[{"scopus_import":"1","corr_author":"1","author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1011376","type":"journal_article","pmid":1,"publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"oa":1,"title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","article_number":"e1011376","volume":20,"language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","month":"08","date_created":"2024-09-08T22:01:11Z","supplementarymaterial":"yes","APC_amount":"3145,39 EUR","article_processing_charge":"Yes","quality_controlled":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project"}],"record":[{"status":"public","relation":"research_data","id":"17362"},{"status":"public","relation":"dissertation_contains","id":"19386"}]},"project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"date_updated":"2026-10-26T23:30:56Z","abstract":[{"text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.","lang":"eng"}],"file_date_updated":"2024-09-11T07:54:12Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1371/journal.pgen.1011376","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2024-08-30T00:00:00Z","has_accepted_license":"1","OA_type":"gold","OA_place":"publisher","DOAJ_listed":"1","oa_version":"Published Version","_id":"17890","researchdata_availability":"yes","status":"public","acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","year":"2024","citation":{"ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024)."},"publisher":"Public Library of Science","das_tickbox":"1","day":"30","isi":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"dataavailabilitystatement":"The scripts used in the analysis can be accessed on the GitHub page: https://github.com/Melkrewi/Artemia-snRNAseq Project. The raw data are available on the NCBI short read archive (BioProject number PRJNA1128544). The Seurat objects produced in the analysis, the loom files generated by Velocyto, the reciprocal best hits used for the SAMap analysis, and the module tables and their GO enrichment results are available for download on ISTA Research Explorer (ISTA REx) using the following link: https://doi.org/10.15479/AT: ISTA:17362. The single nucleus atlas can be viewed with this link on the UCSC Cell Browser: https://brine-shrimp-repro.cells.ucsc.edu","file":[{"relation":"main_file","checksum":"f5d96b9af57126fc1063e951440477d6","access_level":"open_access","creator":"dernst","date_updated":"2024-09-11T07:54:12Z","content_type":"application/pdf","file_id":"18056","success":1,"file_size":8962687,"date_created":"2024-09-11T07:54:12Z","file_name":"2024_PloSGenetics_Elkrewi.pdf"}],"intvolume":"        20","external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"issue":"8"},{"OA_place":"publisher","ddc":["570"],"date_published":"2024-09-26T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/at:ista:18101","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies."}],"ec_funded":1,"file_date_updated":"2025-03-25T23:30:03Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T11:20:53Z","file":[{"relation":"source_file","checksum":"3b8b0bacfe61112f3852744f3170e468","access_level":"closed","creator":"dporley","date_updated":"2025-03-25T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18149","embargo_to":"open_access","file_size":14213128,"date_created":"2024-09-26T13:40:33Z","file_name":"PhD_thesis_DPorley_final_20240919.docx"},{"file_size":18583031,"date_created":"2024-09-26T13:41:39Z","embargo":"2025-03-25","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","file_id":"18150","creator":"dporley","content_type":"application/pdf","date_updated":"2025-03-25T23:30:03Z","checksum":"6c3a652a8eede874118e11d66a63652f","access_level":"open_access","relation":"main_file"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"day":"26","supervisor":[{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"year":"2024","citation":{"apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>","mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>."},"publisher":"Institute of Science and Technology Austria","researchdata_availability":"unclear","_id":"18101","status":"public","oa_version":"Published Version","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"oa":1,"title":"Structural characterization of spumavirus capsid assemblies","doi":"10.15479/at:ista:18101","type":"dissertation","author":[{"first_name":"Dario J","full_name":"Porley, Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","last_name":"Porley"}],"corr_author":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","grant_number":"25762"}],"degree_awarded":"PhD","date_created":"2024-09-20T10:21:03Z","supplementarymaterial":"unclear","article_processing_charge":"No","month":"09","page":"131","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-11-11T09:31:00Z","abstract":[{"lang":"eng","text":"As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects."}],"date_updated":"2026-10-26T23:30:58Z","OA_place":"publisher","ddc":["570"],"date_published":"2024-10-29T00:00:00Z","has_accepted_license":"1","OA_type":"hybrid","fulldoi":"https://doi.org/10.1073/pnas.2402340121","article_type":"original","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"das_tickbox":"1","day":"29","isi":1,"year":"2024","acknowledgement":"N.R.acknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew R. Robinson for fruitful discussions.","citation":{"short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>.","chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>.","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","apa":"Ruzickova, N., Hledik, M., &#38; Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>","ista":"Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2402340121."},"publisher":"National Academy of Sciences","_id":"18525","status":"public","researchdata_availability":"not applicable","oa_version":"Published Version","external_id":{"isi":["001349462600001"],"pmid":["39441639"]},"issue":"44","file":[{"file_size":25529709,"date_created":"2024-11-11T09:31:00Z","file_name":"2024_PNAS_Ruzickova.pdf","file_id":"18536","success":1,"creator":"dernst","date_updated":"2024-11-11T09:31:00Z","content_type":"application/pdf","relation":"main_file","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","access_level":"open_access"}],"intvolume":"       121","dataavailabilitystatement":"Previously published data were used for this work (34).\r\n34 F. W. Albert, J. S. Bloom, J. Siegel, L. Day, L. Kruglyak, Genetics of trans-regulatory variation in gene expression. eLife 7, e35471 (2018).","publication":"Proceedings of the National Academy of Sciences of the United States of America","author":[{"full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia"},{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"corr_author":"1","scopus_import":"1","article_number":"e2402340121","pmid":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa":1,"title":"Quantitative omnigenic model discovers interpretable genome-wide associations","doi":"10.1073/pnas.2402340121","type":"journal_article","month":"10","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"volume":121,"publication_status":"published","project":[{"name":"Collective behaviour of cells in pancreatic Islets of Langerhans","_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"20357","relation":"dissertation_contains"}]},"date_created":"2024-11-10T23:01:59Z","supplementarymaterial":"yes","APC_amount":"3062,93 EUR","article_processing_charge":"Yes"},{"abstract":[{"lang":"eng","text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices."}],"file_date_updated":"2025-03-13T23:30:04Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:12:07Z","alternative_title":["ISTA Thesis"],"OA_place":"publisher","fulldoi":"https://doi.org/10.15479/at:ista:17881","date_published":"2024-09-10T00:00:00Z","has_accepted_license":"1","ddc":["539"],"publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>."},"supervisor":[{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","first_name":"Andrew P"}],"day":"10","oa_version":"Published Version","researchdata_availability":"unclear","_id":"17881","status":"public","file":[{"creator":"smukhopa","date_updated":"2025-03-13T23:30:04Z","content_type":"application/pdf","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","access_level":"open_access","relation":"main_file","date_created":"2024-09-12T10:46:04Z","file_size":10297052,"embargo":"2025-03-13","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","file_id":"18059"},{"date_created":"2024-09-12T10:50:58Z","file_size":29178634,"file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","embargo_to":"open_access","file_id":"18060","creator":"smukhopa","date_updated":"2025-03-13T23:30:04Z","content_type":"application/zip","access_level":"closed","checksum":"e352667482701dd18a9a0e7418aef465","relation":"source_file"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","first_name":"Soham","orcid":"0000-0001-5263-5559"}],"corr_author":"1","doi_confirm":"1","type":"dissertation","doi":"10.15479/at:ista:17881","oa":1,"title":"Thermal effects in one dimensional Josephson chains","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"month":"09","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"page":"82","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14032"},{"status":"public","id":"18057","relation":"part_of_dissertation"}]},"project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"}],"degree_awarded":"PhD","article_processing_charge":"No","supplementarymaterial":"unclear","date_created":"2024-09-08T10:23:25Z"},{"month":"01","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"volume":16,"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"14705"},{"relation":"dissertation_contains","id":"19386","status":"public"},{"relation":"dissertation_contains","id":"20449","status":"public"},{"status":"deleted","relation":"dissertation_contains","id":"20444"}]},"article_processing_charge":"Yes","supplementarymaterial":"yes","date_created":"2024-02-18T23:01:02Z","author":[{"last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","first_name":"Vincent K"},{"first_name":"Ariana","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"publication":"Genome Biology and Evolution","scopus_import":"1","corr_author":"1","article_number":"evae006","type":"journal_article","doi":"10.1093/gbe/evae006","oa":1,"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","publication_identifier":{"eissn":["1759-6653"]},"pmid":1,"publisher":"Oxford University Press","citation":{"apa":"Bett, V. K., Macon, A., Vicoso, B., &#38; Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” <i>Genome Biology and Evolution</i>, vol. 16, no. 1. Oxford University Press, 2024.