[{"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"ec_funded":1,"publication":"Nature Biotechnology","quality_controlled":"1","OA_type":"hybrid","date_created":"2023-09-03T22:01:15Z","oa":1,"volume":42,"article_processing_charge":"Yes (in subscription journal)","publisher":"Springer Nature","article_type":"original","file_date_updated":"2025-01-09T07:48:01Z","ddc":["570"],"license":"https://creativecommons.org/licenses/by/4.0/","page":"1051-1064","month":"07","status":"public","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","project":[{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600"},{"grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"}],"corr_author":"1","OA_place":"publisher","publication_status":"published","citation":{"ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>"},"author":[{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","first_name":"Julia M"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"full_name":"Korinkova, Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","full_name":"Cenameri, Alban"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"first_name":"Karl","last_name":"Roessler","full_name":"Roessler, Karl"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"first_name":"Romana","last_name":"Höftberger","full_name":"Höftberger, Romana"},{"last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"intvolume":"        42","_id":"14257","oa_version":"Published Version","type":"journal_article","scopus_import":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"status":"deleted","id":"18660","relation":"dissertation_contains"},{"id":"13126","relation":"research_data","status":"public"},{"status":"public","id":"18674","relation":"dissertation_contains"}]},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","language":[{"iso":"eng"}],"isi":1,"date_updated":"2026-04-14T08:34:35Z","date_published":"2024-07-01T00:00:00Z","file":[{"date_updated":"2025-01-09T07:48:01Z","relation":"main_file","file_size":26065165,"content_type":"application/pdf","file_name":"2024_NatureBiotech_Michalska.pdf","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","date_created":"2025-01-09T07:48:01Z","creator":"dernst","access_level":"open_access","file_id":"18784","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"pmid":1,"year":"2024","day":"01","doi":"10.1038/s41587-023-01911-8"},{"_id":"14979","intvolume":"        31","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"type":"journal_article","oa_version":"Published Version","OA_place":"publisher","corr_author":"1","project":[{"grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"author":[{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse"},{"last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Thader, Andreas"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"id":"0c894dcf-897b-11ed-a09c-8186353224b0","last_name":"Bauer","first_name":"Lukas W","full_name":"Bauer, Lukas W"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"publication_status":"published","citation":{"ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123."},"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"file":[{"date_updated":"2024-07-22T11:27:22Z","relation":"main_file","file_size":17485494,"content_type":"application/pdf","checksum":"bda7bf65d81455480efaed8ca293b0db","file_name":"2024_NatureStrucBio_Datler.pdf","date_created":"2024-07-22T11:27:22Z","creator":"dernst","access_level":"open_access","file_id":"17307","success":1}],"date_published":"2024-07-01T00:00:00Z","date_updated":"2026-04-07T12:59:44Z","doi":"10.1038/s41594-023-01201-6","pmid":1,"day":"01","year":"2024","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"keyword":["Molecular Biology","Structural Biology"],"scopus_import":"1","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}],"record":[{"status":"public","id":"18766","relation":"dissertation_contains"}]},"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","language":[{"iso":"eng"}],"APC_amount":"11700 EUR","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publication":"Nature Structural & Molecular Biology","page":"1114-1123","status":"public","abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"month":"07","article_processing_charge":"Yes (in subscription journal)","volume":31,"quality_controlled":"1","date_created":"2024-02-12T09:59:45Z","OA_type":"hybrid","oa":1,"ddc":["570"],"publisher":"Springer Nature","file_date_updated":"2024-07-22T11:27:22Z","article_type":"original"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","id":"7606","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12081"},{"status":"public","relation":"part_of_dissertation","id":"7553"}]},"keyword":["Theoretical biology","Optimality","Evolution","Information"],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"relation":"main_file","date_updated":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","checksum":"b2d3da47c98d481577a4baf68944fe41","content_type":"application/pdf","file_size":7102089,"access_level":"open_access","creator":"mhledik","date_created":"2024-02-23T13:50:53Z","success":1,"file_id":"15021"},{"date_updated":"2024-02-23T14:20:16Z","relation":"source_file","file_size":14014790,"content_type":"application/zip","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_name":"hledik thesis source.zip","date_created":"2024-02-23T13:50:54Z","creator":"mhledik","access_level":"closed","file_id":"15022"}],"date_updated":"2026-04-07T12:59:25Z","date_published":"2024-02-23T00:00:00Z","doi":"10.15479/at:ista:15020","day":"23","year":"2024","publication_status":"published","author":[{"full_name":"Hledik, Michal","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik"}],"citation":{"mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"OA_place":"publisher","corr_author":"1","title":"Genetic information and biological optimization","_id":"15020","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"type":"dissertation","oa_version":"Published Version","article_processing_charge":"No","oa":1,"date_created":"2024-02-23T14:02:04Z","ddc":["576","519"],"file_date_updated":"2024-02-23T14:20:16Z","publisher":"Institute of Science and Technology Austria","page":"158","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"status":"public","month":"02","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","ec_funded":1},{"file":[{"relation":"main_file","date_updated":"2024-03-25T12:52:04Z","checksum":"90d1984a93660735e506c2a304bc3f73","file_name":"2024_JCB_Zens.pdf","content_type":"application/pdf","file_size":11907016,"access_level":"open_access","creator":"dernst","date_created":"2024-03-25T12:52:04Z","success":1,"file_id":"15188"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["38506714"],"isi":["001264190100001"]},"date_updated":"2025-09-04T13:17:16Z","date_published":"2024-03-20T00:00:00Z","doi":"10.1083/jcb.202309125","year":"2024","day":"20","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","isi":1,"issue":"6","language":[{"iso":"eng"}],"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","_id":"15146","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"intvolume":"       223","type":"journal_article","oa_version":"Published Version","citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024."