"40th International Symposium on Computational Geometry","arxiv":1,"month":"06","quality_controlled":"1","has_accepted_license":"1","acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nSupported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Cô d'Azur.\r\nWe are greatly indebted to Fred Chazal for sharing his insights. We further thank Erin Chambers, Christopher Fillmore, and Elizabeth Stephenson for early discussions and all members of the Edelsbrunner group (Institute of Science and Technology Austria) and the Datashape team (Inria) for the atmosphere in which this research was conducted.","publication_status":"published","oa":1,"file_date_updated":"2024-06-17T08:33:40Z","citation":{"mla":"Kourimska, Hana, et al. “The Medial Axis of Any Closed Bounded Set Is Lipschitz Stable with Respect to the Hausdorff Distance Under Ambient Diffeomorphisms.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">10.4230/LIPIcs.SoCG.2024.69</a>.","short":"H. Kourimska, A. Lieutier, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Kourimska, Hana, André Lieutier, and Mathijs Wintraecken. “The Medial Axis of Any Closed Bounded Set Is Lipschitz Stable with Respect to the Hausdorff Distance Under Ambient Diffeomorphisms.” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">https://doi.org/10.4230/LIPIcs.SoCG.2024.69</a>.","ieee":"H. Kourimska, A. Lieutier, and M. Wintraecken, “The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293.","ista":"Kourimska H, Lieutier A, Wintraecken M. 2024. The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 69.","apa":"Kourimska, H., Lieutier, A., &#38; Wintraecken, M. (2024). The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">https://doi.org/10.4230/LIPIcs.SoCG.2024.69</a>","ama":"Kourimska H, Lieutier A, Wintraecken M. The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.69\">10.4230/LIPIcs.SoCG.2024.69</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Hana","full_name":"Kourimska, Hana","orcid":"0000-0001-7841-0091","last_name":"Kourimska","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E"},{"first_name":"André","full_name":"Lieutier, André","last_name":"Lieutier"},{"full_name":"Wintraecken, Mathijs","first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"doi":"10.4230/LIPIcs.SoCG.2024.69","oa_version":"Published Version","status":"public","external_id":{"arxiv":["2212.01118"]},"article_number":"69","title":"The medial axis of any closed bounded set Is Lipschitz stable with respect to the Hausdorff distance Under ambient diffeomorphisms","date_published":"2024-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We prove that the medial axis of closed sets is Hausdorff stable in the following sense: Let 𝒮 ⊆ ℝ^d be a fixed closed set that contains a bounding sphere. That is, the bounding sphere is part of the set 𝒮. Consider the space of C^{1,1} diffeomorphisms of ℝ^d to itself, which keep the bounding sphere invariant. The map from this space of diffeomorphisms (endowed with a Banach norm) to the space of closed subsets of ℝ^d (endowed with the Hausdorff distance), mapping a diffeomorphism F to the closure of the medial axis of F(𝒮), is Lipschitz. This extends a previous stability result of Chazal and Soufflet on the stability of the medial axis of C² manifolds under C² ambient diffeomorphisms."}],"type":"conference","ddc":["510"],"department":[{"_id":"HeEd"}],"article_processing_charge":"No","alternative_title":["LIPIcs"],"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773164"]},"scopus_import":"1","ec_funded":1,"file":[{"file_size":1612558,"date_created":"2024-06-17T08:33:40Z","relation":"main_file","access_level":"open_access","checksum":"b40ff456c19294adb5d9613fcfd751c6","content_type":"application/pdf","file_name":"2024_LIPICS_Kourimska.pdf","file_id":"17150","success":1,"creator":"dernst","date_updated":"2024-06-17T08:33:40Z"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"17144","language":[{"iso":"eng"}],"intvolume":"       293","day":"01","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2024-06-14","location":"Athens, Greece"},"year":"2024","date_created":"2024-06-16T22:01:06Z"},{"oa":1,"file_date_updated":"2024-06-17T08:40:04Z","publication_status":"published","acknowledgement":"Part of this work was done while G.R. enjoyed the hospitality of the Institute of Science and Technology Austria (ISTA) as a visiting professor during his sabbatical in the winter semester 2022/23.","has_accepted_license":"1","arxiv":1,"month":"06","quality_controlled":"1","publication":"40th International Symposium on Computational Geometry","date_updated":"2024-06-17T08:41:56Z","volume":293,"abstract":[{"lang":"eng","text":"Grid peeling is the process of repeatedly removing the convex hull vertices of the grid points that lie inside a given convex curve. It has been conjectured that, for a more and more refined grid, grid peeling converges to a continuous process, the affine curve-shortening flow, which deforms the curve based on the curvature. We prove this conjecture for one class of curves, parabolas with a vertical axis, and we determine the value of the constant factor in the formula that relates the two processes."}],"type":"conference","department":[{"_id":"HeEd"}],"ddc":["510"],"external_id":{"arxiv":["2402.15787"]},"date_published":"2024-06-01T00:00:00Z","article_number":"76","title":"Grid peeling of parabolas","status":"public","doi":"10.4230/LIPIcs.SoCG.2024.76","oa_version":"Published Version","citation":{"chicago":"Rote, Günter, Moritz Rüber, and Morteza Saghafian. “Grid Peeling of Parabolas.” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">https://doi.org/10.4230/LIPIcs.SoCG.2024.76</a>.","short":"G. Rote, M. Rüber, M. Saghafian, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Rote, Günter, et al. “Grid Peeling of Parabolas.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 76, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">10.4230/LIPIcs.SoCG.2024.76</a>.","ama":"Rote G, Rüber M, Saghafian M. Grid peeling of parabolas. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">10.4230/LIPIcs.SoCG.2024.76</a>","ieee":"G. Rote, M. Rüber, and M. Saghafian, “Grid peeling of parabolas,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293.","apa":"Rote, G., Rüber, M., &#38; Saghafian, M. (2024). Grid peeling of parabolas. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.76\">https://doi.org/10.4230/LIPIcs.SoCG.2024.76</a>","ista":"Rote G, Rüber M, Saghafian M. 2024. Grid peeling of parabolas. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 76."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Günter","full_name":"Rote, Günter","last_name":"Rote"},{"last_name":"Rüber","full_name":"Rüber, Moritz","first_name":"Moritz"},{"first_name":"Morteza","full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"scopus_import":"1","publication_identifier":{"isbn":["9783959773164"],"issn":["1868-8969"]},"alternative_title":["LIPIcs"],"article_processing_charge":"No","date_created":"2024-06-16T22:01:06Z","year":"2024","conference":{"location":"Athens, Greece","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry","start_date":"2024-06-11"},"intvolume":"       293","_id":"17145","language":[{"iso":"eng"}],"day":"01","file":[{"file_id":"17151","creator":"dernst","success":1,"date_updated":"2024-06-17T08:40:04Z","file_name":"2024_LIPICS_Rote.pdf","checksum":"fbad1de06383a6b7e8a1cb3e8c7205ce","content_type":"application/pdf","access_level":"open_access","file_size":1430896,"date_created":"2024-06-17T08:40:04Z","relation":"main_file"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}}]