[{"article_processing_charge":"Yes","quality_controlled":"1","isi":1,"citation":{"ista":"Podlaski WF, Agnes EJ, Vogels TP. 2025. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. Physical Review X. 15, 011057.","apa":"Podlaski, W. F., Agnes, E. J., &#38; Vogels, T. P. (2025). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">https://doi.org/10.1103/PhysRevX.15.011057</a>","ieee":"W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” <i>Physical Review X</i>, vol. 15. American Physical Society, 2025.","chicago":"Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>Physical Review X</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">https://doi.org/10.1103/PhysRevX.15.011057</a>.","mla":"Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>Physical Review X</i>, vol. 15, 011057, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">10.1103/PhysRevX.15.011057</a>.","ama":"Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>Physical Review X</i>. 2025;15. doi:<a href=\"https://doi.org/10.1103/PhysRevX.15.011057\">10.1103/PhysRevX.15.011057</a>","short":"W.F. Podlaski, E.J. Agnes, T.P. Vogels, Physical Review X 15 (2025)."},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"publication_status":"published","title":"High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating","month":"03","language":[{"iso":"eng"}],"has_accepted_license":"1","related_material":{"link":[{"url":"https://github.com/wpodlaski/contextual-memory-nets","relation":"software"}]},"oa":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2160-3308"]},"scopus_import":"1","article_type":"original","volume":15,"license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","doi":"10.1103/PhysRevX.15.011057","date_created":"2020-07-16T12:24:28Z","publisher":"American Physical Society","abstract":[{"text":"Biological memory is known to be flexible—memory formation and recall depend on factors such as the behavioral context of the organism. However, this property is often ignored in associative memory models, leaving it unclear how memories can be organized and recalled when subject to contextual control. Because of the lack of a rigorous analytical framework, it is also unknown how contextual control affects memory stability, storage capacity, and information content. Here, we bring the dynamic nature of memory to the fore by introducing a novel model of associative memory, which we refer to as the context-modular memory network. In our model, stored memory patterns are associated to one of several background network states, or contexts. Memories are accessible when their corresponding context is active, and are otherwise inaccessible. Context modulates the effective network connectivity by imposing a specific\r\nconfiguration of neuronal and synaptic gating—gated neurons (synapses) have their activity (weights) momentarily silenced, thereby reducing interference from memories belonging to other contexts. Memory patterns are randomly and independently chosen, while neuronal and synaptic gates may be selected randomly or optimized through a process of contextual synaptic refinement. Through analytic and numerical results, we show that context-modular memory networks can exhibit both improved memory capacity and differential control of memory stability with random gating (especially for neuronal gating). For contextual synaptic refinement, we devise a method in which synapses are gated off for a given context if they destabilize the memory patterns in that context, drastically improving memory capacity and enabling even more precise control over memory stability. Notably, synaptic refinement allows for patterns to be\r\naccessible in multiple contexts, stabilizing memory patterns even for weight matrices that alone do not contain any information about the memory patterns, such as Gaussian random matrices. Overall, our model integrates recent ideas about context-dependent memory organization with classic associative memory models and proposes a rigorous theory which can act as a framework for future work. Furthermore, our work carries important implications for the understanding of biological memory storage and recall in the brain, such as highlighting an intriguing trade-off between memory capacity and accessibility.","lang":"eng"}],"author":[{"last_name":"Podlaski","orcid":"0000-0001-6619-7502","first_name":"William F.","full_name":"Podlaski, William F."},{"orcid":"0000-0001-7184-7311","last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P"}],"year":"2025","OA_type":"gold","file_date_updated":"2025-03-20T12:47:17Z","corr_author":"1","file":[{"relation":"main_file","success":1,"file_name":"2025_PhysReviewX_Podlaski.pdf","file_id":"19432","checksum":"1f27ee469ab51a3e1ce1e2df0022e81d","creator":"dernst","date_created":"2025-03-20T12:47:17Z","date_updated":"2025-03-20T12:47:17Z","file_size":1373704,"access_level":"open_access","content_type":"application/pdf"}],"acknowledgement":"We thank Helen Barron, Vezha Boboeva, Adam Packer, João Sacramento, Andrew Saxe, Misha Tsodyks, and Friedemann Zenke for helpful comments at various stages of this work, and Rubem Erichsen, Jr. for carefully reading the manuscript and valuable comments. This work was\r\nsupported by a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society [No. WT100000 (W. F. P., E. J. A., and T. P. V.)], a Wellcome Trust Senior Research Fellowship [No. 214316/Z/18/Z (E. J. A. and T. P. V.)], and a Research Project Grant by the Leverhulme Trust\r\n[No. RPG-2016-446 (E. J. A.)]. ","OA_place":"publisher","article_number":"011057","_id":"8125","publication":"Physical Review X","department":[{"_id":"TiVo"}],"external_id":{"isi":["001451378900002"]},"date_updated":"2026-05-06T12:44:27Z","ddc":["530"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"13","intvolume":"        15","date_published":"2025-03-13T00:00:00Z","locked":"1","APC_amount":"4910,08 EUR"},{"type":"journal_article","article_type":"original","scopus_import":"1","volume":16,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2020-10-06T08:58:59Z","doi":"10.1038/s41467-025-60308-0","publication_identifier":{"eissn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"ec_funded":1,"title":"Reduction of neuronal activity mediated by blood-vessel regression in the brain","month":"07","oa":1,"oa_version":"Published Version","has_accepted_license":"1","citation":{"ista":"Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. 2025. Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. 16, 5840.","apa":"Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (2025). Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-60308-0\">https://doi.org/10.1038/s41467-025-60308-0</a>","ieee":"X. Gao <i>et al.</i>, “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","chicago":"Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-60308-0\">https://doi.org/10.1038/s41467-025-60308-0</a>.","mla":"Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>Nature Communications</i>, vol. 16, 5840, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-60308-0\">10.1038/s41467-025-60308-0</a>.","ama":"Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-60308-0\">10.1038/s41467-025-60308-0</a>","short":"X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, Nature Communications 16 (2025)."},"isi":1,"project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","article_processing_charge":"Yes","publication_status":"published","ddc":["570"],"DOAJ_listed":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","external_id":{"isi":["001523450500035"]},"date_updated":"2025-09-04T07:08:37Z","date_published":"2025-07-01T00:00:00Z","day":"01","intvolume":"        16","publication":"Nature Communications","department":[{"_id":"SiHi"}],"acknowledgement":"The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies.  Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.","file":[{"relation":"main_file","success":1,"file_name":"2025_NatureComm_Gao.pdf","file_id":"19971","date_created":"2025-07-07T09:52:46Z","creator":"dernst","checksum":"f59748cb67232cfb210035d9aef60836","date_updated":"2025-07-07T09:52:46Z","file_size":17018106,"content_type":"application/pdf","access_level":"open_access"}],"OA_place":"publisher","_id":"8616","article_number":"5840","abstract":[{"lang":"eng","text":"The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we report that a substantial proportion of blood vessels in the adult mouse brain sporadically occlude and regress. Their regression proceeds through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels are found to be widespread in mouse, monkey and human brains. We further reveal that blood vessel regression cause a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain."}],"author":[{"last_name":"Gao","full_name":"Gao, Xiaofei","first_name":"Xiaofei"},{"last_name":"Li","full_name":"Li, Jun-Liszt","first_name":"Jun-Liszt"},{"last_name":"Chen","full_name":"Chen, Xingjun","first_name":"Xingjun"},{"last_name":"Ci","first_name":"Bo","full_name":"Ci, Bo"},{"first_name":"Fei","full_name":"Chen, Fei","last_name":"Chen"},{"full_name":"Lu, Nannan","first_name":"Nannan","last_name":"Lu"},{"full_name":"Shen, Bo","first_name":"Bo","last_name":"Shen"},{"full_name":"Zheng, Lijun","first_name":"Lijun","last_name":"Zheng"},{"first_name":"Jie-Min","full_name":"Jia, Jie-Min","last_name":"Jia"},{"first_name":"Yating","full_name":"Yi, Yating","last_name":"Yi"},{"full_name":"Zhang, Shiwen","first_name":"Shiwen","last_name":"Zhang"},{"first_name":"Ying-Chao","full_name":"Shi, Ying-Chao","last_name":"Shi"},{"first_name":"Kaibin","full_name":"Shi, Kaibin","last_name":"Shi"},{"first_name":"Nicholas E","full_name":"Propson, Nicholas E","last_name":"Propson"},{"last_name":"Huang","full_name":"Huang, Yubin","first_name":"Yubin"},{"last_name":"Poinsatte","first_name":"Katherine","full_name":"Poinsatte, Katherine"},{"full_name":"Zhang, Zhaohuan","first_name":"Zhaohuan","last_name":"Zhang"},{"first_name":"Yuanlei","full_name":"Yue, Yuanlei","last_name":"Yue"},{"full_name":"Bosco, Dale B","first_name":"Dale B","last_name":"Bosco"},{"first_name":"Ying-mei","full_name":"Lu, Ying-mei","last_name":"Lu"},{"full_name":"Yang, Shi-bing","first_name":"Shi-bing","last_name":"Yang"},{"last_name":"Adams","first_name":"Ralf H.","full_name":"Adams, Ralf H."},{"full_name":"Lindner, Volkhard","first_name":"Volkhard","last_name":"Lindner"},{"last_name":"Huang","first_name":"Fen","full_name":"Huang, Fen"},{"full_name":"Wu, Long-Jun","first_name":"Long-Jun","last_name":"Wu"},{"last_name":"Zheng","first_name":"Hui","full_name":"Zheng, Hui"},{"full_name":"Han, Feng","first_name":"Feng","last_name":"Han"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"last_name":"Stowe","full_name":"Stowe, Ann M.","first_name":"Ann M."