},"author":[{"orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina"},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler"},{"first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","full_name":"Hansen, Jesse","orcid":"0000-0001-7967-2085"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin"},{"orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden"},{"orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","first_name":"Jonna H","last_name":"Alanko","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"publication_status":"published","corr_author":"1","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435"},{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"grant_number":"21317","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis","_id":"2615199A-B435-11E9-9278-68D0E5697425"},{"grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308"}],"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"status":"public","month":"03","volume":223,"article_processing_charge":"Yes (via OA deal)","oa":1,"date_created":"2024-03-21T06:45:51Z","quality_controlled":"1","article_number":"e202309125","ddc":["570"],"file_date_updated":"2024-03-25T12:52:04Z","article_type":"original","publisher":"Rockefeller University Press","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"publication":"Journal of Cell Biology","ec_funded":1},{"date_created":"2024-04-14T22:01:01Z","oa":1,"OA_type":"hybrid","quality_controlled":"1","volume":134,"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-01-09T09:05:31Z","article_type":"original","publisher":"Elsevier","ddc":["550"],"article_number":"108011","month":"07","abstract":[{"text":"Our goal is to investigate fundamental properties of the system of internally cooled convection. The system consists of an upward thermal flux at the lower boundary, a mean temperature lapse-rate and a constant cooling term in the bulk with the bulk cooling in thermal equilibrium with the input heat flux. This simple model represents idealised dry convection in the atmospheric boundary layer, where the cooling mimics the radiative cooling to space notably through longwave radiation. We perform linear stability analysis of the model for different values of the mean stratification to derive the critical forcing above which the fluid is convectively unstable to small perturbations. The dynamic behavior of the fluid system is described and the scaling of various important measured quantities such as the total vertical convective heat flux and the upward mass flux is measured. We introduce a lapse-rate dependent dimensionless Rayleigh-number Ray that determines the behavior of the system, finding that the convective heat-flux and mass-flux scale approximately as Ray0.5 and Ray0.7 respectively. The area-fraction of the domain that is occupied by upward and downward moving fluid and the skewness of the vertical velocity are studied to understand the asymmetry inherent in the system. We conclude with a short discussion on the relevance to atmospheric convection and the scope for further investigations of atmospheric convection using similar simplified approaches.","lang":"eng"}],"status":"public","publication_identifier":{"issn":["1007-5704"]},"ec_funded":1,"publication":"Communications in Nonlinear Science and Numerical Simulation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska–Curie grant agreement No. 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","isi":1,"date_published":"2024-07-01T00:00:00Z","date_updated":"2025-09-04T13:37:48Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2311.04114"],"isi":["001238294600001"]},"file":[{"access_level":"open_access","creator":"dernst","date_created":"2025-01-09T09:05:31Z","success":1,"file_id":"18795","relation":"main_file","date_updated":"2025-01-09T09:05:31Z","file_name":"2024_CommNonlinear_Agasthya.pdf","checksum":"9b7c2b8281d0b7bc7f08e0468168324c","content_type":"application/pdf","file_size":1257925}],"year":"2024","day":"01","doi":"10.1016/j.cnsns.2024.108011","title":"Dynamics and scaling of internally cooled convection","citation":{"ieee":"L. N. Agasthya and C. J. Muller, “Dynamics and scaling of internally cooled convection,” <i>Communications in Nonlinear Science and Numerical Simulation</i>, vol. 134. Elsevier, 2024.","apa":"Agasthya, L. N., &#38; Muller, C. J. (2024). Dynamics and scaling of internally cooled convection. <i>Communications in Nonlinear Science and Numerical Simulation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">https://doi.org/10.1016/j.cnsns.2024.108011</a>","ama":"Agasthya LN, Muller CJ. Dynamics and scaling of internally cooled convection. <i>Communications in Nonlinear Science and Numerical Simulation</i>. 2024;134. doi:<a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">10.1016/j.cnsns.2024.108011</a>","ista":"Agasthya LN, Muller CJ. 2024. Dynamics and scaling of internally cooled convection. Communications in Nonlinear Science and Numerical Simulation. 134, 108011.","chicago":"Agasthya, Lokahith N, and Caroline J Muller. “Dynamics and Scaling of Internally Cooled Convection.” <i>Communications in Nonlinear Science and Numerical Simulation</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">https://doi.org/10.1016/j.cnsns.2024.108011</a>.","short":"L.N. Agasthya, C.J. Muller, Communications in Nonlinear Science and Numerical Simulation 134 (2024).","mla":"Agasthya, Lokahith N., and Caroline J. Muller. “Dynamics and Scaling of Internally Cooled Convection.” <i>Communications in Nonlinear Science and Numerical Simulation</i>, vol. 134, 108011, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">10.1016/j.cnsns.2024.108011</a>."