[{"month":"07","department":[{"_id":"TiBr"}],"author":[{"last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sutherland, Andrew","last_name":"Sutherland","first_name":"Andrew"}],"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"orcid":"0000-0001-7302-8256","last_name":"Wilsch","id":"560601DA-8D36-11E9-A136-7AC1E5697425","first_name":"Florian Alexander"}],"day":"22","ddc":["500"],"article_processing_charge":"No","oa_version":"Published Version","year":"2024","_id":"22234","date_published":"2024-07-22T00:00:00Z","date_created":"2026-07-02T10:38:53Z","OA_place":"repository","oa":1,"tmp":{"image":"/images/cc_by.png","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)"},"doi":"10.25625/4FLFH8","date_updated":"2026-08-12T12:15:33Z","status":"public","main_file_link":[{"url":"https://doi.org/10.25625/4FLFH8","open_access":"1"}],"OA_type":"green","citation":{"chicago":"Browning, Timothy D, and Andrew Sutherland. “Data and Code for: Integral Points on Cubic Surfaces: Heuristics and Numerics.” Göttingen Research Online Data, 2024. <a href=\"https://doi.org/10.25625/4FLFH8\">https://doi.org/10.25625/4FLFH8</a>.","ieee":"T. D. Browning and A. Sutherland, “Data and code for: Integral points on cubic surfaces: heuristics and numerics.” Göttingen Research Online Data, 2024.","mla":"Browning, Timothy D., and Andrew Sutherland. <i>Data and Code for: Integral Points on Cubic Surfaces: Heuristics and Numerics</i>. Göttingen Research Online Data, 2024, doi:<a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>.","ista":"Browning TD, Sutherland A. 2024. Data and code for: Integral points on cubic surfaces: heuristics and numerics, Göttingen Research Online Data, <a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>.","ama":"Browning TD, Sutherland A. Data and code for: Integral points on cubic surfaces: heuristics and numerics. 2024. doi:<a href=\"https://doi.org/10.25625/4FLFH8\">10.25625/4FLFH8</a>","apa":"Browning, T. D., &#38; Sutherland, A. (2024). Data and code for: Integral points on cubic surfaces: heuristics and numerics. Göttingen Research Online Data. <a href=\"https://doi.org/10.25625/4FLFH8\">https://doi.org/10.25625/4FLFH8</a>","short":"T.D. Browning, A. Sutherland, (2024)."},"corr_author":"1","related_material":{"record":[{"id":"20249","status":"public","relation":"used_in_publication"}]},"title":"Data and code for: Integral points on cubic surfaces: heuristics and numerics","abstract":[{"lang":"eng","text":"Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)"}],"has_accepted_license":"1","publisher":"Göttingen Research Online Data"},{"OA_place":"publisher","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2023.10.04.560631"}]},"has_accepted_license":"1","OA_type":"gold","issue":"5","citation":{"ieee":"A. Ritzau-Jost <i>et al.</i>, “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024.","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer, 2024. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>.","mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>.","ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology &#38; Neuroinflammation. 11(5), e200284.","ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. 2024;11(5):e200284. doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology &#38; Neuroinflammation 11 (2024) e200284."},"acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","ddc":["570"],"intvolume":"        11","scopus_import":"1","month":"09","volume":11,"isi":1,"publication_status":"published","author":[{"full_name":"Ritzau-Jost, Andreas","last_name":"Ritzau-Jost","first_name":"Andreas"},{"first_name":"Felix","full_name":"Gsell, Felix","last_name":"Gsell"},{"last_name":"Sell","full_name":"Sell, Josefine","first_name":"Josefine"},{"first_name":"Stefan","full_name":"Sachs, Stefan","last_name":"Sachs"},{"first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"last_name":"Kirmann","full_name":"Kirmann, Toni","first_name":"Toni"},{"first_name":"Sebastian","last_name":"Maaß","full_name":"Maaß, Sebastian"},{"first_name":"Sarosh R.","full_name":"Irani, Sarosh R.","last_name":"Irani"},{"last_name":"Werner","full_name":"Werner, Christian","first_name":"Christian"},{"first_name":"Christian","last_name":"Geis","full_name":"Geis, Christian"},{"first_name":"Markus","last_name":"Sauer","full_name":"Sauer, Markus"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"last_name":"Hallermann","full_name":"Hallermann, Stefan","first_name":"Stefan"}],"department":[{"_id":"RySh"}],"page":"e200284","oa_version":"Published Version","language":[{"iso":"eng"}],"project":[{"_id":"05970B30-7A3F-11EA-A408-12923DDC885E","name":"LGI1 antibody-induced pathophysiology in synapses","grant_number":"I04638"}],"DOAJ_listed":"1","date_updated":"2026-08-12T14:17:59Z","status":"public","doi":"10.1212/NXI.0000000000200284","oa":1,"tmp":{"image":"/images/cc_by.png","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)"},"article_type":"original","file":[{"access_level":"open_access","file_size":855818,"creator":"dernst","relation":"main_file","date_created":"2025-01-09T13:42:42Z","file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf","date_updated":"2025-01-09T13:42:42Z","checksum":"1e6d1230e0387f72752e3268f5330c9e","file_id":"18815","content_type":"application/pdf","success":1}],"publisher":"Wolters Kluwer","quality_controlled":"1","abstract":[{"text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening.","lang":"eng"}],"title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","publication_identifier":{"eissn":["2332-7812"]},"article_processing_charge":"Yes","day":"01","publication":"Neurology, Neuroimmunology & Neuroinflammation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2024-09-01T00:00:00Z","external_id":{"pmid":["39141878"],"isi":["001291908600001"]},"_id":"17457","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"date_created":"2024-08-25T22:01:07Z","pmid":1,"file_date_updated":"2025-01-09T13:42:42Z","year":"2024"},{"OA_place":"repository","citation":{"short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.).","apa":"Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., &#38; Lampert, C. (n.d.). Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>","ama":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>","ista":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833.","mla":"Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, 2403.06833, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>.","ieee":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate instructions from data? And what do we even mean by that?,” <i>arXiv</i>. .","chicago":"Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>."},"corr_author":"1","article_number":"2403.06833","OA_type":"green","has_accepted_license":"1","related_material":{"link":[{"relation":"software","url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed"}]},"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"author":[{"full_name":"Zverev, Egor","last_name":"Zverev","first_name":"Egor","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc"},{"first_name":"Sahar","full_name":"Abdelnabi, Sahar","last_name":"Abdelnabi"},{"orcid":"0009-0003-4119-6281","full_name":"Tabesh, Soroush","last_name":"Tabesh","first_name":"Soroush","id":"06000900-6068-11ef-8d61-c2472ef2e752"},{"first_name":"Mario","last_name":"Fritz","full_name":"Fritz, Mario"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"submitted","month":"03","ddc":["000"],"acknowledgement":"The authors would like to sincerely thank Juan Rocamonde for valuable feedback to our manuscript. We acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We thank Dan Alistarh for providing us with computational resources. This work was partially funded by the German Federal Ministry of Education and Research (BMBF) under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and Safe AI funded by the European Union under grant agreement No. 101070617. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them.","language":[{"iso":"eng"}],"oa_version":"Preprint","tmp":{"image":"/images/cc_by.png","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)"},"oa":1,"arxiv":1,"doi":"10.48550/arXiv.2403.06833","status":"public","date_updated":"2026-08-13T07:26:54Z","abstract":[{"text":"Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n","lang":"eng"}],"title":"Can LLMs separate instructions from data? And what do we even mean by that?","file":[{"date_updated":"2025-02-20T10:11:45Z","checksum":"35eb43968684b87be59144603ef10af0","content_type":"application/pdf","file_id":"19064","success":1,"access_level":"open_access","file_size":530972,"creator":"ezverev","relation":"main_file","date_created":"2025-02-20T10:11:45Z","file_name":"2403.06833v3.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","publication":"arXiv","day":"01","article_processing_charge":"No","year":"2024","file_date_updated":"2025-02-20T10:11:45Z","date_created":"2025-02-20T10:13:42Z","_id":"19063","external_id":{"arxiv":["2403.06833"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2024-03-01T00:00:00Z"},{"citation":{"short":"F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49.","apa":"Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C., &#38; Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>","ama":"Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. 2024;5(1):33-49. doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>","ista":"Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 5(1), 33–49.","mla":"Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>.","ieee":"F. Napoli <i>et al.</i>, “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024.","chicago":"Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>."},"corr_author":"1","OA_type":"gold","issue":"1","has_accepted_license":"1","OA_place":"publisher","APC_amount":"1530 EUR","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"33-49","author":[{"first_name":"Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","orcid":"0000-0002-9043-136X","last_name":"Napoli","full_name":"Napoli, Federico"},{"first_name":"Jia-Ying","full_name":"Guan, Jia-Ying","last_name":"Guan"},{"first_name":"Charles-Adrien","full_name":"Arnaud, Charles-Adrien","last_name":"Arnaud"},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"},{"first_name":"Cécile","last_name":"Breyton","full_name":"Breyton, Cécile"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"department":[{"_id":"PaSc"}],"publication_status":"published","month":"04","volume":5,"scopus_import":"1","intvolume":"         5","ddc":["530"],"acknowledgement":"We thank Dominique Madern (IBS Grenoble) for providing the plasmid for MalDH and feedback on the article, Alicia Vallet for excellent support at the Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of Max Perutz Labs for the mass spectrometry analysis using the instruments of the Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University Dortmund) for sharing a paper draft describing a similar study. This work was supported by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis (Lyon) and the reviewers for constructive input.\r\nThis research has been supported by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien Arnaud was funded by GRAL.","publication_identifier":{"issn":["2699-0016"]},"abstract":[{"lang":"eng","text":"Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with a H2O-based culture medium doped with deuterated cell lysate allow scientists to overcome this “reprotonation bottleneck” while retaining a high level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence lifetimes of several proteins prepared with this labeling pattern over a range of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range, many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and we show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments."}],"quality_controlled":"1","title":"Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck","publisher":"Copernicus Publications","file":[{"date_updated":"2024-05-22T07:01:15Z","content_type":"application/pdf","checksum":"80ea50114e428461ca9530d3bd5d89e4","file_id":"15413","success":1,"creator":"dernst","access_level":"open_access","file_size":6657865,"date_created":"2024-05-22T07:01:15Z","relation":"main_file","file_name":"2024_MagneticResonance_Napoli.pdf"}],"article_type":"original","tmp":{"image":"/images/cc_by.png","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)"},"oa":1,"doi":"10.5194/mr-5-33-2024","date_updated":"2025-07-17T08:12:23Z","status":"public","project":[{"_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812","name":"AlloSpace. The emergence and mechanisms of allostery"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"year":"2024","file_date_updated":"2024-05-22T07:01:15Z","pmid":1,"date_created":"2024-05-16T15:02:43Z","acknowledged_ssus":[{"_id":"NMR"}],"_id":"15401","external_id":{"pmid":["40384771"]},"date_published":"2024-04-19T00:00:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Magnetic Resonance","day":"19","article_processing_charge":"Yes"},{"ddc":["514","500","516"],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"}],"publication_status":"published","month":"03","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"108","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"OA_place":"publisher","has_accepted_license":"1","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"15091"},{"status":"public","id":"15090","relation":"part_of_dissertation"},{"status":"public","id":"15093","relation":"part_of_dissertation"},{"id":"13182","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11658"},{"status":"public","id":"11660","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"ec_funded":1,"citation":{"mla":"Cultrera di Montesano, Sebastiano. <i>Persistence and Morse Theory for Discrete Geometric Structures</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","apa":"Cultrera di Montesano, S. (2024). <i>Persistence and Morse theory for discrete geometric structures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024."},"corr_author":"1","day":"08","article_processing_charge":"No","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2024-03-08T15:28:10Z","_id":"15094","date_published":"2024-03-08T00:00:00Z","year":"2024","file_date_updated":"2024-03-14T14:14:35Z","status":"public","doi":"10.15479/at:ista:15094","date_updated":"2026-08-13T09:41:57Z","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry","grant_number":"I4887"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa":1,"title":"Persistence and Morse theory for discrete geometric structures","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","file":[{"success":1,"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_id":"15112","content_type":"application/pdf","date_updated":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","relation":"main_file","date_created":"2024-03-14T08:55:07Z","file_size":4106872,"creator":"scultrer","access_level":"open_access"},{"checksum":"bcbd213490f5a7e68855a092bbce93f1","content_type":"application/zip","file_id":"15113","date_updated":"2024-03-14T14:14:35Z","file_name":"Thesis (1).zip","access_level":"closed","file_size":4746234,"creator":"scultrer","relation":"source_file","date_created":"2024-03-14T08:56:24Z"}],"publication_identifier":{"issn":["2663-337X"]}},{"volume":8,"month":"10","author":[{"last_name":"Biswas","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cultrera Di Montesano, Sebastiano","last_name":"Cultrera Di Montesano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35. The authors of this paper thank anonymous reviewers for their constructive criticism and Monika Henzinger for detailed comments on an earlier version of this paper.","scopus_import":"1","intvolume":"         8","ddc":["000"],"oa_version":"Published Version","page":"1101-1119","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"hybrid","citation":{"mla":"Biswas, Ranita, et al. “Geometric Characterization of the Persistence of 1D Maps.” <i>Journal of Applied and Computational Topology</i>, vol. 8, Springer Nature, 2024, pp. 1101–19, doi:<a href=\"https://doi.org/10.1007/s41468-023-00126-9\">10.1007/s41468-023-00126-9</a>.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Geometric characterization of the persistence of 1D maps,” <i>Journal of Applied and Computational Topology</i>, vol. 8. Springer Nature, pp. 1101–1119, 2024.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Geometric Characterization of the Persistence of 1D Maps.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s41468-023-00126-9\">https://doi.org/10.1007/s41468-023-00126-9</a>.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2024. Geometric characterization of the persistence of 1D maps. Journal of Applied and Computational Topology. 8, 1101–1119.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2024). Geometric characterization of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00126-9\">https://doi.org/10.1007/s41468-023-00126-9</a>","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Geometric characterization of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>. 2024;8:1101-1119. doi:<a href=\"https://doi.org/10.1007/s41468-023-00126-9\">10.1007/s41468-023-00126-9</a>","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal of Applied and Computational Topology 8 (2024) 1101–1119."