},{"full_name":"Peng, Bo","first_name":"Bo","last_name":"Peng"},{"full_name":"Margeta, Marta","first_name":"Marta","last_name":"Margeta"},{"first_name":"Xiaoqun","full_name":"Wang, Xiaoqun","last_name":"Wang"},{"full_name":"Liu, Qiang","first_name":"Qiang","last_name":"Liu"},{"full_name":"Körbelin, Jakob","first_name":"Jakob","last_name":"Körbelin"},{"full_name":"Trepel, Martin","first_name":"Martin","last_name":"Trepel"},{"first_name":"Hui","full_name":"Lu, Hui","last_name":"Lu"},{"full_name":"Zhou, Bo O.","first_name":"Bo O.","last_name":"Zhou"},{"last_name":"Zhao","first_name":"Hu","full_name":"Zhao, Hu"},{"full_name":"Su, Wenzhi","first_name":"Wenzhi","last_name":"Su"},{"first_name":"Robert M.","full_name":"Bachoo, Robert M.","last_name":"Bachoo"},{"first_name":"Woo-ping","full_name":"Ge, Woo-ping","last_name":"Ge"}],"publisher":"Springer Nature","OA_type":"gold","file_date_updated":"2025-07-07T09:52:46Z","year":"2025"},{"type":"journal_article","volume":26,"scopus_import":"1","article_type":"original","date_created":"2024-07-14T22:01:12Z","doi":"10.1007/s00023-024-01450-1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication_identifier":{"issn":["1424-0637"]},"PlanS_conform":"1","language":[{"iso":"eng"}],"title":"Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion","month":"01","oa_version":"Published Version","oa":1,"related_material":{"record":[{"status":"public","id":"18135","relation":"dissertation_contains"}]},"has_accepted_license":"1","project":[{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"citation":{"mla":"Lauritsen, Asbjørn Bækgaard. “Almost Optimal Upper Bound for the Ground State Energy of a Dilute Fermi Gas via Cluster Expansion.” <i>Annales Henri Poincare</i>, vol. 26, Springer Nature, 2025, pp. 203–43, doi:<a href=\"https://doi.org/10.1007/s00023-024-01450-1\">10.1007/s00023-024-01450-1</a>.","chicago":"Lauritsen, Asbjørn Bækgaard. “Almost Optimal Upper Bound for the Ground State Energy of a Dilute Fermi Gas via Cluster Expansion.” <i>Annales Henri Poincare</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00023-024-01450-1\">https://doi.org/10.1007/s00023-024-01450-1</a>.","apa":"Lauritsen, A. B. (2025). Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-024-01450-1\">https://doi.org/10.1007/s00023-024-01450-1</a>","ieee":"A. B. Lauritsen, “Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion,” <i>Annales Henri Poincare</i>, vol. 26. Springer Nature, pp. 203–243, 2025.","ista":"Lauritsen AB. 2025. Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. 26, 203–243.","short":"A.B. Lauritsen, Annales Henri Poincare 26 (2025) 203–243.","ama":"Lauritsen AB. Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. <i>Annales Henri Poincare</i>. 2025;26:203-243. doi:<a href=\"https://doi.org/10.1007/s00023-024-01450-1\">10.1007/s00023-024-01450-1</a>"},"isi":1,"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication_status":"published","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["510"],"external_id":{"isi":["001261197700002"],"pmid":["39926012"]},"date_updated":"2026-04-07T13:01:40Z","date_published":"2025-01-01T00:00:00Z","intvolume":"        26","day":"01","department":[{"_id":"RoSe"}],"publication":"Annales Henri Poincare","OA_place":"publisher","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nWe thank Alessandro Giuliani and Robert Seiringer for helpful discussions and Robert Seiringer for his comments on the manuscript. Financial support by the Austrian Science Fund (FWF) through Grant https://doi.org/10.55776/I6427 (as part of the SFB/TRR 352) is gratefully acknowledged.","file":[{"success":1,"relation":"main_file","file_name":"2025_AnnalesHenriPoincare_Lauritsen.pdf","date_created":"2025-08-05T11:42:27Z","creator":"dernst","checksum":"01b6572f55f721e97498522c85072ed2","file_id":"20125","content_type":"application/pdf","access_level":"open_access","file_size":797241,"date_updated":"2025-08-05T11:42:27Z"}],"corr_author":"1","_id":"17240","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"abstract":[{"lang":"eng","text":"We prove an upper bound on the energy density of the dilute spin-\\(\\frac {1}{2}\\) Fermi gas capturing the leading correction to the kinetic energy\\(8\\pi a\\rho _\\uparrow\\rho _\\downarrow\\) with an error of size smaller than\\(a\\rho^{2}(a^ 3\\rho)^{1/3-\\varepsilon}\\) for any\\(\\varepsilon> 0\\), where a denotes the scattering length of the interaction. The result is valid for a large class of interactions including interactions with a hard core. A central ingredient in the proof is a rigorous version of a fermionic cluster expansion adapted from the formal expansion of Gaudin et al. (Nucl Phys A 176(2):237–260, 1971. https://doi.org/10.1016/0375-9474(71)90267-3)."}],"publisher":"Springer Nature","file_date_updated":"2025-08-05T11:42:27Z","OA_type":"hybrid","page":"203-243","year":"2025"},{"scopus_import":"1","article_type":"original","volume":35,"type":"journal_article","doi":"10.1111/bpa.13279","date_created":"2024-07-22T07:48:20Z","publication_identifier":{"eissn":["1750-3639"],"issn":["1015-6305"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"title":"Nanoarchitecture of CaV>2.1 channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology","month":"03","language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"issue":"2","oa_version":"Published Version","article_processing_charge":"Yes","quality_controlled":"1","citation":{"ama":"Martín‐Belmonte A, Aguado C, Alfaro‐Ruiz R, et al. Nanoarchitecture of CaV&#62;2.1 channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology. <i>Brain Pathology</i>. 2025;35(2). doi:<a href=\"https://doi.org/10.1111/bpa.13279\">10.1111/bpa.13279</a>","short":"A. Martín‐Belmonte, C. Aguado, R. Alfaro‐Ruiz, A. Kulik, L. de la Ossa, A.E. Moreno‐Martínez, S. Alberquilla, L. García‐Carracedo, M. Fernández, A. Fajardo‐Serrano, E. Aso, R. Shigemoto, E.D. Martín, Y. Fukazawa, F. Ciruela, R. Luján, Brain Pathology 35 (2025).","ista":"Martín‐Belmonte A, Aguado C, Alfaro‐Ruiz R, Kulik A, de la Ossa L, Moreno‐Martínez AE, Alberquilla S, García‐Carracedo L, Fernández M, Fajardo‐Serrano A, Aso E, Shigemoto R, Martín ED, Fukazawa Y, Ciruela F, Luján R. 2025. Nanoarchitecture of CaV&#62;2.1 channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology. Brain Pathology. 35(2), e13279.","apa":"Martín‐Belmonte, A., Aguado, C., Alfaro‐Ruiz, R., Kulik, A., de la Ossa, L., Moreno‐Martínez, A. E., … Luján, R. (2025). Nanoarchitecture of CaV&#62;2.1 channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology. <i>Brain Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/bpa.13279\">https://doi.org/10.1111/bpa.13279</a>","ieee":"A. Martín‐Belmonte <i>et al.</i>, “Nanoarchitecture of CaV&#62;2.1 channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology,” <i>Brain Pathology</i>, vol. 35, no. 2. Wiley, 2025.","chicago":"Martín‐Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro‐Ruiz, Akos Kulik, Luis de la Ossa, Ana Esther Moreno‐Martínez, Samuel Alberquilla, et al. “Nanoarchitecture of CaV&#62;2.1 Channels and GABAB Receptors in the Mouse Hippocampus: Impact of APP/PS1 Pathology.” <i>Brain Pathology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/bpa.13279\">https://doi.org/10.1111/bpa.13279</a>.","mla":"Martín‐Belmonte, Alejandro, et al. “Nanoarchitecture of CaV&#62;2.1 Channels and GABAB Receptors in the Mouse Hippocampus: Impact of APP/PS1 Pathology.” <i>Brain Pathology</i>, vol. 35, no. 2, e13279, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/bpa.13279\">10.1111/bpa.13279</a>."},"isi":1,"publication_status":"published","external_id":{"isi":["001250034200001"],"pmid":["38887180"]},"date_updated":"2025-05-19T13:58:12Z","DOAJ_listed":"1","ddc":["570"],"status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"01","intvolume":"        35","date_published":"2025-03-01T00:00:00Z","publication":"Brain Pathology","department":[{"_id":"RySh"}],"file":[{"date_created":"2025-04-16T09:56:08Z","creator":"dernst","checksum":"75a172800ab2e949abb66fba97cf70f0","file_id":"19582","content_type":"application/pdf","access_level":"open_access","file_size":8767863,"date_updated":"2025-04-16T09:56:08Z","success":1,"relation":"main_file","file_name":"2025_BrainPathology_MartinBelmonte.pdf"}],"acknowledgement":"Funding sources were Spanish Ministerio de Economía y Competitividad, Junta de Comunidades de Castilla-La Mancha (Spain), Life Science Innovation Center at University of Fukui and German Research Foundation.\r\nGrants RTI2018-095812-B-I00 and PID2021-125875OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe” to Rafael Luján. This study was also supported by a grant from Junta de Comunidades de Castilla-La Mancha (SBPLY/17/180501/000229 and SBPLY/21/180501/000064) and Universidad de Castilla-La Mancha (2023-GRIN-34187) to Rafael Luján, and Life Science Innovation Center (Research and Education Program for Life Science) at University of Fukui and JSPS KAKENHI Grant Numbers 16H04662, 17K19446, 18H05120 to Yugo Fukazawa and Margarita Salas fellowship from Ministerio de Universidades and Universidad de Castilla-La Mancha to Alejandro Martín-Belmonte. German Research Foundation (DFG FOR 2143) and BIOSS-2 to Akos Kulik.","OA_place":"publisher","article_number":"e13279","_id":"17293","publisher":"Wiley","abstract":[{"text":"Voltage-gated CaV2.1 (P/Q-type) Ca2+ channels play a crucial role in regulating neurotransmitter release, thus contributing to synaptic plasticity and to processes such as learning and memory. Despite their recognized importance in neural function, there is limited information on their potential involvement in neurodegenerative conditions such as Alzheimer's disease (AD). Here, we aimed to explore the impact of AD pathology on the density and nanoscale compartmentalization of CaV2.1 channels in the hippocampus in association with GABAB receptors. Histoblotting experiments showed that the density of CaV2.1 channel was significantly reduced in the hippocampus of APP/PS1 mice in a laminar-dependent manner. CaV2.1 channel was enriched in the active zone of the axon terminals and was present at a very low density over the surface of dendritic tree of the CA1 pyramidal cells, as shown by quantitative SDS-digested freeze-fracture replica labelling (SDS-FRL). In APP/PS1 mice, the density of CaV2.1 channel in the active zone was significantly reduced in the strata radiatum and lacunosum-moleculare, while it remained unaltered in the stratum oriens. The decline in Cav2.1 channel density was found to be associated with a corresponding impairment in the GABAergic synaptic function, as evidenced by electrophysiological experiments carried out in the hippocampus of APP/PS1 mice. Remarkably, double SDS-FRL showed a co-clustering of CaV2.1 channel and GABAB1 receptor in nanodomains (~40–50 nm) in wild type mice, while in APP/PS1 mice this nanoarchitecture was absent. Together, these findings suggest that the AD pathology-induced reduction in CaV2.1 channel density and CaV2.1-GABAB1 de-clustering may play a role in the synaptic transmission alterations shown in the AD hippocampus. Therefore, uncovering these layer-dependent changes in P/Q calcium currents associated with AD pathology can benefit the development of future strategies for AD