},"author":[{"full_name":"Agasthya, Lokahith N","first_name":"Lokahith N","last_name":"Agasthya","id":"cd100965-0804-11ed-9c55-f4878ff4e877"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"}],"publication_status":"published","OA_place":"publisher","corr_author":"1","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"grant_number":"805041","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"arxiv":1,"intvolume":"       134","department":[{"_id":"CaMu"}],"_id":"15313","oa_version":"Published Version","type":"journal_article"},{"publication":"The Plant Cell","publication_identifier":{"eissn":["1532-298X"]},"article_type":"original","file_date_updated":"2025-04-23T07:43:12Z","publisher":"Oxford University Press","ddc":["580"],"OA_type":"hybrid","oa":1,"date_created":"2024-05-12T22:01:01Z","quality_controlled":"1","volume":36,"article_processing_charge":"Yes (via OA deal)","month":"05","abstract":[{"text":"In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA.","lang":"eng"}],"status":"public","page":"1829-1843","title":"Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis","publication_status":"published","citation":{"ama":"He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. <i>The Plant Cell</i>. 2024;36(5):1829-1843. doi:<a href=\"https://doi.org/10.1093/plcell/koae034\">10.1093/plcell/koae034</a>","apa":"He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koae034\">https://doi.org/10.1093/plcell/koae034</a>","ieee":"S. He <i>et al.</i>, “Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis,” <i>The Plant Cell</i>, vol. 36, no. 5. Oxford University Press, pp. 1829–1843, 2024.","mla":"He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” <i>The Plant Cell</i>, vol. 36, no. 5, Oxford University Press, 2024, pp. 1829–43, doi:<a href=\"https://doi.org/10.1093/plcell/koae034\">10.1093/plcell/koae034</a>.","short":"S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant Cell 36 (2024) 1829–1843.","chicago":"He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” <i>The Plant Cell</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/plcell/koae034\">https://doi.org/10.1093/plcell/koae034</a>.","ista":"He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. 36(5), 1829–1843."},"author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"last_name":"Yu","id":"318e643b-8b61-11ed-b69e-aafa103ec8dd","first_name":"Yiming","full_name":"Yu, Yiming"},{"first_name":"Liang","last_name":"Wang","full_name":"Wang, Liang"},{"full_name":"Zhang, Jingyi","first_name":"Jingyi","last_name":"Zhang"},{"full_name":"Bai, Zhengyong","first_name":"Zhengyong","last_name":"Bai"},{"full_name":"Li, Guohong","first_name":"Guohong","last_name":"Li"},{"full_name":"Li, Pilong","first_name":"Pilong","last_name":"Li"},{"first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"corr_author":"1","OA_place":"publisher","oa_version":"Published Version","type":"journal_article","department":[{"_id":"XiFe"}],"intvolume":"        36","_id":"15375","language":[{"iso":"eng"}],"acknowledgement":"This work was funded by ISTA core support (Y.Y. and X.F.) and grants from the National Natural Science Foundation of China (31871443 to L.W. and P.L.; 32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance with microscopy and the ISTA Scientific Computing Facility for high-performance computing resources.","isi":1,"issue":"5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"year":"2024","day":"01","pmid":1,"doi":"10.1093/plcell/koae034","date_updated":"2025-09-08T07:21:17Z","date_published":"2024-05-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","date_updated":"2025-04-23T07:43:12Z","checksum":"eed76c848fe3d8fe9a53943181aaa53c","file_name":"2024_PlantCell_He.pdf","content_type":"application/pdf","file_size":50791962,"access_level":"open_access","creator":"dernst","date_created":"2025-04-23T07:43:12Z","success":1,"file_id":"19611"}],"external_id":{"isi":["001180817000001"],"pmid":["38309957"]}},{"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","OA_type":"gold","date_created":"2024-11-06T21:25:37Z","oa":1,"article_processing_charge":"No","file_date_updated":"2024-11-07T10:59:42Z","publisher":"Institute of Science and Technology Austria","ddc":["576"],"page":"219","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"11","abstract":[{"lang":"eng","text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations."}],"status":"public","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","citation":{"chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024."},"publication_status":"published","author":[{"full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","corr_author":"1","project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"_id":"18515","oa_version":"Published Version","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T12:56:52Z","date_published":"2024-11-07T00:00:00Z","file":[{"access_level":"open_access","date_created":"2024-11-07T10:59:29Z","creator":"psurendr","success":1,"file_id":"18519","relation":"main_file","date_updated":"2024-11-07T10:59:29Z","content_type":"application/pdf","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","checksum":"c32cf7bc75748d9c551d8eb70178bbec","file_size":37019760},{"content_type":"application/zip","file_name":"PhD Thesis- Parvathy_071124.zip","checksum":"4417e02d54084d89e75734e18caaa96d","file_size":41198857,"relation":"source_file","date_updated":"2024-11-07T10:59:42Z","file_id":"18520","access_level":"closed","date_created":"2024-11-07T10:59:42Z","creator":"psurendr"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","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"},"day":"07","year":"2024","doi":"10.15479/at:ista:18515"},{"file_date_updated":"2024-12-09T12:54:55Z","publisher":"Institute of Science and Technology Austria","ddc":["570"],"date_created":"2024-11-22T13:48:12Z","oa":1,"article_processing_charge":"No","month":"12","abstract":[{"text":"Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. ","lang":"eng"}],"status":"public","ec_funded":1,"acknowledgement":"Freyja Lange, Michael Schunn, and Todor