},"corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"15094","status":"public"},{"relation":"earlier_version","status":"public","id":"11660"}]},"ec_funded":1,"has_accepted_license":"1","publication":"Journal of Applied and Computational Topology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"01","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-01-09T07:39:41Z","year":"2024","external_id":{"pmid":["39678706"]},"_id":"13182","date_published":"2024-10-01T00:00:00Z","pmid":1,"date_created":"2023-07-02T22:00:44Z","oa":1,"tmp":{"image":"/images/cc_by.png","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)"},"article_type":"original","date_updated":"2026-08-13T09:41:57Z","doi":"10.1007/s41468-023-00126-9","status":"public","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887","name":"Persistent Homology, Algorithms and Stochastic Geometry"},{"call_identifier":"FWF","grant_number":"Z00342","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"file":[{"success":1,"checksum":"d493df5088c222b88d9ca46b623ad0ee","file_id":"18783","content_type":"application/pdf","date_updated":"2025-01-09T07:39:41Z","file_name":"2024_JourApplCompTopo_Biswas.pdf","relation":"main_file","date_created":"2025-01-09T07:39:41Z","file_size":476896,"creator":"dernst","access_level":"open_access"}],"title":"Geometric characterization of the persistence of 1D maps","quality_controlled":"1","abstract":[{"lang":"eng","text":"We characterize critical points of 1-dimensional maps paired in persistent homology\r\ngeometrically and this way get elementary proofs of theorems about the symmetry\r\nof persistence diagrams and the variation of such maps. In particular, we identify\r\nbranching points and endpoints of networks as the sole source of asymmetry and\r\nrelate the cycle basis in persistent homology with a version of the stable marriage\r\nproblem. Our analysis provides the foundations of fast algorithms for maintaining a\r\ncollection of sorted lists together with its persistence diagram."}],"publisher":"Springer Nature"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"130-148.e17","department":[{"_id":"JiFr"}],"author":[{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"first_name":"Sumanth","last_name":"Mutte","full_name":"Mutte, Sumanth"},{"full_name":"Dubey, Shiv Mani","last_name":"Dubey","first_name":"Shiv Mani"},{"first_name":"Vanessa Polet","last_name":"Carrillo Carrasco","full_name":"Carrillo Carrasco, Vanessa Polet"},{"first_name":"Sjef","full_name":"Boeren, Sjef","last_name":"Boeren"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline"},{"first_name":"Jasper","full_name":"Koehorst, Jasper","last_name":"Koehorst"},{"full_name":"Kohchi, Takayuki","last_name":"Kohchi","first_name":"Takayuki"},{"first_name":"Ryuichi","last_name":"Nishihama","full_name":"Nishihama, Ryuichi"},{"orcid":"0000-0002-9767-8699","last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sprakel","full_name":"Sprakel, Joris","first_name":"Joris"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"publication_status":"published","isi":1,"volume":187,"month":"01","scopus_import":"1","ddc":["580"],"intvolume":"       187","acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","citation":{"short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>."},"issue":"1","has_accepted_license":"1","related_material":{"record":[{"id":"19395","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"year":"2024","file_date_updated":"2024-01-22T13:41:41Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2024-01-17T12:45:40Z","pmid":1,"external_id":{"isi":["001152705700001"],"pmid":["38128538"]},"_id":"14826","date_published":"2024-01-04T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publication":"Cell","day":"04","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"abstract":[{"lang":"eng","text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage."}],"quality_controlled":"1","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","publisher":"Elsevier","file":[{"creator":"dernst","access_level":"open_access","file_size":13194060,"relation":"main_file","date_created":"2024-01-22T13:41:41Z","file_name":"2024_Cell_Kuhn.pdf","date_updated":"2024-01-22T13:41:41Z","file_id":"14874","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","content_type":"application/pdf","success":1}],"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"oa":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"status":"public","doi":"10.1016/j.cell.2023.11.021","date_updated":"2026-08-14T09:33:45Z","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF"}]},{"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031780103"]},"main_file_link":[{"url":"https://eprint.iacr.org/2024/1097","open_access":"1"}],"publisher":"Springer Nature","quality_controlled":"1","abstract":[{"text":"In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. ","lang":"eng"}],"title":"The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging","oa":1,"date_updated":"2026-08-21T10:53:16Z","doi":"10.1007/978-3-031-78011-0_14","status":"public","year":"2024","date_created":"2024-12-22T23:01:47Z","date_published":"2024-12-02T00:00:00Z","_id":"18702","external_id":{"isi":["001545628900014"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publication":"22nd International Conference on Theory of Cryptography","article_processing_charge":"No","day":"02","corr_author":"1","citation":{"short":"M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography, Springer Nature, 2024, pp. 413–443.","apa":"Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual Perez, G., &#38; Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In <i>22nd International Conference on Theory of Cryptography</i> (Vol. 15364, pp. 413–443). Milan, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>","ama":"Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In: <i>22nd International Conference on Theory of Cryptography</i>. Vol 15364. Springer Nature; 2024:413-443. doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>","ista":"Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G, Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. 22nd International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.","mla":"Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” <i>22nd International Conference on Theory of Cryptography</i>, vol. 15364, Springer Nature, 2024, pp. 413–43, doi:<a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">10.1007/978-3-031-78011-0_14</a>.","ieee":"M. Anastos <i>et al.