management.","lang":"eng"}],"author":[{"full_name":"Martín‐Belmonte, Alejandro","first_name":"Alejandro","last_name":"Martín‐Belmonte"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"last_name":"Alfaro‐Ruiz","full_name":"Alfaro‐Ruiz, Rocío","first_name":"Rocío"},{"last_name":"Kulik","full_name":"Kulik, Akos","first_name":"Akos"},{"full_name":"de la Ossa, Luis","first_name":"Luis","last_name":"de la Ossa"},{"last_name":"Moreno‐Martínez","full_name":"Moreno‐Martínez, Ana Esther","first_name":"Ana Esther"},{"last_name":"Alberquilla","full_name":"Alberquilla, Samuel","first_name":"Samuel"},{"first_name":"Lucía","full_name":"García‐Carracedo, Lucía","last_name":"García‐Carracedo"},{"last_name":"Fernández","full_name":"Fernández, Miriam","first_name":"Miriam"},{"full_name":"Fajardo‐Serrano, Ana","first_name":"Ana","last_name":"Fajardo‐Serrano"},{"full_name":"Aso, Ester","first_name":"Ester","last_name":"Aso"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Martín, Eduardo D.","first_name":"Eduardo D.","last_name":"Martín"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"first_name":"Francisco","full_name":"Ciruela, Francisco","last_name":"Ciruela"},{"full_name":"Luján, Rafael","first_name":"Rafael","last_name":"Luján"}],"year":"2025","OA_type":"gold","file_date_updated":"2025-04-16T09:56:08Z"},{"publication_identifier":{"issn":["0926-9959"],"eissn":["1468-3083"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-08-25T22:01:07Z","doi":"10.1111/jdv.20291","type":"journal_article","volume":39,"article_type":"original","scopus_import":"1","publication_status":"published","isi":1,"citation":{"short":"Y. Pan, M. Hochgerner, M.A. Cichon, T. Benezeder, T. Bieber, P. Wolf, Journal of the European Academy of Dermatology and Venereology 39 (2025) 278–289.","ama":"Pan Y, Hochgerner M, Cichon MA, Benezeder T, Bieber T, Wolf P. Langerhans cells: Central players in the pathophysiology of atopic dermatitis. <i>Journal of the European Academy of Dermatology and Venereology</i>. 2025;39(2):278-289. doi:<a href=\"https://doi.org/10.1111/jdv.20291\">10.1111/jdv.20291</a>","mla":"Pan, Yi, et al. “Langerhans Cells: Central Players in the Pathophysiology of Atopic Dermatitis.” <i>Journal of the European Academy of Dermatology and Venereology</i>, vol. 39, no. 2, Wiley, 2025, pp. 278–89, doi:<a href=\"https://doi.org/10.1111/jdv.20291\">10.1111/jdv.20291</a>.","chicago":"Pan, Yi, Mathias Hochgerner, Malgorzata Anna Cichon, Theresa Benezeder, Thomas Bieber, and Peter Wolf. “Langerhans Cells: Central Players in the Pathophysiology of Atopic Dermatitis.” <i>Journal of the European Academy of Dermatology and Venereology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/jdv.20291\">https://doi.org/10.1111/jdv.20291</a>.","ista":"Pan Y, Hochgerner M, Cichon MA, Benezeder T, Bieber T, Wolf P. 2025. Langerhans cells: Central players in the pathophysiology of atopic dermatitis. Journal of the European Academy of Dermatology and Venereology. 39(2), 278–289.","ieee":"Y. Pan, M. Hochgerner, M. A. Cichon, T. Benezeder, T. Bieber, and P. Wolf, “Langerhans cells: Central players in the pathophysiology of atopic dermatitis,” <i>Journal of the European Academy of Dermatology and Venereology</i>, vol. 39, no. 2. Wiley, pp. 278–289, 2025.","apa":"Pan, Y., Hochgerner, M., Cichon, M. A., Benezeder, T., Bieber, T., &#38; Wolf, P. (2025). Langerhans cells: Central players in the pathophysiology of atopic dermatitis. <i>Journal of the European Academy of Dermatology and Venereology</i>. Wiley. <a href=\"https://doi.org/10.1111/jdv.20291\">https://doi.org/10.1111/jdv.20291</a>"},"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","issue":"2","oa_version":"Published Version","oa":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"month":"02","title":"Langerhans cells: Central players in the pathophysiology of atopic dermatitis","publication":"Journal of the European Academy of Dermatology and Venereology","department":[{"_id":"MiSi"}],"date_published":"2025-02-01T00:00:00Z","intvolume":"        39","day":"01","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["570"],"external_id":{"isi":["001292894900001"],"pmid":["39157943"]},"date_updated":"2025-05-19T13:58:50Z","file_date_updated":"2025-04-16T09:59:37Z","OA_type":"hybrid","page":"278-289","year":"2025","author":[{"first_name":"Yi","full_name":"Pan, Yi","last_name":"Pan"},{"full_name":"Hochgerner, Mathias","first_name":"Mathias","last_name":"Hochgerner"},{"full_name":"Cichon, Malgorzata Anna","first_name":"Malgorzata Anna","id":"d63197a3-c188-11ed-9387-8d33a3f13871","last_name":"Cichon"},{"full_name":"Benezeder, Theresa","first_name":"Theresa","last_name":"Benezeder"},{"last_name":"Bieber","full_name":"Bieber, Thomas","first_name":"Thomas"},{"full_name":"Wolf, Peter","first_name":"Peter","last_name":"Wolf"}],"abstract":[{"text":"Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide. AD is a highly complex disease with different subtypes. Many elements of AD pathophysiology have been described, but if/how they interact with each other or which mechanisms are important in which patients is still unclear. Langerhans cells (LCs) are antigen-presenting cells (APCs) in the epidermis. Depending on the context, they can act either pro- or anti-inflammatory. Many different studies have investigated LCs in the context of AD and found them to be connected to all major mechanisms of AD pathophysiology. As APCs, LCs recruit other immune cells and shape the immune response, especially adaptive immunity via polarization of T cells. As sentinel cells, LCs are primary sensors of the skin microbiome and are important for the decision of immunity versus tolerance. LCs are also involved with the integrity of the skin barrier by influencing tight junctions. Finally, LCs are important cells in the neuro-immune crosstalk in the skin. In this review, we provide an overview about the many different roles of LCs in AD. Understanding LCs might bring us closer to a more complete understanding of this highly complex disease. Potentially, modulating LCs might offer new options for targeted therapies for AD patients.","lang":"eng"}],"publisher":"Wiley","_id":"17459","OA_place":"publisher","file":[{"file_name":"2025_JEADV_Pan.pdf","relation":"main_file","success":1,"file_size":457698,"date_updated":"2025-04-16T09:59:37Z","access_level":"open_access","content_type":"application/pdf","file_id":"19583","checksum":"12555ddb3490daf10b8d44e334e7312e","creator":"dernst","date_created":"2025-04-16T09:59:37Z"}],"acknowledgement":"This work was supported by the CK-CARE of the KühneFoundation, Switzerland; the China Scholarship Counciland Shanghai Biocelline Enterprise Co. Ltd, China."},{"day":"16","intvolume":"       646","date_published":"2025-10-16T00:00:00Z","external_id":{"isi":["001586378900001"],"pmid":["41044415"]},"date_updated":"2026-04-28T13:18:33Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["540"],"department":[{"_id":"StFr"},{"_id":"Bio"}],"publication":"Nature","_id":"17468","corr_author":"1","OA_place":"publisher","file":[{"checksum":"b507ddd23df0388aa65d04dc9b00fe3d","creator":"dernst","date_created":"2025-10-20T10:26:13Z","file_id":"20500","access_level":"open_access","content_type":"application/pdf","file_size":3809247,"date_updated":"2025-10-20T10:26:13Z","success":1,"relation":"main_file","file_name":"2025_Nature_Mondal.pdf"}],"acknowledgement":"S.A.F. thanks the Institute of Science and Technology Austria (ISTA) for the support. The Scientific Service Units of ISTA supported this research through resources provided by the Imaging and Optics Facility, the Lab Support Facility, the Miba Machine Shop and Scientific Computing. This research was partly funded by the Austrian Science Fund (FWF) (10.55776/P37169 and 10.55776/COE5). For open access purposes, the author has applied for a CC BY public copyright licence to any author-accepted manuscript version arising from this submission. R.H. acknowledges funding through CZI grant DAF2020-225401 (10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (10.13039/100014989). H.T.K.N. acknowledges funding by the European Commission Erasmus Mundus Joint Masters programme. We thank M. Sixt and M. Chinon for the discussions about O-redox in life and R. Jethwa for proofreading. Open access funding was provided by ISTA.","page":"601–605","year":"2025","file_date_updated":"2025-10-20T10:26:13Z","OA_type":"hybrid","publisher":"Springer Nature","author":[{"last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip","first_name":"Soumyadip"},{"last_name":"Nguyen","full_name":"Nguyen, Huyen T.K.","first_name":"Huyen T.K."},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert"},{"first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger"}],"abstract":[{"lang":"eng","text":"Oxygen redox chemistry is central to life1 and many human-made technologies, such as in energy storage2,3,4. The large energy gain from oxygen redox reactions is often connected with the occurrence of harmful reactive oxygen species3,5,6. Key species are superoxide and the highly reactive singlet oxygen3,4,5,6,7, which may evolve from superoxide. However, the factors determining the formation of singlet oxygen, rather than the relatively unreactive triplet oxygen, are unknown. Here we report that the release of triplet or singlet oxygen is governed by individual Marcus normal and inverted region behaviour. We found that as the driving force for the reaction increases, the initially dominant evolution of triplet oxygen slows down, and singlet oxygen evolution becomes predominant with higher maximum kinetics. This behaviour also applies to the widely observed superoxide disproportionation, in which one superoxide is oxidized by another, in both non-aqueous and aqueous systems, with Lewis and Brønsted acidity controlling the driving forces. Singlet oxygen yields governed by these conditions are relevant, for example, in batteries or cellular organelles in which superoxide forms. Our findings suggest ways to understand and control spin states and kinetics in oxygen redox chemistry, with implications for fields, including life sciences, pure chemistry and energy storage."}],"doi":"10.1038/s41586-025-09587-7","date_created":"2024-08-29T10:40:23Z","volume":646,"scopus_import":"1","article_type":"original","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"PlanS_conform":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pmid":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/taming-the-bad-oxygen/","relation":"press_release","description":"News on ISTA website"}]},"has_accepted_license":"1","oa_version":"Published Version","issue":"8085","oa":1,"month":"10","title":"Marcus kinetics control singlet and triplet oxygen evolving from superoxide","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"P37169","name":"Singlet oxygen in non-aqueous oxygen redox chemistry","_id":"8df062be-16d5-11f0-9cad-f559b6612c7e"},{"grant_number":"CZI01","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy"}],"isi":1,"citation":{"apa":"Mondal, S., Nguyen, H. T. K., Hauschild, R., &#38; Freunberger, S. A. (2025). Marcus kinetics control singlet and triplet oxygen evolving from superoxide. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09587-7\">https://doi.org/10.1038/s41586-025-09587-7</a>","ieee":"S. Mondal, H. T. K. Nguyen, R. Hauschild, and S. A. Freunberger, “Marcus kinetics control singlet and triplet oxygen evolving from superoxide,” <i>Nature</i>, vol. 646, no. 8085. Springer Nature, pp. 601–605, 2025.","ista":"Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. 2025. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. Nature. 646(8085), 601–605.","mla":"Mondal, Soumyadip, et al. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” <i>Nature</i>, vol. 646, no. 8085, Springer Nature, 2025, pp. 601–605, doi:<a href=\"https://doi.org/10.1038/s41586-025-09587-7\">10.1038/s41586-025-09587-7</a>.","chicago":"Mondal, Soumyadip, Huyen T.K. Nguyen, Robert Hauschild, and Stefan Alexander Freunberger. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09587-7\">https://doi.org/10.1038/s41586-025-09587-7</a>.","ama":"Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. <i>Nature</i>. 2025;646(8085):601–605. doi:<a href=\"https://doi.org/10.1038/s41586-025-09587-7\">10.1038/s41586-025-09587-7</a>","short":"S. Mondal, H.T.K. Nguyen, R. Hauschild, S.A. Freunberger, Nature 646 (2025) 601–605."}},{"publication_status":"published","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","isi":1,"citation":{"mla":"Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 268–76, doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>.","chicago":"Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick, and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>.","apa":"Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., … Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>","ieee":"M. Obr <i>et al.</i>, “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 268–276, 2025.","ista":"Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural &#38; Molecular Biology. 32, 268–276.","short":"M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural &#38; Molecular Biology 32 (2025) 268–276.","ama":"Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:268-276. doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>"},"project":[{"call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"has_accepted_license":"1","oa":1,"oa_version":"Published Version","month":"02","title":"Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"doi":"10.1038/s41594-024-01390-8","date_created":"2024-09-08T10:29:06Z","article_type":"original","scopus_import":"1","volume":32,"type":"journal_article","page":"268-276","year":"2025","OA_type":"hybrid","file_date_updated":"2025-04-23T07:02:33Z","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct."}],"author":[{"last_name":"Obr","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","first_name":"Martin"},{"id":"4986e21c-eb97-11eb-a6c2-a4ef0b629971","last_name":"Percipalle","first_name":"Mathias","full_name":"Percipalle, Mathias"},{"first_name":"Darya","full_name":"Chernikova, Darya","id":"7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0","last_name":"Chernikova"},{"full_name":"Yang, Huixin","first_name":"Huixin","last_name":"Yang"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","full_name":"Thader, Andreas","first_name":"Andreas"},{"full_name":"Pinke, Gergely","first_name":"Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","last_name":"Pinke"},{"id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","last_name":"Porley","first_name":"Dario J","full_name":"Porley, Dario J"},{"first_name":"Louis M.","full_name":"Mansky, Louis M.","last_name":"Mansky"},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"_id":"17884","corr_author":"1","oaworkid":1,"file":[{"access_level":"open_access","content_type":"application/pdf","file_size":13724041,"date_updated":"2025-04-23T07:02:33Z","checksum":"c641ad94afb28917b20425db676fc3ee","creator":"dernst","date_created":"2025-04-23T07:02:33Z","file_id":"19608","file_name":"2025_NatureStrucBio_Obr.pdf","success":1,"relation":"main_file"}],"acknowledgement":"This work was funded by the Institute of Science and Technology Austria (ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This research was also supported by the scientific service units of ISTA through resources provided by Scientific Computing, the Life Science Facility, and the EM Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775 and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P. was supported by the DOC doctoral fellowship program of the Austrian Academy of Sciences. R.A.D was supported by the National Institute of Allergy and Infectious Diseases (grant R01AI147890). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Specifically, we also want to thank A. Schlögl for computational support and J. Hansen and V. Vogt for critical comments on the manuscript. We also thank the other members of the Schur lab for helpful discussions and experimental advice.","OA_place":"publisher","department":[{"_id":"FlSc"},{"_id":"LeSa"}],"publication":"Nature Structural & Molecular Biology","day":"01","intvolume":"        32","date_published":"2025-02-01T00:00:00Z","APC_amount":"12348 EUR","date_updated":"2026-03-16T12:55:18Z","external_id":{"isi":["001306564000001"],"pmid":["39242978"],"oaworkid":["W4402316284"]},"ddc":["570"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"publisher":"Springer Nature","author":[{"last_name":"Fialova","id":"e9c9844d-9e21-11ec-b482-f96fc09f7c4d","full_name":"Fialova, Marie","first_name":"Marie"}],"abstract":[{"text":"The Aharonov–Casher theorem is a result on the number of the so-called zero modes of a system described by the magnetic Pauli operator in R2. In this paper we address the same question for the Dirac operator on a flat two-dimensional manifold with boundary and Atiyah–Patodi–Singer boundary condition. More concretely we are interested in the plane and a disc with a finite number of circular holes cut out. We consider a smooth compactly supported magnetic field on the manifold and an arbitrary magnetic field inside the holes.","lang":"eng"}],"year":"2025","page":"2859-2900","file_date_updated":"2025-08-05T11:24:25Z","OA_type":"hybrid","corr_author":"1","OA_place":"publisher","acknowledgement":"First and foremost I am grateful to Jan Philip Solovej for fruitful meetings during (and after) my PhD programme, when this work was done. Further I would like to thank Joshua Hunt, Anna Sisak, Jakub Löwit, Błażej Ruba, Volodymir Riabov, Lukas Schimmer and Georgios Koutentakis for valuable discussions. Many thanks belong to Rafael Benguria for hosting my visit, during which some of the work has been done. I am also grateful to Marina Prokhorova who first initiated the discussion of this project topic and to Annemarie Luger for her valuable comments during my PhD defence and in particular pointing out the qualitative difference in our two main results. I would like to acknowledge support for research on this paper from VILLUM FONDEN through the QMATH Centre of Excellence grant. nr. 10059. This project also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. I am grateful to the two reviewers for reading carefully my manuscript and pointing out several issues contributing thus significantly to the readability and clarity of this paper.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","file":[{"file_name":"2025_AnnalesHenriPoincare_Fialova.pdf","relation":"main_file","success":1,"date_updated":"2025-08-05T11:24:25Z","file_size":728124,"access_level":"open_access","content_type":"application/pdf","file_id":"20124","checksum":"d8d2d6dbce293c9ee6eaa9262e597147","creator":"dernst","date_created":"2025-08-05T11:24:25Z"}],"_id":"18074","publication":"Annales Henri Poincare","department":[{"_id":"RoSe"}],"external_id":{"isi":["001304370000001"],"arxiv":["2304.13373"]},"date_updated":"2025-09-30T10:22:14Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["510"],"intvolume":"        26","day":"01","date_published":"2025-08-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"isi":1,"citation":{"ista":"Fialova M. 2025. Aharonov–Casher theorems for Dirac operators on manifolds with boundary and APS boundary condition. Annales Henri Poincare. 26, 2859–2900.","ieee":"M. Fialova, “Aharonov–Casher theorems for Dirac operators on manifolds with boundary and APS boundary condition,” <i>Annales Henri Poincare</i>, vol. 26. Springer Nature, pp. 2859–2900, 2025.","apa":"Fialova, M. (2025). Aharonov–Casher theorems for Dirac operators on manifolds with boundary and APS boundary condition. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-024-01482-7\">https://doi.org/10.1007/s00023-024-01482-7</a>","chicago":"Fialova, Marie. “Aharonov–Casher Theorems for Dirac Operators on Manifolds with Boundary and APS Boundary Condition.” <i>Annales Henri Poincare</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00023-024-01482-7\">https://doi.org/10.1007/s00023-024-01482-7</a>.","mla":"Fialova, Marie. “Aharonov–Casher Theorems for Dirac Operators on Manifolds with Boundary and APS Boundary Condition.” <i>Annales Henri Poincare</i>, vol. 26, Springer Nature, 2025, pp. 2859–900, doi:<a href=\"https://doi.org/10.1007/s00023-024-01482-7\">10.1007/s00023-024-01482-7</a>.","ama":"Fialova M. Aharonov–Casher theorems for Dirac operators on manifolds with boundary and APS boundary condition. <i>Annales Henri Poincare</i>. 2025;26:2859-2900. doi:<a href=\"https://doi.org/10.1007/s00023-024-01482-7\">10.1007/s00023-024-01482-7</a>","short":"M. Fialova, Annales Henri Poincare 26 (2025) 2859–2900."},"publication_status":"published","month":"08","title":"Aharonov–Casher theorems for Dirac operators on manifolds with boundary and APS boundary condition","ec_funded":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1424-0637"]},"PlanS_conform":"1","arxiv":1,"volume":26,"scopus_import":"1","article_type":"original","type":"journal_article","doi":"10.1007/s00023-024-01482-7","date_created":"2024-09-15T22:01:42Z"},{"page":"81-118","year":"2025","file_date_updated":"2025-01-13T08:57:57Z","OA_type":"hybrid","publisher":"Elsevier","author":[{"id":"e3b80ae2-eb8e-11eb-b029-9aef4a9108a0","last_name":"Löwit","full_name":"Löwit, Jakub","first_name":"Jakub"}],"abstract":[{"text":"In 1976, Deligne and Lusztig realized the representation theory of finite groups of Lie type inside étale cohomology of certain algebraic varieties. Recently, a p-adic version of this theory started to emerge: there are p-adic Deligne–Lusztig spaces, whose cohomology encodes representation theoretic information for p-adic groups – for instance, it partially realizes the local Langlands correspondence with characteristic zero coefficients. However, the parallel case of coefficients of positive characteristic  ℓ≠p has not been inspected so far. The purpose of this article is to initiate such an inspection. In particular, we relate cohomology of certain p-adic Deligne–Lusztig spaces to Vignéras's modular local Langlands correspondence for GLn.","lang":"eng"}],"_id":"18154","corr_author":"1","OA_place":"publisher","file":[{"success":1,"relation":"main_file","file_name":"2024_JourAlgebra_Loewit.pdf","creator":"dernst","date_created":"2025-01-13T08:57:57Z","checksum":"eb240e93c178e48429ad918c9058f1fe","file_id":"18830","content_type":"application/pdf","access_level":"open_access","file_size":731175,"date_updated":"2025-01-13T08:57:57Z"}],"publication":"Journal of Algebra","department":[{"_id":"TaHa"}],"day":"01","intvolume":"       663","date_published":"2025-02-01T00:00:00Z","date_updated":"2025-02-27T12:32:40Z","external_id":{"isi":["001325207800001"],"arxiv":["2404.11176"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["510"],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","citation":{"short":"J. Löwit, Journal of Algebra 663 (2025) 81–118.","ama":"Löwit J. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. <i>Journal of Algebra</i>. 2025;663(2):81-118. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">10.1016/j.jalgebra.2024.08.033</a>","mla":"Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for GLn.” <i>Journal of Algebra</i>, vol. 663, no. 2, Elsevier, 2025, pp. 81–118, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">10.1016/j.jalgebra.2024.08.033</a>.","chicago":"Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for GLn.” <i>Journal of Algebra</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">https://doi.org/10.1016/j.jalgebra.2024.08.033</a>.","ieee":"J. Löwit, “On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn,” <i>Journal of Algebra</i>, vol. 663, no. 2. Elsevier, pp. 81–118, 2025.","apa":"Löwit, J. (2025). On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2024.08.033\">https://doi.org/10.1016/j.jalgebra.2024.08.033</a>","ista":"Löwit J. 2025. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn. Journal of Algebra. 663(2), 81–118."},"isi":1,"has_accepted_license":"1","issue":"2","oa_version":"Published Version","oa":1,"title":"On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn","month":"02","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1090-266X"],"issn":["0021-8693"]},"doi":"10.1016/j.jalgebra.2024.08.033","date_created":"2024-09-29T22:01:37Z","volume":663,"arxiv":1,"scopus_import":"1","article_type":"original","type":"journal_article"},{"intvolume":"        47","day":"01","date_published":"2025-03-01T00:00:00Z","external_id":{"isi":["001318056000001"],"arxiv":["2303.09459"]},"date_updated":"2025-05-19T14:00:09Z","ddc":["510"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"Mathematical Intelligencer","department":[{"_id":"UlWa"},{"_id":"MaKw"}],"_id":"18157","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2025-04-08T11:17:45Z","file_size":1760643,"creator":"dernst","date_created":"2025-04-08T11:17:45Z","checksum":"c932ebe45c460d4a73f5b2dcca643db1","file_id":"19530","file_name":"2025_MathIntelligencer_Brunck.pdf","success":1,"relation":"main_file"}],"acknowledgement":"Open access funding provided by Copenhagen University.","OA_place":"publisher","year":"2025","page":"52-65","OA_type":"hybrid","file_date_updated":"2025-04-08T11:17:45Z","publisher":"Springer Nature","abstract":[{"text":"Interest in sliding block puzzles dates back to the 15-puzzle, seemingly invented by Noyes Chapman in 1874 (see [23] for an account of the fascinating history of the puzzle). The game consists of fifteen movable square blocks numbered \r\n and arranged within a \r\n square box, leaving one empty space (see Figure 1). The task at hand is to start from a given configuration of the numbered blocks and reach the desired target configuration, where the only allowed move is to slide a numbered block into an adjacent empty space. This task seemed to be unpredictably either very easy to accomplish, or completely impossible, and the puzzle turned into a worldwide sensation in the spring of 1880. A particularly challenging instance, known as the 13-15-14 puzzle, consisted of initial and target configurations that differed by a single swap (historically this swap involved the blocks labeled 14 and 15). The craze of this puzzle was such that it consistently made newspaper headlines in 1880, with an article in the New York Times lamenting that it was “threatening our free institutions” [23, p. 9]. Various prizes were offered for anyone who could solve this challenge, beginning with a $25 set of teeth and culminating with Sam Loyd’s famous $1,000 cash prize.","lang":"eng"}],"author":[{"id":"6ab6e556-f394-11eb-9cf6-9dfb78f00d8d","last_name":"Brunck","first_name":"Florestan R","full_name":"Brunck, Florestan R"},{"first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","last_name":"Kwan"}],"doi":"10.1007/s00283-024-10358-x","date_created":"2024-09-29T22:01:38Z","scopus_import":"1","article_type":"original","volume":47,"arxiv":1,"type":"journal_article","publication_identifier":{"issn":["0343-6993"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","oa":1,"oa_version":"Published Version","title":"Books, Hallways, and social butterflies: A note on sliding block puzzles","month":"03","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","isi":1,"citation":{"ama":"Brunck FR, Kwan MA. Books, Hallways, and social butterflies: A note on sliding block puzzles. <i>Mathematical Intelligencer</i>. 2025;47:52-65. doi:<a href=\"https://doi.org/10.1007/s00283-024-10358-x\">10.1007/s00283-024-10358-x</a>","short":"F.R. Brunck, M.A. Kwan, Mathematical Intelligencer 47 (2025) 52–65.","ista":"Brunck FR, Kwan MA. 2025. Books, Hallways, and social butterflies: A note on sliding block puzzles. Mathematical Intelligencer. 47, 52–65.","ieee":"F. R. Brunck and M. A. Kwan, “Books, Hallways, and social butterflies: A note on sliding block puzzles,” <i>Mathematical Intelligencer</i>, vol. 47. Springer Nature, pp. 52–65, 2025.","apa":"Brunck, F. R., &#38; Kwan, M. A. (2025). Books, Hallways, and social butterflies: A note on sliding block puzzles. <i>Mathematical Intelligencer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00283-024-10358-x\">https://doi.org/10.1007/s00283-024-10358-x</a>","chicago":"Brunck, Florestan R, and Matthew Alan Kwan. “Books, Hallways, and Social Butterflies: A Note on Sliding Block Puzzles.” <i>Mathematical Intelligencer</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00283-024-10358-x\">https://doi.org/10.1007/s00283-024-10358-x</a>.","mla":"Brunck, Florestan R., and Matthew Alan Kwan. “Books, Hallways, and Social Butterflies: A Note on Sliding Block Puzzles.” <i>Mathematical Intelligencer</i>, vol. 47, Springer Nature, 2025, pp. 52–65, doi:<a href=\"https://doi.org/10.1007/s00283-024-10358-x\">10.1007/s00283-024-10358-x</a>."}},{"department":[{"_id":"ToHe"}],"publication":"Science of Computer Programming","intvolume":"       240","day":"01","date_published":"2025-02-01T00:00:00Z","date_updated":"2025-09-09T12:25:29Z","external_id":{"isi":["001327852600001"]},"ddc":["000"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","year":"2025","OA_type":"hybrid","file_date_updated":"2025-01-13T09:02:47Z","publisher":"Elsevier","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of runtime monitoring. Third-party and best-effort monitoring are especially valuable, yet under-explored areas of runtime monitoring. In this context, third-party monitoring means monitoring with a limited knowledge of the monitored software (as it has been developed by a third party). Best-effort monitoring keeps pace with the monitored software at the cost of possibly imprecise verdicts when keeping up with the monitored software would not be feasible. Most existing monitoring frameworks do not support the combination of third-party and best-effort monitoring because they either require the full access to the monitored code or the ability to process all observable events, or both.\r\nWe present a middleware framework, Vamos, for the runtime monitoring of software. Vamos is explicitly designed to support third-party and best-effort scenarios. The design goals of Vamos are (i) efficiency (tracing events with low overhead), (ii) flexibility (the ability to monitor a variety of different event channels, and to connect to a wide range of monitors), and (iii) ease-of-use. To achieve its goals, Vamos combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for Vamos and conducted a set of experiments demonstrating the usability of the scheme. The results indicate that Vamos enables writing useful yet efficient monitors, and simplifies key aspects of setting up a monitoring system from scratch."}],"author":[{"last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","full_name":"Chalupa, Marek"},{"full_name":"Mühlböck, Fabian","first_name":"Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck"},{"last_name":"Muroya Lei","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","first_name":"Stefanie"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"article_number":"103212","_id":"18169","corr_author":"1","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the STTT reviewers for their valuable feedback and suggestions.","file":[{"file_size":1173677,"date_updated":"2025-01-13T09:02:47Z","access_level":"open_access","content_type":"application/pdf","file_id":"18831","checksum":"cd93c0c356e479ffccfbe8499b6ba8e2","date_created":"2025-01-13T09:02:47Z","creator":"dernst","file_name":"2024_ScienceCompProg_Chalupa.pdf","relation":"main_file","success":1}],"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0167-6423"]},"doi":"10.1016/j.scico.2024.103212","date_created":"2024-10-06T22:01:10Z","article_type":"original","scopus_import":"1","volume":240,"type":"journal_article","publication_status":"published","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","citation":{"mla":"Chalupa, Marek, et al. “VAMOS: Middleware for Best-Effort Third-Party Monitoring.” <i>Science of Computer Programming</i>, vol. 240, no. 2, 103212, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.scico.2024.103212\">10.1016/j.scico.2024.103212</a>.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “VAMOS: Middleware for Best-Effort Third-Party Monitoring.” <i>Science of Computer Programming</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.scico.2024.103212\">https://doi.org/10.1016/j.scico.2024.103212</a>.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2025. VAMOS: Middleware for best-effort third-party monitoring. Science of Computer Programming. 240(2), 103212.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “VAMOS: Middleware for best-effort third-party monitoring,” <i>Science of Computer Programming</i>, vol. 240, no. 2. Elsevier, 2025.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2025). VAMOS: Middleware for best-effort third-party monitoring. <i>Science of Computer Programming</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scico.2024.103212\">https://doi.org/10.1016/j.scico.2024.103212</a>","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, Science of Computer Programming 240 (2025).","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for best-effort third-party monitoring. <i>Science of Computer Programming</i>. 