Asenov","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"19076","relation":"used_in_publication"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2024","day":"09","doi":"10.15479/AT:ISTA:18579","date_updated":"2026-06-18T18:12:08Z","date_published":"2024-12-09T00:00:00Z","file":[{"date_created":"2024-12-06T13:28:18Z","creator":"symonova","access_level":"open_access","file_id":"18625","date_updated":"2024-12-09T10:24:25Z","relation":"main_file","file_size":800647957,"content_type":"application/x-zip-compressed","file_name":"electro_physiology_data.zip","checksum":"8b13990ca1a458ae3f3ae54c2e888564"},{"creator":"symonova","date_created":"2024-12-09T10:21:10Z","access_level":"open_access","file_id":"18636","success":1,"date_updated":"2024-12-09T10:21:10Z","relation":"main_file","file_size":828410832,"checksum":"c5a4d71c5f29c009c3d96a3244532afa","file_name":"NN_vLGN_Ca_data.zip","content_type":"application/x-zip-compressed"},{"file_name":"readme.txt","checksum":"63651df0186196969553dc48b467f6ab","content_type":"text/plain","file_size":505,"relation":"main_file","date_updated":"2024-12-09T12:54:55Z","success":1,"file_id":"18637","access_level":"open_access","creator":"symonova","date_created":"2024-12-09T12:54:55Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","citation":{"chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>.","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024).","ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","mla":"Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024."},"author":[{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A"},{"orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser","first_name":"Anton L"},{"first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga","orcid":"0000-0003-2012-9947"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"},{"full_name":"Schmidt, Florian","id":"A2EF226A-AF19-11E9-924C-0525E6697425","last_name":"Schmidt","first_name":"Florian"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A"}],"OA_place":"publisher","project":[{"name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017"},{"grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580"}],"corr_author":"1","oa_version":"Published Version","type":"research_data","department":[{"_id":"MaJö"}],"_id":"18579"},{"ec_funded":1,"publication":"bioRxiv","date_created":"2024-12-18T14:48:24Z","oa":1,"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"07","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner."}],"status":"public","title":"Light-microscopy based dense connectomic reconstruction of mammalian brain tissue","citation":{"ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” <i>bioRxiv</i>. .","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.).","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>."},"author":[{"full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"},{"full_name":"Januszewski, Michał","first_name":"Michał","last_name":"Januszewski"},{"last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali","full_name":"Vistunou, Vitali"},{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","orcid":"0009-0000-7590-3501","full_name":"Vorlaufer, Jakob"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"full_name":"Oliveira, Bárbara","last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","first_name":"Bárbara"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"full_name":"Jain, Viren","last_name":"Jain","first_name":"Viren"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"draft","project":[{"grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865"},{"grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"OA_place":"repository","corr_author":"1","department":[{"_id":"GaNo"},{"_id":"JoDa"}],"_id":"18677","oa_version":"Preprint","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"18681","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"18674"},{"status":"public","relation":"later_version","id":"19704"}]},"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.03.01.582884"}],"date_published":"2024-07-08T00:00:00Z","date_updated":"2026-04-28T13:33:34Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"year":"2024","day":"08","doi":"10.1101/2024.03.01.582884"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_created":"2024-12-19T11:35:08Z","related_material":{"record":[{"status":"public","id":"18681","relation":"dissertation_contains"},{"id":"18879","relation":"later_version","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","main_file_link":[{"url":"https://doi.org/10.1101/2024.05.02.592169","open_access":"1"}],"date_updated":"2026-04-14T08:34:32Z","date_published":"2024-05-02T00:00:00Z","month":"05","day":"02","year":"2024","abstract":[{"lang":"eng","text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits."}],"doi":"10.1101/2024.05.02.592169","status":"public","title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","publication_status":"draft","author":[{"full_name":"Watson, Jake F.","first_name":"Jake F.","last_name":"Watson"},{"full_name":"Vargas-Barroso, Victor","first_name":"Victor","last_name":"Vargas-Barroso"},{"last_name":"Morse-Mora","first_name":"Rebecca J.","full_name":"Morse-Mora, Rebecca J."},{"full_name":"Navas-Olive, Andrea","last_name":"Navas-Olive","first_name":"Andrea"},{"orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tomschik, Matthias","last_name":"Tomschik","first_name":"Matthias"},{"full_name":"Rössler, Karl","last_name":"Rössler","first_name":"Karl"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"citation":{"ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>."},"OA_place":"repository","project":[{"grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"}],"corr_author":"1","department":[{"_id":"JoDa"},{"_id":"PeJo"}],"_id":"18688","oa_version":"Preprint","ec_funded":1,"publication":"bioRxiv","type":"preprint"},{"publisher":"Oxford University Press","article_type":"original","file_date_updated":"2025-01-08T08:28:07Z","ddc":["570"],"article_number":"evae265","quality_controlled":"1","oa":1,"OA_type":"gold","date_created":"2025-01-05T23:01:58Z","volume":16,"article_processing_charge":"Yes","month":"12","status":"public","abstract":[{"text":"Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication":"Genome Biology and Evolution","DOAJ_listed":"1","publication_identifier":{"eissn":["1759-6653"]},"acknowledgement":"urthermore, we thank all lab members and collaborators for feedback on the project. Specifically, Dino McMahon provided R. flavipes males and females, Judith Korb provided C. secundus males and females, gave feedback on the project and discussed questions on termite reproduction, Mireille Vasseur-Cognet provided M. natalensis males and females, Ariana Macon performed the lab work for sequencing and the Vicoso group gave critical feedback on the project. We furthermore thank the HPC group at IST Austria and Christian Meesters at JGU Mainz for their technical support.