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. 2024;16(1). doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>."},"year":"2024","isi":1,"day":"20","das_tickbox":"1","oa_version":"Published Version","researchdata_availability":"yes","_id":"15009","status":"public","intvolume":"        16","file":[{"file_name":"2024_GBE_Bett.pdf","file_size":5213306,"date_created":"2024-02-26T09:54:59Z","file_id":"15029","success":1,"date_updated":"2024-02-26T09:54:59Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"106a40f10443b2e7ba66749844ebbdf1"}],"issue":"1","external_id":{"pmid":["38245839"],"isi":["001153952800001"]},"dataavailabilitystatement":"The assembly pipeline and the scripts used in the analysis can be accessed on the gitpage (https://github.com/Melkrewi/Artemia_franciscana_genome/). The raw data are available on the National Center for Biotechnology Information (NCBI) short-read archive (BioProject number PRJNA1017357). The final assembly, the annotation, and the supplementary data sets are available on (https://doi.org/10.15479/AT:ISTA:14705). All genomic and transcriptomic samples used for this study and the steps of the analysis they were used in are described in supplementary table S3, Supplementary Material online.","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"file_date_updated":"2024-02-26T09:54:59Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-26T23:30:57Z","DOAJ_listed":"1","OA_place":"publisher","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1093/gbe/evae006","article_type":"original","date_published":"2024-01-20T00:00:00Z","OA_type":"gold","has_accepted_license":"1","ddc":["570"]},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"external_id":{"arxiv":["2408.07829"]},"researchdata_availability":"no","_id":"18057","status":"public","oa_version":"Preprint","day":"14","arxiv":1,"das_tickbox":"0","year":"2024","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","citation":{"ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. .","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>."},"date_published":"2024-08-14T00:00:00Z","fulldoi":"https://doi.org/10.48550/arXiv.2408.07829","OA_place":"repository","date_updated":"2026-10-26T23:30:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations."}],"ec_funded":1,"date_created":"2024-09-11T09:25:22Z","supplementarymaterial":"no","article_processing_charge":"No","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"related_material":{"record":[{"status":"public","id":"20324","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"17881"}]},"department":[{"_id":"AnHi"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"publication_status":"draft","month":"08","title":"Dual relaxation oscillations in a Josephson junction array","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.07829","open_access":"1"}],"doi":"10.48550/arXiv.2408.07829","type":"preprint","article_number":"2408.07829","corr_author":"1","publication":"arXiv","author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","first_name":"Soham","orcid":"0000-0001-5263-5559"},{"full_name":"Lancheros Naranjo, Diego A","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","last_name":"Lancheros Naranjo","first_name":"Diego A"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","full_name":"Senior, Jorden L","first_name":"Jorden L","orcid":"0000-0002-0672-9295"},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363"}]},{"oa_version":"Published Version","researchdata_availability":"unclear","_id":"17119","status":"public","citation":{"chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024."},"year":"2024","publisher":"Institute of Science and Technology Austria","day":"20","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"file":[{"file_name":"thesis.zip","date_created":"2024-06-07T16:09:17Z","file_size":180557931,"embargo_to":"open_access","file_id":"17121","content_type":"application/zip","date_updated":"2025-01-10T23:30:10Z","creator":"rkelemen","checksum":"fab59146e3b3dc2e5d214576984a2a63","access_level":"closed","relation":"source_file"},{"creator":"rkelemen","date_updated":"2025-01-10T23:30:10Z","content_type":"application/pdf","access_level":"open_access","checksum":"91cc4c25a792239e8a7688e8aec7c62a","relation":"main_file","file_size":19405484,"embargo":"2025-01-10","date_created":"2024-07-10T08:00:20Z","file_name":"thesis_to_archive.pdf","file_id":"17213"}],"date_updated":"2026-10-02T11:14:33Z","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research.","lang":"eng"}],"file_date_updated":"2025-01-10T23:30:10Z","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.15479/at:ista:17119","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"ddc":["576"],"date_published":"2024-06-20T00:00:00Z","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","page":"105","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"06","supplementarymaterial":"unclear","date_created":"2024-06-07T16:14:13Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"542","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10767"}]},"degree_awarded":"PhD","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"corr_author":"1","author":[{"first_name":"Réka