2025;240(2). doi:<a href=\"https://doi.org/10.1016/j.scico.2024.103212\">10.1016/j.scico.2024.103212</a>"},"isi":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"earlier_version","id":"12856","status":"public"}]},"oa":1,"oa_version":"Published Version","issue":"2","ec_funded":1,"title":"VAMOS: Middleware for best-effort third-party monitoring","month":"02","language":[{"iso":"eng"}]},{"publisher":"Elsevier","abstract":[{"text":"This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.","lang":"eng"}],"author":[{"full_name":"Herdina, Anna Nele","first_name":"Anna Nele","last_name":"Herdina"},{"last_name":"Bozdogan","full_name":"Bozdogan, Anil","first_name":"Anil"},{"first_name":"Patrik","full_name":"Aspermair, Patrik","last_name":"Aspermair"},{"last_name":"Dostalek","first_name":"Jakub","full_name":"Dostalek, Jakub"},{"last_name":"Klausberger","full_name":"Klausberger, Miriam","first_name":"Miriam"},{"last_name":"Lingg","full_name":"Lingg, Nico","first_name":"Nico"},{"first_name":"Monika","full_name":"Cserjan-Puschmann, Monika","last_name":"Cserjan-Puschmann"},{"last_name":"Aguilar","full_name":"Aguilar, Patricia Pereira","first_name":"Patricia Pereira"},{"first_name":"Simone","full_name":"Auer, Simone","last_name":"Auer"},{"full_name":"Demirtas, Halil","first_name":"Halil","last_name":"Demirtas"},{"first_name":"Jakob","full_name":"Andersson, Jakob","last_name":"Andersson","id":"3a5f4167-9bd9-11ed-bd12-a1446d38776f"},{"first_name":"Felix","full_name":"Lötsch, Felix","last_name":"Lötsch"},{"first_name":"Barbara","full_name":"Holzer, Barbara","last_name":"Holzer"},{"last_name":"Steinrigl","full_name":"Steinrigl, Adi","first_name":"Adi"},{"full_name":"Thalhammer, Florian","first_name":"Florian","last_name":"Thalhammer"},{"last_name":"Schellnegger","full_name":"Schellnegger, Julia","first_name":"Julia"},{"first_name":"Monika","full_name":"Breuer, Monika","last_name":"Breuer"},{"last_name":"Knoll","full_name":"Knoll, Wolfgang","first_name":"Wolfgang"},{"first_name":"Robert","full_name":"Strassl, Robert","last_name":"Strassl"}],"year":"2025","OA_type":"hybrid","file_date_updated":"2025-01-13T11:14:32Z","acknowledgement":"This research was funded in whole by the Austrian Science Fund (FWF) [P 35103-B, Grant-DOI: 10.55776/P35103]. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. We would like to thank Olfert Landt for advice on ssDNA probe design; Rui Qiang Chen, Jennifer Stock, and Christine Wukotitsch for their excellent support with ONT sequencing; Christoph Köppl and Andreas Fischer for excellent support in recombinant N protein expression and purification; and the whole team at the division of clinical virology for their support with standard diagnostics.","file":[{"file_id":"18843","checksum":"208ac27dab27af792d198fcb74af8756","date_created":"2025-01-13T11:14:32Z","creator":"dernst","file_size":4135372,"date_updated":"2025-01-13T11:14:32Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","success":1,"file_name":"2025_BiosensorsBioelectronics_Herdina.pdf"}],"OA_place":"publisher","article_number":"116807","_id":"18170","publication":"Biosensors and Bioelectronics","department":[{"_id":"LeSa"}],"date_updated":"2025-02-27T12:34:07Z","external_id":{"pmid":["39341071"],"isi":["001328413700001"]},"ddc":["570"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","intvolume":"       267","date_published":"2025-01-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","citation":{"short":"A.N. Herdina, A. Bozdogan, P. Aspermair, J. Dostalek, M. Klausberger, N. Lingg, M. Cserjan-Puschmann, P.P. Aguilar, S. Auer, H. Demirtas, J. Andersson, F. Lötsch, B. Holzer, A. Steinrigl, F. Thalhammer, J. Schellnegger, M. Breuer, W. Knoll, R. Strassl, Biosensors and Bioelectronics 267 (2025).","ama":"Herdina AN, Bozdogan A, Aspermair P, et al. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. <i>Biosensors and Bioelectronics</i>. 2025;267. doi:<a href=\"https://doi.org/10.1016/j.bios.2024.116807\">10.1016/j.bios.2024.116807</a>","mla":"Herdina, Anna Nele, et al. “Bridging Basic Science and Applied Diagnostics: Comprehensive Viral Diagnostics Enabled by Graphene-Based Electronic Biosensor Technology Advancements.” <i>Biosensors and Bioelectronics</i>, vol. 267, 116807, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.bios.2024.116807\">10.1016/j.bios.2024.116807</a>.","chicago":"Herdina, Anna Nele, Anil Bozdogan, Patrik Aspermair, Jakub Dostalek, Miriam Klausberger, Nico Lingg, Monika Cserjan-Puschmann, et al. “Bridging Basic Science and Applied Diagnostics: Comprehensive Viral Diagnostics Enabled by Graphene-Based Electronic Biosensor Technology Advancements.” <i>Biosensors and Bioelectronics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.bios.2024.116807\">https://doi.org/10.1016/j.bios.2024.116807</a>.","ista":"Herdina AN, Bozdogan A, Aspermair P, Dostalek J, Klausberger M, Lingg N, Cserjan-Puschmann M, Aguilar PP, Auer S, Demirtas H, Andersson J, Lötsch F, Holzer B, Steinrigl A, Thalhammer F, Schellnegger J, Breuer M, Knoll W, Strassl R. 2025. Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. Biosensors and Bioelectronics. 267, 116807.","ieee":"A. N. Herdina <i>et al.</i>, “Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements,” <i>Biosensors and Bioelectronics</i>, vol. 267. Elsevier, 2025.","apa":"Herdina, A. N., Bozdogan, A., Aspermair, P., Dostalek, J., Klausberger, M., Lingg, N., … Strassl, R. (2025). Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements. <i>Biosensors and Bioelectronics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bios.2024.116807\">https://doi.org/10.1016/j.bios.2024.116807</a>"},"isi":1,"publication_status":"published","month":"01","title":"Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements","language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"oa_version":"Published Version","publication_identifier":{"eissn":["1873-4235"],"issn":["0956-5663"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_type":"original","volume":267,"type":"journal_article","doi":"10.1016/j.bios.2024.116807","date_created":"2024-10-06T22:01:11Z"},{"date_published":"2025-05-14T00:00:00Z","date_created":"2026-06-22T12:17:47Z","day":"14","doi":"10.5194/egusphere-egu25-17446","ddc":["550"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"conference_abstract","date_updated":"2026-07-02T06:41:43Z","conference":{"start_date":"2025-04-27","name":"EGU General Assembly","location":"Vienna, Austria & Virtual","end_date":"2025-05-02"},"department":[{"_id":"FrPe"},{"_id":"GradSch"}],"publication":"EGU General Assembly 2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22120","oa":1,"oa_version":"Published Version","has_accepted_license":"1","article_number":"EGU25-17446","language":[{"iso":"eng"}],"OA_place":"publisher","title":"Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier","month":"05","OA_type":"gold","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/egusphere-egu25-17446"}],"publication_status":"published","year":"2025","citation":{"mla":"Muñoz Hermosilla, José M., et al. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” <i>EGU General Assembly 2025</i>, EGU25-17446, European Geosciences Union, 2025, doi:<a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">10.5194/egusphere-egu25-17446</a>.","chicago":"Muñoz Hermosilla, José M, Evan Miles, Michael McCarthy, Florian Hardmeier, Juan Vicente Melo Velasco, Guillaume Jouvet, and Francesca Pellicciotti. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” In <i>EGU General Assembly 2025</i>. European Geosciences Union, 2025. <a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">https://doi.org/10.5194/egusphere-egu25-17446</a>.","ista":"Muñoz Hermosilla JM, Miles E, McCarthy M, Hardmeier F, Melo Velasco JV, Jouvet G, Pellicciotti F. 2025. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. EGU General Assembly 2025. EGU General Assembly, EGU25-17446.","apa":"Muñoz Hermosilla, J. M., Miles, E., McCarthy, M., Hardmeier, F., Melo Velasco, J. V., Jouvet, G., &#38; Pellicciotti, F. (2025). Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In <i>EGU General Assembly 2025</i>. Vienna, Austria &#38; Virtual: European Geosciences Union. <a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">https://doi.org/10.5194/egusphere-egu25-17446</a>","ieee":"J. M. Muñoz Hermosilla <i>et al.</i>, “Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier,” in <i>EGU General Assembly 2025</i>, Vienna, Austria &#38; Virtual, 2025.","short":"J.M. Muñoz Hermosilla, E. Miles, M. McCarthy, F. Hardmeier, J.V. Melo Velasco, G. Jouvet, F. Pellicciotti, in:, EGU General Assembly 2025, European Geosciences Union, 2025.","ama":"Muñoz Hermosilla JM, Miles E, McCarthy M, et al. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In: <i>EGU General Assembly 2025</i>. European Geosciences Union; 2025. doi:<a href=\"https://doi.org/10.5194/egusphere-egu25-17446\">10.5194/egusphere-egu25-17446</a>"},"author":[{"orcid":"0000-0002-1990-8508","id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","last_name":"Muñoz Hermosilla","full_name":"Muñoz Hermosilla, José M","first_name":"José M"},{"first_name":"Evan","full_name":"Miles, Evan","last_name":"Miles"},{"last_name":"McCarthy","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","full_name":"McCarthy, Michael","first_name":"Michael"},{"last_name":"Hardmeier","full_name":"Hardmeier, Florian","first_name":"Florian"},{"id":"2611dec0-b9c6-11ed-9bea-a81c2b17a549","last_name":"Melo Velasco","full_name":"Melo Velasco, Juan Vicente","first_name":"Juan Vicente"},{"full_name":"Jouvet, Guillaume","first_name":"Guillaume","last_name":"Jouvet"},{"first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087"}],"article_processing_charge":"No","publisher":"European Geosciences Union"},{"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"DOAJ_listed":"1","ddc":["510"],"date_updated":"2026-07-06T11:51:31Z","external_id":{"arxiv":["2303.05435"]},"date_published":"2025-09-02T00:00:00Z","day":"02","das_tickbox":"1","department":[{"_id":"MaKw"}],"publication":"Journal of the European Mathematical Society","OA_place":"publisher","acknowledgement":"We would like to thank Noga Alon for suggesting that our main result gives\r\na linear-time algorithm for computing the rank. We also thank the referees for a number of thoughtful comments and suggestions. Glasgow was supported by NSF graduate research fellowship program award DGE1656518. Kwan was supported by ERC Starting Grant “RANDSTRUCT” No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302.