\r\nThis work was supported by a Österreichischer Wissenschaftsfonds (FWF) grant of the Meitner Programme to A.K.H. (project number M 2484), funding by the Deutsche Forschungsgemeinschaft (DFG) of the Research Training Group GenEvo (project number 407023052) to A.K.H., R.F., and A.D., and funding of the DFG within the Schwerpunktprogramm Gevol to A.K.H. and R.M. (project number 503256468).","language":[{"iso":"eng"}],"issue":"12","isi":1,"scopus_import":"1","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"year":"2024","day":"01","doi":"10.1093/gbe/evae265","date_updated":"2025-09-09T11:58:41Z","date_published":"2024-12-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"content_type":"application/pdf","checksum":"9cf8fd14580dd694dd810ccca808ad0e","file_name":"2024_GBE_Fraser.pdf","file_size":795106,"relation":"main_file","date_updated":"2025-01-08T08:28:07Z","success":1,"file_id":"18772","access_level":"open_access","date_created":"2025-01-08T08:28:07Z","creator":"dernst"}],"external_id":{"isi":["001380841100001"],"pmid":["39658246"]},"title":"Evidence for a novel X chromosome in termites","OA_place":"publisher","corr_author":"1","project":[{"call_identifier":"FWF","_id":"26641CAC-B435-11E9-9278-68D0E5697425","name":"Sex Determination in Termites","grant_number":"M02484"}],"citation":{"ama":"Fraser R, Moraa R, Djolai A, et al. Evidence for a novel X chromosome in termites. <i>Genome Biology and Evolution</i>. 2024;16(12). doi:<a href=\"https://doi.org/10.1093/gbe/evae265\">10.1093/gbe/evae265</a>","ieee":"R. Fraser <i>et al.</i>, “Evidence for a novel X chromosome in termites,” <i>Genome Biology and Evolution</i>, vol. 16, no. 12. Oxford University Press, 2024.","apa":"Fraser, R., Moraa, R., Djolai, A., Meisenheimer, N., Laube, S., Vicoso, B., &#38; Huylmans, A. K. (2024). Evidence for a novel X chromosome in termites. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae265\">https://doi.org/10.1093/gbe/evae265</a>","short":"R. Fraser, R. Moraa, A. Djolai, N. Meisenheimer, S. Laube, B. Vicoso, A.K. Huylmans, Genome Biology and Evolution 16 (2024).","chicago":"Fraser, Roxanne, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube, Beatriz Vicoso, and Ann K Huylmans. “Evidence for a Novel X Chromosome in Termites.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae265\">https://doi.org/10.1093/gbe/evae265</a>.","ista":"Fraser R, Moraa R, Djolai A, Meisenheimer N, Laube S, Vicoso B, Huylmans AK. 2024. Evidence for a novel X chromosome in termites. Genome Biology and Evolution. 16(12), evae265.","mla":"Fraser, Roxanne, et al. “Evidence for a Novel X Chromosome in Termites.” <i>Genome Biology and Evolution</i>, vol. 16, no. 12, evae265, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae265\">10.1093/gbe/evae265</a>."},"publication_status":"published","author":[{"full_name":"Fraser, Roxanne","first_name":"Roxanne","last_name":"Fraser"},{"last_name":"Moraa","first_name":"Ruth","full_name":"Moraa, Ruth"},{"full_name":"Djolai, Annika","first_name":"Annika","last_name":"Djolai"},{"first_name":"Nils","last_name":"Meisenheimer","full_name":"Meisenheimer, Nils"},{"full_name":"Laube, Sophie","first_name":"Sophie","last_name":"Laube"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K"}],"oa_version":"Published Version","type":"journal_article","department":[{"_id":"BeVi"}],"intvolume":"        16","_id":"18761"},{"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"_id":"18766","oa_version":"Published Version","type":"dissertation","title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","citation":{"apa":"Datler, J. (2024). <i>Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>","ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria.","chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>.","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","mla":"Datler, Julia. <i>Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>."},"publication_status":"published","author":[{"first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia","orcid":"0000-0002-3616-8580"}],"project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}],"corr_author":"1","OA_place":"publisher","date_updated":"2026-04-07T12:59:44Z","date_published":"2024-12-30T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"file":[{"file_id":"18769","creator":"jstanger","date_created":"2025-01-07T12:15:11Z","access_level":"closed","file_size":38814932,"file_name":"PhD_thesis_Julia_Datler.docx","checksum":"3e51cab327c754045c3d29c1a50cc9a9","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-01-07T12:15:11Z","relation":"source_file"},{"file_id":"18770","success":1,"creator":"jstanger","date_created":"2025-01-07T12:15:14Z","access_level":"open_access","file_size":12044865,"checksum":"22fabe5b97950bf852212f6edb555173","file_name":"PhD_thesis_Julia_Datler.pdf","content_type":"application/pdf","date_updated":"2025-01-07T12:15:14Z","relation":"main_file"}],"day":"30","year":"2024","doi":"10.15479/at:ista:18766","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12334"},{"status":"public","id":"14979","relation":"part_of_dissertation"}]},"keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample.","alternative_title":["ISTA thesis"],"publication_identifier":{"isbn":["978-3-99078-049-7"],"issn":["2663-337X"]},"degree_awarded":"PhD","page":"106","month":"12","abstract":[{"lang":"eng","text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses."}],"status":"public","date_created":"2025-01-07T10:23:12Z","oa":1,"article_processing_charge":"No","file_date_updated":"2025-01-07T12:15:14Z","publisher":"Institute of Science and Technology Austria","ddc":["570"]},{"citation":{"ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","apa":"Súkeník, P., Lampert, C., &#38; Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024."