</i>, “The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging,” in <i>22nd International Conference on Theory of Cryptography</i>, Milan, Italy, 2024, vol. 15364, pp. 413–443.","chicago":"Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” In <i>22nd International Conference on Theory of Cryptography</i>, 15364:413–43. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-78011-0_14\">https://doi.org/10.1007/978-3-031-78011-0_14</a>."},"OA_type":"green","alternative_title":["LNCS"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"22664"}]},"OA_place":"repository","language":[{"iso":"eng"}],"page":"413-443","oa_version":"Preprint","isi":1,"publication_status":"published","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael","last_name":"Anastos"},{"first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","orcid":"0000-0002-7553-6606","last_name":"Auerbach","full_name":"Auerbach, Benedikt"},{"first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","full_name":"Pascual Perez, Guillermo"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"department":[{"_id":"MaKw"},{"_id":"KrPi"}],"conference":{"start_date":"2024-12-02","location":"Milan, Italy","end_date":"2024-12-06","name":"TCC: Theory of Cryptography"},"volume":15364,"month":"12","intvolume":"     15364","scopus_import":"1"},{"file":[{"file_size":2537502,"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2024-08-05T08:19:58Z","file_name":"2024_JourApplPhysics_Lenton.pdf","date_updated":"2024-08-05T08:19:58Z","checksum":"6141d05cd68d540a7446dce9490975db","file_id":"17386","content_type":"application/pdf","success":1}],"quality_controlled":"1","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging","abstract":[{"text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results.","lang":"eng"}],"publisher":"AIP Publishing","publication_identifier":{"issn":["0021-8979"],"eissn":["1089-7550"]},"doi":"10.1063/5.0215151","date_updated":"2026-08-27T11:42:44Z","status":"public","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","call_identifier":"H2020"}],"oa":1,"article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"17373","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"external_id":{"isi":["001281681100003"]},"date_published":"2024-07-28T00:00:00Z","date_created":"2024-08-04T22:01:21Z","file_date_updated":"2024-08-05T08:19:58Z","year":"2024","day":"28","article_processing_charge":"No","publication":"Journal of Applied Physics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"22684","status":"public"}]},"ec_funded":1,"has_accepted_license":"1","issue":"4","citation":{"mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>.","ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” <i>Journal of Applied Physics</i>, vol. 136, no. 4. AIP Publishing, 2024.","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>.","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. 2024;136(4). doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024)."},"article_number":"045305","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","scopus_import":"1","intvolume":"       136","ddc":["530"],"month":"07","volume":136,"author":[{"first_name":"Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb","orcid":"0000-0002-5010-6984","last_name":"Lenton","full_name":"Lenton, Isaac C"},{"orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix"},{"first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","last_name":"Shafeek","full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"isi":1,"publication_status":"published"},{"type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Neuronal Morphogenesis","article_processing_charge":"No","day":"13","place":"New York, NY","year":"2024","pmid":1,"date_created":"2024-08-13T12:16:41Z","date_published":"2024-08-13T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"}],"_id":"17425","external_id":{"pmid":["39134857"]},"project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"status":"public","date_updated":"2026-08-28T22:30:04Z","doi":"10.1007/978-1-0716-3969-6_19","publication_identifier":{"eisbn":["9781071639696"],"eissn":["1940-6029"],"isbn":["9781071639689"],"issn":["1064-3745"]},"series_title":"MIMB","publisher":"Springer Nature","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","quality_controlled":"1","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology."}],"publication_status":"published","author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","last_name":"Miranda","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889"},{"full_name":"Cheung, Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"volume":2831,"month":"08","intvolume":"      2831","scopus_import":"1","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","language":[{"iso":"eng"}],"page":"283-299","oa_version":"None","editor":[{"first_name":"Kazuhito","last_name":"Toyooka","full_name":"Toyooka, Kazuhito"}],"edition":"1","corr_author":"1","citation":{"short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299."},"alternative_title":["Methods in Molecular Biology"],"related_material":{"record":[{"status":"public","id":"20212","relation":"dissertation_contains"}]}},{"OA_place":"repository","supervisor":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"citation":{"ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria."},"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"11420","relation":"part_of_dissertation"},{"id":"14459","status":"public","relation":"part_of_dissertation"},{"id":"9198","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"17469"}]},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"}],"publication_status":"published","month":"08","ddc":["519"],"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"232","oa":1,"status":"public","doi":"10.15479/at:ista:17465","date_updated":"2026-06-18T17:55:53Z","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"title":"High-dimensional limits in artificial neural networks","publisher":"Institute of Science and Technology Austria","file":[{"file_id":"17482","content_type":"application/pdf","checksum":"da6dd3166078934577f6af93d27000e2","date_updated":"2024-10-05T22:30:05Z","file_name":"thesis_a2b.pdf","embargo":"2024-10-04","file_size":4468610,"access_level":"open_access","creator":"ashevche","date_created":"2024-09-02T09:23:32Z","relation":"main_file"},{"date_updated":"2024-10-05T22:30:05Z","checksum":"76a39ef252239560923cdda4ce0a31a4","file_id":"17483","content_type":"application/zip","embargo_to":"open_access","date_created":"2024-09-02T09:23:46Z","relation":"source_file","access_level":"closed","creator":"ashevche","file_size":15930999,"file_name":"Thesis Alex - ISTA.zip"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","day":"29","article_processing_charge":"No","year":"2024","file_date_updated":"2024-10-05T22:30:05Z","date_created":"2024-08-28T15:14:25Z","_id":"17465","acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2024-08-29T00:00:00Z"},{"oa":1,"arxiv":1,"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"status":"public","date_updated":"2026-08-28T22:30:16Z","main_file_link":[{"url":"https://proceedings.mlr.press/v235/kogler24a.html","open_access":"1"}],"publisher":"ML Research Press","abstract":[{"lang":"eng","text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST."}],"quality_controlled":"1","title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 41st International Conference on Machine Learning","article_processing_charge":"No","day":"01","year":"2024","date_created":"2024-08-29T11:47:57Z","date_published":"2024-07-01T00:00:00Z","_id":"17469","external_id":{"arxiv":["2402.05013"]},"corr_author":"1","citation":{"ista":"Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.","mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015.","apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015."},"alternative_title":["PMLR"],"related_material":{"record":[{"id":"17465","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","conference":{"start_date":"2024-07-21","location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning"},"department":[{"_id":"DaAl"},{"_id":"MaMo"}],"author":[{"id":"94ec913c-dc85-11ea-9058-e5051ab2428b","first_name":"Kevin","full_name":"Kögler, Kevin","last_name":"Kögler"},{"first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"month":"07","volume":235,"intvolume":"       235","ddc":["000"],"scopus_import":"1","acknowledgement":"Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","language":[{"iso":"eng"}],"page":"24964-25015","oa_version":"Published Version"},{"citation":{"ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria."},"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"14032","relation":"part_of_dissertation"},{"id":"18057","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"OA_place":"publisher","supervisor":[{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"82","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham","orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay"}],"publication_status":"published","month":"09","ddc":["539"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"abstract":[{"lang":"eng","text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices."}],"title":"Thermal effects in one dimensional Josephson chains","publisher":"Institute of Science and Technology Austria","file":[{"file_id":"18059","content_type":"application/pdf","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","date_updated":"2025-03-13T23:30:04Z","embargo":"2025-03-13","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","date_created":"2024-09-12T10:46:04Z","relation":"main_file","access_level":"open_access","creator":"smukhopa","file_size":10297052},{"date_updated":"2025-03-13T23:30:04Z","checksum":"e352667482701dd18a9a0e7418aef465","file_id":"18060","content_type":"application/zip","access_level":"closed","file_size":29178634,"creator":"smukhopa","relation":"source_file","date_created":"2024-09-12T10:50:58Z","embargo_to":"open_access","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip"}],"oa":1,"doi":"10.15479/at:ista:17881","date_updated":"2026-06-03T07:16:04Z","status":"public","project":[{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"year":"2024","file_date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-08T10:23:25Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"_id":"17881","date_published":"2024-09-10T00:00:00Z","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"10","article_processing_charge":"No"},{"ec_funded":1,"related_material":{"record":[{"id":"20324","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"17881","status":"public"}]},"corr_author":"1","article_number":"2408.07829","citation":{"ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>.","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. .","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>"},"OA_place":"repository","language":[{"iso":"eng"}],"oa_version":"Preprint","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","publication_status":"draft","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559"},{"full_name":"Lancheros Naranjo, Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","first_name":"Diego A"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","orcid":"0000-0002-0672-9295","last_name":"Senior","full_name":"Senior, Jorden L"},{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"}],"month":"08","abstract":[{"text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations.","lang":"eng"}],"title":"Dual relaxation oscillations in a Josephson junction array","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.07829"}],"arxiv":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"doi":"10.48550/arXiv.2408.07829","date_updated":"2026-08-28T22:30:18Z","status":"public","oa":1,"date_created":"2024-09-11T09:25:22Z","date_published":"2024-08-14T00:00:00Z","external_id":{"arxiv":["2408.07829"]},"_id":"18057","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"year":"2024","article_processing_charge":"No","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","publication":"arXiv"},{"OA_place":"publisher","APC_amount":"3145,39 EUR","has_accepted_license":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project"}],"record":[{"id":"17362","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"19386"}]},"citation":{"ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376."