\r\n","corr_author":"1","_id":"21263","author":[{"first_name":"Margalit","full_name":"Glasgow, Margalit","last_name":"Glasgow"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan"},{"first_name":"Ashwin","full_name":"Sah, Ashwin","last_name":"Sah"},{"last_name":"Sawhney","first_name":"Mehtaab","full_name":"Sawhney, Mehtaab"}],"abstract":[{"text":"Two landmark results in combinatorial random matrix theory, due to Komlós and Costello–Tao–Vu, show that discrete random matrices and symmetric discrete random matrices are typically nonsingular. In particular, in the language of graph theory, when p is a fixed constant, the biadjacency matrix of a random Erdős–Rényi bipartite graph G(n,n,p) and the adjacency matrix of an Erdős–Rényi random graph G(n,p) are both nonsingular with high probability. However, very sparse random graphs (i.e., where p is allowed to decay rapidly with n) are typically singular, due to the presence of “local” dependencies such as isolated vertices and pairs of degree-1 vertices with the same neighbour. In this paper, we give a combinatorial description of the rank of a sparse random graph G(n,n,c/n) or G(n,c/n) in terms of such local dependencies, for all constants c=e (and we present some evidence that the situation is very different for c=e). This gives an essentially complete answer to a question raised by Vu (2014). As applications of our main theorem and its proof, we also determine the asymptotic singularity probability of the 2-core of a sparse random graph, we show that the rank of a sparse random graph is extremely well approximated by its matching number, and we deduce a central limit theorem for the rank of G(n,c/n).","lang":"eng"}],"publisher":"EMS Press","OA_type":"diamond","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4171/JEMS/1692"}],"year":"2025","type":"journal_article","arxiv":1,"article_type":"original","date_created":"2026-02-17T07:41:59Z","doi":"10.4171/jems/1692","PlanS_conform":"1","publication_identifier":{"eissn":["1435-9863"],"issn":["1435-9855"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"month":"09","title":"The exact rank of sparse random graphs","oa_version":"Published Version","oa":1,"has_accepted_license":"1","project":[{"name":"Randomness and structure in combinatorics","_id":"bd95085b-d553-11ed-ba76-e55d3349be45","grant_number":"101076777"}],"citation":{"ama":"Glasgow M, Kwan MA, Sah A, Sawhney M. The exact rank of sparse random graphs. <i>Journal of the European Mathematical Society</i>. 2025. doi:<a href=\"https://doi.org/10.4171/jems/1692\">10.4171/jems/1692</a>","short":"M. Glasgow, M.A. Kwan, A. Sah, M. Sawhney, Journal of the European Mathematical Society (2025).","ista":"Glasgow M, Kwan MA, Sah A, Sawhney M. 2025. The exact rank of sparse random graphs. Journal of the European Mathematical Society.","apa":"Glasgow, M., Kwan, M. A., Sah, A., &#38; Sawhney, M. (2025). The exact rank of sparse random graphs. <i>Journal of the European Mathematical Society</i>. EMS Press. <a href=\"https://doi.org/10.4171/jems/1692\">https://doi.org/10.4171/jems/1692</a>","ieee":"M. Glasgow, M. A. Kwan, A. Sah, and M. Sawhney, “The exact rank of sparse random graphs,” <i>Journal of the European Mathematical Society</i>. EMS Press, 2025.","mla":"Glasgow, Margalit, et al. “The Exact Rank of Sparse Random Graphs.” <i>Journal of the European Mathematical Society</i>, EMS Press, 2025, doi:<a href=\"https://doi.org/10.4171/jems/1692\">10.4171/jems/1692</a>.","chicago":"Glasgow, Margalit, Matthew Alan Kwan, Ashwin Sah, and Mehtaab Sawhney. “The Exact Rank of Sparse Random Graphs.” <i>Journal of the European Mathematical Society</i>. EMS Press, 2025. <a href=\"https://doi.org/10.4171/jems/1692\">https://doi.org/10.4171/jems/1692</a>."},"quality_controlled":"1","article_processing_charge":"No","publication_status":"epub_ahead"},{"title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","month":"09","language":[{"iso":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"21423","relation":"dissertation_contains"},{"status":"public","id":"21439","relation":"research_data"}]},"oa":1,"oa_version":"Preprint","article_processing_charge":"No","citation":{"ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.)."},"project":[{"grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces"},{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"publication_status":"draft","type":"preprint","doi":"10.1101/2025.05.20.655037","date_created":"2026-03-11T08:40:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","OA_place":"repository","_id":"21427","abstract":[{"lang":"eng","text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo."}],"author":[{"last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Dunajova, Zuzana"},{"last_name":"Tasciyan","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","first_name":"Saren"},{"last_name":"Majek","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","first_name":"Juraj","full_name":"Majek, Juraj"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"full_name":"Sahai, Erik","first_name":"Erik","last_name":"Sahai"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"}],"year":"2025","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.20.655037"}],"date_updated":"2026-07-06T12:38:17Z","ddc":["539","570"],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","day":"25","date_published":"2025-09-25T00:00:00Z","publication":"bioRxiv","department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"das_tickbox":"1"},{"citation":{"short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, I. Kulich, Y. Jaillais, J. Friml, Cell 188 (2025) 6138–6150.e17.","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. <i>Cell</i>. 2025;188(22):6138-6150.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">10.1016/j.cell.2025.08.026</a>","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>Cell</i>, vol. 188, no. 22, Elsevier, 2025, p. 6138–6150.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">10.1016/j.cell.2025.08.026</a>.","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">https://doi.org/10.1016/j.cell.2025.08.026</a>.","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism,” <i>Cell</i>, vol. 188, no. 22. Elsevier, p. 6138–6150.e17, 2025.","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (2025). ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.08.026\">https://doi.org/10.1016/j.cell.2025.08.026</a>","ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Kulich I, Jaillais Y, Friml J. 2025. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell. 188(22), 6138–6150.e17."},"isi":1,"project":[{"grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants"},{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123"},{"grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425","name":"Cell surface receptor complexes for auxin signaling in plants"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication_status":"published","language":[{"iso":"eng"}],"title":"ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism","ec_funded":1,"month":"10","oa":1,"issue":"22","oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"19399"}]},"publication_identifier":{"issn":["0092-8674"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"type":"journal_article","article_type":"original","volume":188,"date_created":"2025-11-19T09:44:31Z","doi":"10.1016/j.cell.2025.08.026","abstract":[{"lang":"eng","text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a prerequisite for (1) self-organizing processes, including vascular tissue formation, and (2) directional growth responses such as gravitropism. Here, we identify a mechanism by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1) receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably for other self-organizing developmental phenomena."}],"author":[{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler","first_name":"Lukas","full_name":"Fiedler, Lukas"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","full_name":"Zou, Minxia","first_name":"Minxia"},{"full_name":"Giannini, Caterina","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"},{"full_name":"Monzer, Aline","first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii","full_name":"Vladimirtsev, Dmitrii"},{"last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","full_name":"Randuch, Marek"},{"full_name":"Yu, Yongfan","first_name":"Yongfan","last_name":"Yu"},{"full_name":"Gelová, Zuzana","first_name":"Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová"},{"full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Meng","first_name":"Meng","last_name":"Chen"},{"last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","full_name":"Tan, Shutang"},{"full_name":"Hörmayer, Lukas","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin"},{"last_name":"Marques-Bueno","first_name":"Maria Mar","full_name":"Marques-Bueno, Maria Mar"},{"full_name":"Quddoos, Zainab","first_name":"Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","last_name":"Quddoos"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","full_name":"Molnar, Gergely","first_name":"Gergely"},{"first_name":"Ivan","full_name":"Kulich, Ivan","last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54"},{"full_name":"Jaillais, Yvon","first_name":"Yvon","last_name":"Jaillais"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"publisher":"Elsevier","OA_type":"hybrid","file_date_updated":"2025-11-24T10:55:18Z","page":"6138-6150.e17","year":"2025","acknowledgement":"We gratefully acknowledge Tongda Xu for experimental, material, and conceptual support. We thank William Gray for providing material, Nataliia Gnyliukh and Ema Cervenova for help with manuscript preparation, and Julia Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at the Institute of Science and Technology Austria (ISTA) for their excellent service and assistance. The research leading to these results has received funding from the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; I 6123-B) to J.F., and Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by the FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985-2016). S.T. was supported by the National Natural Science Foundation of China (32321001, 32570366). The work of J.H. was supported by the project JG_2024_003 implemented within the Palacký University Young Researcher Grant.","file":[{"file_name":"2025_Cell_Rodriguez.pdf","relation":"main_file","success":1,"date_updated":"2025-11-24T10:55:18Z","file_size":17825465,"access_level":"open_access","content_type":"application/pdf","file_id":"20679","checksum":"8ac396a0806ad7f2e4e7a0c1eed712ce","date_created":"2025-11-24T10:55:18Z","creator":"dernst"}],"OA_place":"publisher","corr_author":"1","_id":"20656","publication":"Cell","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"ddc":["580"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","date_updated":"2026-07-06T12:51:13Z","external_id":{"pmid":["41043433"],"isi":["001616077900005"]},"date_published":"2025-10-30T00:00:00Z","intvolume":"       188","day":"30"},{"language":[{"iso":"eng"}],"month":"09","title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"12291","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"19399"}]},"citation":{"chicago":"Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>.","mla":"Giannini, Caterina. <i>Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>.","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025.","apa":"Giannini, C. (2025). <i>Nuclear and cell surface auxin signaling in A. thaliana developmental transitions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>","ista":"Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria.","short":"C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025.","ama":"Giannini C. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>"},"article_processing_charge":"No","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"}],"publication_status":"published","type":"dissertation","keyword":["Auxin Signaling","Plant Development"],"date_created":"2025-09-19T12:23:38Z","doi":"10.15479/AT-ISTA-20364","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file":[{"relation":"main_file","file_name":"2025_Giannini_Caterina_Thesis...pdf","date_created":"2025-09-24T14:46:34Z","embargo":"2026-09-30","creator":"cgiannin","checksum":"536ba1701453b0b2346be14c046b2911","file_id":"20390","content_type":"application/pdf","access_level":"closed","date_updated":"2025-09-30T14:31:29Z","embargo_to":"open_access","file_size":14278965},{"file_size":24499022,"date_updated":"2025-09-24T14:46:35Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20391","checksum":"192f55262f2da2ea0a59d9c23a1b8573","date_created":"2025-09-24T14:46:35Z","creator":"cgiannin","file_name":"2025_Giannini_Caterina_Thesis...docx","relation":"source_file"}],"acknowledgement":"Plant Facility,\r\nProtein Service Facility","OA_place":"publisher","degree_awarded":"PhD","corr_author":"1","_id":"20364","author":[{"first_name":"Caterina","full_name":"Giannini, Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2025-09-30T14:31:29Z","year":"2025","page":"151","ddc":["580"],"status":"public","date_updated":"2026-07-06T12:51:13Z","date_published":"2025-09-19T00:00:00Z","day":"19","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}]},{"month":"10","title":"Keratins act as global coordinators of tissue spreading through mechanosensitive feedback","language":[{"iso":"eng"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"20465","relation":"part_of_dissertation"}]},"oa":1,"oa_version":"Published Version","article_processing_charge":"No","citation":{"ama":"Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>","short":"S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025.","apa":"Naik, S. (2025). <i>Keratins act as global coordinators of tissue spreading through mechanosensitive feedback</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>","ieee":"S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025.","ista":"Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria.","chicago":"Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>.","mla":"Naik, Suyash. <i>Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>."},"project":[{"_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading","grant_number":"PAT 5044023"},{"name":"Nano-Analytics of Cellular Systems","_id":"25AA5F24-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W 1250-B20"}],"supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-sa/4.0/","type":"dissertation","doi":"10.15479/AT-ISTA-20441","date_created":"2025-10-10T14:58:30Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-069-5"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"corr_author":"1","degree_awarded":"PhD","acknowledgement":"I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences.","file":[{"file_name":"Thesis_PDFA_.pdf","relation":"main_file","success":1,"file_size":6846189,"date_updated":"2025-10-28T13:10:08Z","access_level":"open_access","content_type":"application/pdf","file_id":"20567","checksum":"2892f04d4a5c18677871c3e06ac1244a","creator":"snaik","date_created":"2025-10-28T13:10:08Z"},{"access_level":"open_access","content_type":"application/zip","file_size":8839300,"date_updated":"2025-10-28T13:10:26Z","checksum":"15934d4465cd0e9b7c32678da9a33a2f","creator":"snaik","date_created":"2025-10-28T13:10:26Z","file_id":"20568","file_name":"Thesis.zip","relation":"source_file"}],"OA_place":"publisher","_id":"20441","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium."}],"author":[{"id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","last_name":"Naik","first_name":"Suyash","full_name":"Naik, Suyash"}],"page":"105","year":"2025","file_date_updated":"2025-10-28T13:10:26Z","date_updated":"2026-07-06T12:51:41Z","ddc":["596","597","532"],"status":"public","tmp":{"short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png"},"day":"12","date_published":"2025-10-12T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}]},{"date_updated":"2026-07-06T12:58:58Z","status":"public","ddc":["580"],"day":"04","date_published":"2025-04-04T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"degree_awarded":"PhD","corr_author":"1","OA_place":"publisher","acknowledgement":"This project was funded by the European Research Council Advanced Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian Science Fund (FWF; P\r\n37051-B).","file":[{"file_id":"19526","checksum":"b154973663a1bba505683faab7ae5ead","date_created":"2025-04-08T08:00:07Z","creator":"hchen","date_updated":"2025-04-08T08:22:37Z","file_size":16344814,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_0403_Huihuang.docx"},{"file_name":"Thesis_0406_PDFA_Huihuang_1.pdf","relation":"main_file","content_type":"application/pdf","access_level":"closed","embargo_to":"local","date_updated":"2025-04-09T13:53:38Z","file_size":8482147,"date_created":"2025-04-08T08:00:06Z","embargo":"2026-10-08","creator":"hchen","checksum":"0099565f024388830c125ec17375c1a0","file_id":"19527"}],"_id":"19478","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Chen, Huihuang","first_name":"Huihuang","last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f"}],"page":"118","year":"2025","file_date_updated":"2025-04-09T13:53:38Z","type":"dissertation","doi":"10.15479/AT-ISTA-19478","date_created":"2025-04-04T07:48:24Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"title":"The cAMP second messenger in auxin signalling","month":"04","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"19421","status":"public"},{"relation":"part_of_dissertation","id":"13212","status":"public"}]},"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","article_processing_charge":"No","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"},{"grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"citation":{"mla":"Chen, Huihuang. <i>The CAMP Second Messenger in Auxin Signalling</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19478\">10.15479/AT-ISTA-19478</a>.","chicago":"Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19478\">https://doi.org/10.15479/AT-ISTA-19478</a>.","ista":"Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria.","ieee":"H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science and Technology Austria, 2025.","apa":"Chen, H. (2025). <i>The cAMP second messenger in auxin signalling</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19478\">https://doi.org/10.15479/AT-ISTA-19478</a>","short":"H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science and Technology Austria, 2025.","ama":"Chen H. The cAMP second messenger in auxin signalling. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19478\">10.15479/AT-ISTA-19478</a>"},"publication_status":"published","supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"}]},{"language":[{"iso":"eng"}],"month":"12","title":"Theory and applications of verifiable delay functions","oa":1,"oa_version":"Published Version","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"13143","relation":"part_of_dissertation"},{"id":"12176","status":"public","relation":"part_of_dissertation"},{"relation":"earlier_version","status":"public","id":"20556"},{"id":"19778","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"20701","relation":"part_of_dissertation"}]},"citation":{"ama":"Hoffmann C. Theory and applications of verifiable delay functions. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20920\">10.15479/AT-ISTA-20920</a>","short":"C. Hoffmann, Theory and Applications of Verifiable Delay Functions, Institute of Science and Technology Austria, 2025.","ieee":"C. Hoffmann, “Theory and applications of verifiable delay functions,” Institute of Science and Technology Austria, 2025.","apa":"Hoffmann, C. (2025). <i>Theory and applications of verifiable delay functions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20920\">https://doi.org/10.15479/AT-ISTA-20920</a>","ista":"Hoffmann C. 2025. Theory and applications of verifiable delay functions. Institute of Science and Technology Austria.","chicago":"Hoffmann, Charlotte. “Theory and Applications of Verifiable Delay Functions.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20920\">https://doi.org/10.15479/AT-ISTA-20920</a>.","mla":"Hoffmann, Charlotte. <i>Theory and Applications of Verifiable Delay Functions</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20920\">10.15479/AT-ISTA-20920</a>."},"article_processing_charge":"No","publication_status":"published","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"type":"dissertation","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_created":"2026-01-02T10:46:47Z","doi":"10.15479/AT-ISTA-20920","publication_identifier":{"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"2025_Hoffmann_Charlotte_Source.zip","relation":"source_file","date_updated":"2026-01-02T10:39:16Z","file_size":8355494,"content_type":"application/x-zip-compressed","access_level":"closed","file_id":"20921","date_created":"2026-01-02T10:39:16Z","creator":"choffman","checksum":"8a099fbf54963bd0be38f7ce73658682"},{"file_name":"2025_Hoffmann_Charlotte_Thesis.pdf","success":1,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":2258804,"date_updated":"2026-01-02T10:39:26Z","checksum":"9521c07bfb2bb5b14a49c09fcfc96474","creator":"choffman","date_created":"2026-01-02T10:39:26Z","file_id":"20922"}],"OA_place":"publisher","corr_author":"1","degree_awarded":"PhD","_id":"20920","abstract":[{"lang":"eng","text":"Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality.\r\n\r\nThe only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).\r\nThe iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \\pi. Given \\pi, the output of VDF can be verified in time much less than T.\r\n\r\nWe first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications.\r\n\r\nSecondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources.\r\n\r\nWe then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions).\r\n\r\nFinally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory.\r\n\r\nTogether, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications."}],"author":[{"full_name":"Hoffmann, Charlotte","first_name":"Charlotte","last_name":"Hoffmann","orcid":"0000-0003-2027-5549","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-01-02T10:39:26Z","year":"2025","page":"116","ddc":["004"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"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"},"date_updated":"2026-07-06T13:15:27Z","date_published":"2025-12-31T00:00:00Z","day":"31","department":[{"_id":"GradSch"},{"_id":"KrPi"}]}]