},"author":[{"full_name":"Súkeník, Peter","first_name":"Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","last_name":"Súkeník"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"publication_status":"published","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"OA_place":"publisher","corr_author":"1","title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","arxiv":1,"_id":"18891","intvolume":"        37","department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"type":"conference","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Advances in Neural Information Processing Systems"],"language":[{"iso":"eng"}],"acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"18989","success":1,"date_created":"2025-02-04T08:11:25Z","creator":"dernst","access_level":"open_access","file_size":1784118,"content_type":"application/pdf","checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","file_name":"2024_NeurIPS_Sukenik.pdf","date_updated":"2025-02-04T08:11:25Z","relation":"main_file"}],"external_id":{"arxiv":["2405.14468"]},"date_updated":"2025-06-04T07:19:21Z","date_published":"2024-12-01T00:00:00Z","day":"01","year":"2024","conference":{"end_date":"2024-12-16","location":"Vancouver, Canada","start_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems"},"publication":"38th Annual Conference on Neural Information Processing Systems","article_processing_charge":"No","volume":37,"oa":1,"OA_type":"gold","date_created":"2025-01-27T11:15:18Z","quality_controlled":"1","ddc":["000"],"file_date_updated":"2025-02-04T08:11:25Z","publisher":"Neural Information Processing Systems Foundation","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent."}],"status":"public","month":"12"},{"license":"https://creativecommons.org/licenses/by-sa/4.0/","status":"public","abstract":[{"lang":"eng","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"}],"month":"03","article_processing_charge":"No","oa":1,"date_created":"2025-02-20T10:13:42Z","OA_type":"green","ddc":["000"],"article_number":"2403.06833","file_date_updated":"2025-02-20T10:11:45Z","publication":"arXiv","file":[{"content_type":"application/pdf","checksum":"35eb43968684b87be59144603ef10af0","file_name":"2403.06833v3.pdf","file_size":530972,"relation":"main_file","date_updated":"2025-02-20T10:11:45Z","success":1,"file_id":"19064","access_level":"open_access","date_created":"2025-02-20T10:11:45Z","creator":"ezverev"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"external_id":{"arxiv":["2403.06833"]},"date_published":"2024-03-01T00:00:00Z","date_updated":"2025-02-24T12:52:23Z","doi":"10.48550/arXiv.2403.06833","year":"2024","day":"01","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"link":[{"url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed","relation":"software"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.06833"}],"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"}],"_id":"19063","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"type":"preprint","oa_version":"Preprint","OA_place":"repository","corr_author":"1","publication_status":"published","citation":{"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>. 2024. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>","apa":"Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., &#38; Lampert, C. (2024). 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>","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>. 2024.","mla":"Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” <i>ArXiv</i>, 2403.06833, 2024, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.06833\">10.48550/arXiv.2403.06833</a>.","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>, 2024. <a href=\"https://doi.org/10.48550/arXiv.2403.06833\">https://doi.org/10.48550/arXiv.2403.06833</a>.","short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (2024).","ista":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. 2024. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833."},"author":[{"full_name":"Zverev, Egor","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc","last_name":"Zverev","first_name":"Egor"},{"full_name":"Abdelnabi, Sahar","first_name":"Sahar","last_name":"Abdelnabi"},{"full_name":"Tabesh, Soroush","orcid":"0009-0003-4119-6281","last_name":"Tabesh","id":"06000900-6068-11ef-8d61-c2472ef2e752","first_name":"Soroush"},{"full_name":"Fritz, Mario","last_name":"Fritz","first_name":"Mario"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"title":"Can LLMs separate instructions from data? And what do we even mean by that?","arxiv":1},{"publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"DOAJ_listed":"1","abstract":[{"lang":"eng","text":"Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material."}],"status":"public","month":"07","article_number":"6400","ddc":["530"],"article_type":"original","file_date_updated":"2024-08-05T08:38:01Z","publisher":"Springer Nature","article_processing_charge":"Yes","volume":15,"date_created":"2024-07-04T11:40:45Z","OA_type":"gold","oa":1,"quality_controlled":"1","type":"journal_article","oa_version":"Published Version","_id":"17202","intvolume":"        15","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"arxiv":1,"publication_status":"published","citation":{"ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>","ieee":"O. Sagi <i>et al.</i>, “A gate tunable transmon qubit in planar Ge,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>, vol. 15, 6400, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>.","short":"O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","chicago":"Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>.","ista":"Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400."},"author":[{"first_name":"Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver"},{"orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro","first_name":"Alessandro","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"full_name":"Valentini, Marco","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini"},{"full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian"},{"first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","last_name":"Baghumyan","full_name":"Baghumyan, Levon"},{"full_name":"Fabris, Giorgio","last_name":"Fabris","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","first_name":"Giorgio"},{"full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","first_name":"Lucky"},{"first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"project":[{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"OA_place":"publisher","corr_author":"1","title":"A gate tunable transmon qubit in planar