},"article_number":"e1011376","corr_author":"1","issue":"8","OA_type":"gold","scopus_import":"1","ddc":["570"],"intvolume":"        20","acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","author":[{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"department":[{"_id":"BeVi"}],"isi":1,"publication_status":"published","month":"08","volume":20,"language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1371/journal.pgen.1011376","status":"public","date_updated":"2026-08-28T22:30:30Z","DOAJ_listed":"1","project":[{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"tmp":{"image":"/images/cc_by.png","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)"},"article_type":"original","oa":1,"title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","quality_controlled":"1","abstract":[{"text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.","lang":"eng"}],"publisher":"Public Library of Science","file":[{"file_name":"2024_PloSGenetics_Elkrewi.pdf","date_created":"2024-09-11T07:54:12Z","relation":"main_file","access_level":"open_access","file_size":8962687,"creator":"dernst","success":1,"file_id":"18056","checksum":"f5d96b9af57126fc1063e951440477d6","content_type":"application/pdf","date_updated":"2024-09-11T07:54:12Z"}],"publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"day":"30","article_processing_charge":"Yes","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"PLoS Genetics","date_created":"2024-09-08T22:01:11Z","pmid":1,"_id":"17890","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"date_published":"2024-08-30T00:00:00Z","year":"2024","file_date_updated":"2024-09-11T07:54:12Z"},{"citation":{"mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024."},"corr_author":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"542","status":"public"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","ec_funded":1,"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","OA_place":"publisher","supervisor":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","page":"105","language":[{"iso":"eng"}],"month":"06","author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","last_name":"Kelemen"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","ddc":["576"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"file":[{"file_name":"thesis.zip","creator":"rkelemen","access_level":"closed","file_size":180557931,"embargo_to":"open_access","date_created":"2024-06-07T16:09:17Z","relation":"source_file","checksum":"fab59146e3b3dc2e5d214576984a2a63","content_type":"application/zip","file_id":"17121","date_updated":"2025-01-10T23:30:10Z"},{"file_id":"17213","content_type":"application/pdf","checksum":"91cc4c25a792239e8a7688e8aec7c62a","date_updated":"2025-01-10T23:30:10Z","file_name":"thesis_to_archive.pdf","embargo":"2025-01-10","access_level":"open_access","file_size":19405484,"creator":"rkelemen","relation":"main_file","date_created":"2024-07-10T08:00:20Z"}],"abstract":[{"text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research.","lang":"eng"}],"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","publisher":"Institute of Science and Technology Austria","oa":1,"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"status":"public","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"doi":"10.15479/at:ista:17119","date_updated":"2026-04-07T13:21:37Z","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"file_date_updated":"2025-01-10T23:30:10Z","year":"2024","_id":"17119","date_published":"2024-06-20T00:00:00Z","date_created":"2024-06-07T16:14:13Z","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"20","article_processing_charge":"No"},{"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"29","article_processing_charge":"No","year":"2024","file_date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-27T07:35:13Z","_id":"18477","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_published":"2024-10-29T00:00:00Z","tmp":{"image":"/images/cc_by.png","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)"},"oa":1,"doi":"10.15479/at:ista:18477","status":"public","date_updated":"2026-04-07T13:23:59Z","publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"title":"Biochemical and structural insights into ADAR1 RNA editing","abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"2053294ea4d770c495e4cc501e2a218b","file_id":"18485","date_updated":"2025-10-29T23:30:02Z","file_name":"20241029_PhD_thesis_BKaczmarek.docx","file_size":23136626,"creator":"bkaczmar","access_level":"closed","date_created":"2024-10-29T11:56:36Z","embargo_to":"open_access","relation":"source_file"},{"file_name":"20241029_PhD_thesis_BKaczmarek.pdf","embargo":"2025-10-29","access_level":"open_access","file_size":11707360,"creator":"bkaczmar","relation":"main_file","date_created":"2024-10-29T11:56:44Z","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","file_id":"18486","content_type":"application/pdf","date_updated":"2025-10-29T23:30:02Z"}],"author":[{"full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"publication_status":"published","month":"10","ddc":["572"],"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"124","OA_place":"publisher","supervisor":[{"first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky"}],"citation":{"ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>"},"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","alternative_title":["ISTA Thesis"]},{"ddc":["570"],"author":[{"id":"1d390868-f128-11eb-9611-a0ca5f7833b5","first_name":"Julie Stefanie","full_name":"Murmann, Julie Stefanie","last_name":"Murmann"}],"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"publication_status":"published","month":"05","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"54","supervisor":[{"last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"OA_place":"publisher","has_accepted_license":"1","degree_awarded":"MS","alternative_title":["ISTA Master's Thesis"],"citation":{"ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>"},"corr_author":"1","day":"02","article_processing_charge":"No","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2024-05-02T08:31:38Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"_id":"15352","date_published":"2024-05-02T00:00:00Z","year":"2024","file_date_updated":"2025-05-02T22:30:04Z","doi":"10.15479/at:ista:15352","status":"public","date_updated":"2026-04-07T13:05:00Z","tmp":{"image":"/images/cc_by.png","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)"},"oa":1,"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","abstract":[{"lang":"eng","text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. "}],"publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2025-05-02T22:30:04Z","file_id":"15354","content_type":"application/pdf","checksum":"095817a6c944954ac3f277e547031a33","creator":"cchlebak","access_level":"open_access","file_size":5936142,"relation":"main_file","date_created":"2024-05-02T12:26:13Z","embargo":"2025-05-02","file_name":"Murmann_Thesis_final_2024_2.pdf"},{"date_updated":"2025-05-02T22:30:04Z","file_id":"15355","content_type":"application/x-zip-compressed","checksum":"43b632255372973a437ac87739cfd4db","access_level":"closed","file_size":20645510,"creator":"cchlebak","embargo_to":"open_access","date_created":"2024-05-02T12:37:56Z","relation":"source_file","file_name":"Murmann_Thesis_final_2024.zip"}],"publication_identifier":{"issn":["2791-4585"]}},{"OA_place":"publisher","supervisor":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"}],"corr_author":"1","citation":{"ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"ec_funded":1,"degree_awarded":"PhD","has_accepted_license":"1","month":"01","publication_status":"published","author":[{"full_name":"Chiossi, Heloisa","last_name":"Chiossi","orcid":"0009-0004-2973-278X","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","first_name":"Heloisa"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"ddc":["570"],"page":"89","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.15479/at:ista:14821","date_updated":"2026-04-07T13:21:56Z","status":"public","publication_identifier":{"issn":["2663-337X"]},"file":[{"checksum":"d3fa3de1abd5af5204c13e9d55375615","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14838","date_updated":"2025-01-19T23:30:04Z","file_name":"PhD_Thesis_190124.docx","access_level":"closed","creator":"hchiossi","file_size":8656268,"relation":"source_file","date_created":"2024-01-19T11:04:05Z","embargo_to":"open_access"},{"file_name":"PhD_Thesis_190124.pdf","embargo":"2025-01-19","date_created":"2024-01-19T11:03:59Z","relation":"main_file","file_size":6567275,"creator":"hchiossi","access_level":"open_access","content_type":"application/pdf","file_id":"14839","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","date_updated":"2025-01-19T23:30:04Z"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour."}],"title":"Adaptive hierarchical representations in the hippocampus","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","article_processing_charge":"No","day":"19","file_date_updated":"2025-01-19T23:30:04Z","year":"2024","date_published":"2024-01-19T00:00:00Z","_id":"14821","date_created":"2024-01-16T14:25:21Z"},{"month":"03","volume":112,"publication_status":"published","isi":1,"author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","last_name":"Chen","full_name":"Chen, JingJing"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong","full_name":"Chen, Chong","last_name":"Chen"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","full_name":"Arai, Itaru","last_name":"Arai"},{"orcid":"0000-0003-2344-1039","full_name":"Kim, Olena","last_name":"Kim","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","intvolume":"       112","ddc":["570"],"scopus_import":"1","page":"755-771.e9","oa_version":"Published Version","language":[{"iso":"eng"}],"OA_place":"publisher","issue":"5","OA_type":"hybrid","corr_author":"1","citation":{"short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>."},"ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","description":"News on ISTA Website"}],"record":[{"id":"15101","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","publication":"Neuron","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_processing_charge":"Yes (via OA deal)","day":"06","file_date_updated":"2025-04-23T14:02:08Z","year":"2024","date_published":"2024-03-06T00:00:00Z","external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"_id":"14843","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"pmid":1,"date_created":"2024-01-21T23:00:56Z","oa":1,"tmp":{"image":"/images/cc_by.png","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)"},"article_type":"original","project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-08-28T22:30:33Z","doi":"10.1016/j.neuron.2023.12.002","status":"public","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"file":[{"date_updated":"2025-04-23T14:02:08Z","checksum":"30098b4f0209556ddfb3540a23d07ca5","content_type":"application/pdf","file_id":"19614","success":1,"access_level":"open_access","creator":"dernst","file_size":8192355,"relation":"main_file","date_created":"2025-04-23T14:02:08Z","file_name":"2024_Neuron_Chen.pdf"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"quality_controlled":"1","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","PlanS_conform":"1"}]