Ge","doi":"10.1038/s41467-024-50763-6","year":"2024","day":"30","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"17388","success":1,"date_created":"2024-08-05T08:38:01Z","creator":"dernst","access_level":"open_access","file_size":1928001,"content_type":"application/pdf","checksum":"ddf5361dcb6c543e2cea818501c09910","file_name":"2024_NatureComm_Sagi.pdf","date_updated":"2024-08-05T08:38:01Z","relation":"main_file"}],"external_id":{"arxiv":["2403.16774"],"pmid":["39080279"],"isi":["001281271000022"]},"date_updated":"2026-04-07T13:01:55Z","date_published":"2024-07-30T00:00:00Z","isi":1,"APC_amount":"6828 EUR","language":[{"iso":"eng"}],"acknowledgement":"We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support.","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","scopus_import":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-024-53910-1"}],"record":[{"status":"public","relation":"research_data","id":"17196"},{"id":"18076","relation":"dissertation_contains","status":"public"}]}},{"page":"133","abstract":[{"text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization.  We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration.","lang":"eng"}],"status":"public","month":"07","article_processing_charge":"No","oa":1,"date_created":"2024-07-09T09:14:24Z","ddc":["539"],"file_date_updated":"2024-07-17T09:23:24Z","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","ec_funded":1,"file":[{"content_type":"application/zip","checksum":"6f45273d04f4418bc2adc018baed0525","file_name":"Raimel_Thesis-Final.zip","file_size":"14218691","relation":"source_file","date_updated":"2024-07-10T11:34:09Z","file_id":"17212","access_level":"closed","date_created":"2024-07-09T09:21:44Z","creator":"rmedinar"},{"date_created":"2024-07-17T09:23:24Z","creator":"rmedinar","access_level":"open_access","file_id":"17275","success":1,"date_updated":"2024-07-17T09:23:24Z","relation":"main_file","file_size":11253627,"content_type":"application/pdf","file_name":"Raimel_Thesis-20_pdfa.pdf","checksum":"6724a95bec772dbabc0111b9f08a805e"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2024-07-09T00:00:00Z","date_updated":"2026-04-07T12:43:22Z","doi":"10.15479/at:ista:17208","year":"2024","day":"09","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"related_material":{"record":[{"status":"public","id":"10545","relation":"part_of_dissertation"},{"status":"public","id":"10067","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"17222"},{"status":"public","relation":"part_of_dissertation","id":"13125"},{"relation":"part_of_dissertation","id":"11471","status":"public"}]},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"_id":"17208","supervisor":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"type":"dissertation","oa_version":"Published Version","citation":{"mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>.","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>"},"publication_status":"published","author":[{"first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A"}],"OA_place":"publisher","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"corr_author":"1","title":"Exploring the optimization landscape of variational quantum algorithms"},{"month":"07","year":"2024","status":"public","abstract":[{"text":"This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. ","lang":"eng"}],"doi":"10.15479/AT:ISTA:17344","date_published":"2024-07-01T00:00:00Z","date_updated":"2025-01-14T13:02:59Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","creator":"psurendr","date_created":"2024-07-29T13:51:11Z","success":1,"file_id":"17345","relation":"main_file","date_updated":"2024-07-29T13:51:11Z","checksum":"75bdbc7ad7cc6afe4459bc4a8824a302","file_name":"Submission.nb","content_type":"application/octet-stream","file_size":726132}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-07-29T13:51:11Z","ddc":["576"],"has_accepted_license":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-07-29T14:01:43Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","type":"research_data","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"17344","title":"Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","citation":{"apa":"Surendranadh, P., &#38; Sachdeva, H. (2024). Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>","ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2024.","ama":"Surendranadh P, Sachdeva H. Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>","ista":"Surendranadh P, Sachdeva H. 2024. Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","short":"P. Surendranadh, H. Sachdeva, (2024).","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>.","mla":"Surendranadh, Parvathy, and Himani Sachdeva. <i>Mathematica Notebook for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>."},"author":[{"orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}]},{"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17890"}]},"date_created":"2024-08-02T07:27:45Z","oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-08-05T23:28:52Z","file":[{"creator":"melkrewi","date_created":"2024-08-05T22:24:18Z","access_level":"open_access","file_id":"17394","success":1,"date_updated":"2024-08-05T22:24:18Z","relation":"main_file","file_size":2465,"checksum":"26b5d41b3103f4284dd97d56e370a5b6","file_name":"README.txt","content_type":"text/plain"},{"date_updated":"2024-08-05T23:28:52Z","relation":"main_file","file_size":2526735400,"file_name":"Data_artemia_single_nucleus_atlas.zip","checksum":"95adab5e36148015da313505e3910707","content_type":"application/x-zip-compressed","creator":"melkrewi","date_created":"2024-08-05T23:28:52Z","access_level":"open_access","file_id":"17395","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-04-16T12:20:41Z","date_published":"2024-08-05T00:00:00Z","status":"public","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"doi":"10.15479/AT:ISTA:17362","day":"05","month":"08","year":"2024","project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"corr_author":"1","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"citation":{"ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","short":"M.N. Elkrewi, B. Vicoso, (2024).","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. <i>Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>"},"title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","_id":"17362","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"research_data","oa_version":"Published Version"},{"file":[{"relation":"main_file","date_updated":"2024-08-05T08:19:58Z","content_type":"application/pdf","file_name":"2024_JourApplPhysics_Lenton.pdf","checksum":"6141d05cd68d540a7446dce9490975db","file_size":2537502,"access_level":"open_access","date_created":"2024-08-05T08:19:58Z","creator":"dernst","success":1,"file_id":"17386"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"external_id":{"isi":["001281681100003"]},"date_published":"2024-07-28T00:00:00Z","date_updated":"2025-09-08T08:47:42Z","doi":"10.1063/5.0215151","year":"2024","day":"28","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","scopus_import":"1","isi":1,"issue":"4","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.","_id":"17373","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"intvolume":"       136","type":"journal_article","oa_version":"Published Version","author":[{"orcid":"0000-0002-5010-6984","full_name":"Lenton, Isaac C","first_name":"Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb","last_name":"Lenton"},{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl","first_name":"Felix","orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix"},{"full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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>","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.","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>","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>.","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.","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (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>."},"publication_status":"published","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"corr_author":"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"}],"status":"public","month":"07","article_processing_charge":"No","volume":136,"date_created":"2024-08-04T22:01:21Z","oa":1,"quality_controlled":"1","ddc":["530"],"article_number":"045305","file_date_updated":"2024-08-05T08:19:58Z","article_type":"original","publisher":"AIP Publishing","publication_identifier":{"issn":["0021-8979"],"eissn":["1089-7550"]},"publication":"Journal of Applied Physics","ec_funded":1},{"oa":1,"date_created":"2024-08-11T22:01:12Z","quality_controlled":"1","article_processing_charge":"No","file_date_updated":"2024-08-12T07:38:06Z","publisher":"OpenReview","ddc":["000"],"month":"03","abstract":[{"lang":"eng","text":"We present PeFLL, a new personalized federated learning algorithm that improves\r\nover the state-of-the-art in three aspects: 1) it produces more accurate models,\r\nespecially in the low-data regime, and not only for clients present during its\r\ntraining phase, but also for any that may emerge in the future; 2) it reduces the\r\namount of on-client computation and client-server communication by providing\r\nfuture clients with ready-to-use personalized models that require no additional\r\nfinetuning or optimization; 3) it comes with theoretical guarantees that establish\r\ngeneralization from the observed clients to future ones.\r\nAt the core of PeFLL lies a learning-to-learn approach that jointly trains an\r\nembedding network and a hypernetwork. The embedding network is used to\r\nrepresent clients in a latent descriptor space in a way that reflects their similarity\r\nto each other. The hypernetwork takes as input such descriptors and outputs the\r\nparameters of fully personalized client models. In combination, both networks\r\nconstitute a learning algorithm that achieves state-of-the-art performance in several\r\npersonalized federated learning benchmarks"}],"status":"public","conference":{"end_date":"2024-03-07","location":"Vienna, Austria","name":"ICLR: International Conference on Learning Representations","start_date":"2024-03-07"},"publication":"12th International Conference on Learning Representations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"21198","relation":"dissertation_contains"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).\r\n","date_updated":"2026-04-07T11:46:11Z","date_published":"2024-03-07T00:00:00Z","external_id":{"arxiv":["2306.05515"]},"file":[{"date_updated":"2024-08-12T07:38:06Z","relation":"main_file","file_size":1029219,"file_name":"2024_ICLR_Scott.pdf","checksum":"81b7ea2e667adaf9c7a7b6b376b1f251","content_type":"application/pdf","creator":"dernst","date_created":"2024-08-12T07:38:06Z","access_level":"open_access","file_id":"17415","success":1}],"year":"2024","day":"07","title":"PEFLL: Personalized federated learning by learning to learn","citation":{"apa":"Scott, J. A., Zakerinia, H., &#38; Lampert, C. (2024). PEFLL: Personalized federated learning by learning to learn. In <i>12th International Conference on Learning Representations</i>. Vienna, Austria: OpenReview.","ieee":"J. A. Scott, H. Zakerinia, and C. Lampert, “PEFLL: Personalized federated learning by learning to learn,” in <i>12th International Conference on Learning Representations</i>, Vienna, Austria, 2024.","ama":"Scott JA, Zakerinia H, Lampert C. PEFLL: Personalized federated learning by learning to learn. In: <i>12th International Conference on Learning Representations</i>. OpenReview; 2024.","ista":"Scott JA, Zakerinia H, Lampert C. 2024. PEFLL: Personalized federated learning by learning to learn. 12th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Scott, Jonathan A, Hossein Zakerinia, and Christoph Lampert. “PEFLL: Personalized Federated Learning by Learning to Learn.” In <i>12th International Conference on Learning Representations</i>. OpenReview, 2024.","short":"J.A. Scott, H. Zakerinia, C. Lampert, in:, 12th International Conference on Learning Representations, OpenReview, 2024.","mla":"Scott, Jonathan A., et al. “PEFLL: Personalized Federated Learning by Learning to Learn.” <i>12th International Conference on Learning Representations</i>, OpenReview, 2024."},"author":[{"first_name":"Jonathan A","id":"e499926b-f6e0-11ea-865d-9c63db0031e8","last_name":"Scott","full_name":"Scott, Jonathan A"},{"orcid":"0009-0007-3977-6462","full_name":"Zakerinia, Hossein","id":"653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4","last_name":"Zakerinia","first_name":"Hossein"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"publication_status":"published","corr_author":"1","arxiv":1,"department":[{"_id":"ChLa"}],"_id":"17411","oa_version":"Published Version","type":"conference"}]