K","orcid":"0000-0002-8489-9281","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","full_name":"Kelemen, Réka K"}],"doi":"10.15479/at:ista:17119","type":"dissertation","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","oa":1,"doi_confirm":"1"},{"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"}],"corr_author":"1","doi_confirm":"1","type":"dissertation","doi":"10.15479/at:ista:18531","oa":1,"title":"Early stages of sex chromosome evolution","publication_identifier":{"issn":["2663-337X"]},"month":"11","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"language":[{"iso":"eng"}],"page":"181","related_material":{"record":[{"id":"12521","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18549","status":"public"}]},"degree_awarded":"PhD","article_processing_charge":"No","supplementarymaterial":"unclear","date_created":"2024-11-11T08:40:45Z","file_date_updated":"2025-05-11T22:30:04Z","abstract":[{"text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. ","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_embargo":"6","date_updated":"2026-10-02T11:14:08Z","alternative_title":["ISTA Thesis"],"OA_place":"publisher","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"keyword":["Sex chromosomes","evolution","selection","sheltering"],"fulldoi":"https://doi.org/10.15479/at:ista:18531","date_published":"2024-11-11T00:00:00Z","has_accepted_license":"1","ddc":["576"],"publisher":"Institute of Science and Technology Austria","citation":{"ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>."},"year":"2024","supervisor":[{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"day":"11","oa_version":"Published Version","_id":"18531","status":"public","researchdata_availability":"unclear","file":[{"file_size":26870629,"date_created":"2024-11-13T12:15:28Z","file_name":"AMrnjavac_thesis_library.docx","title":"Early stages of sex chromosome evolution","file_id":"18551","embargo_to":"open_access","creator":"amrnjava","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-05-11T22:30:04Z","relation":"source_file","checksum":"3e48b163c22114ef5d5371f758668289","access_level":"closed"},{"embargo":"2025-05-11","date_created":"2024-11-13T12:15:54Z","file_size":4228766,"title":"Early stages of sex chromosome evolution","file_name":"AMrnjavac_thesis_library.pdf","file_id":"18552","creator":"amrnjava","content_type":"application/pdf","date_updated":"2025-05-11T22:30:04Z","relation":"main_file","access_level":"open_access","checksum":"3ead60c1b678e7dcf018043aef3b5db2"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}]},{"degree_awarded":"PhD","related_material":{"record":[{"id":"18670","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","supplementarymaterial":"unclear","date_created":"2024-12-16T10:53:39Z","month":"12","license":"https://creativecommons.org/licenses/by-sa/4.0/","page":"57","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"language":[{"iso":"eng"}],"doi_confirm":"1","title":"Archaeal membranes: In silico modelling and design","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"type":"dissertation","doi":"10.15479/at:ista:18661","author":[{"last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel"}],"corr_author":"1","file":[{"embargo_to":"open_access","file_id":"18671","file_name":"2024_msfa_thesis.zip","date_created":"2024-12-18T12:27:01Z","file_size":19161387,"access_level":"closed","checksum":"eca06497a29078558395455c890a32d9","relation":"source_file","content_type":"application/zip","date_updated":"2025-06-18T22:30:03Z","creator":"mamaral"},{"file_id":"18672","embargo":"2025-06-18","date_created":"2024-12-18T12:26:30Z","file_size":16530084,"file_name":"2024_msfa_thesis.pdf","relation":"main_file","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","access_level":"open_access","creator":"mamaral","date_updated":"2025-06-18T22:30:03Z","content_type":"application/pdf"}],"supervisor":[{"first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"day":"17","publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes: In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes: In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","short":"M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","ama":"Santana de Freitas Amaral M. Archaeal membranes: In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.","apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes: In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>"},"_id":"18661","status":"public","researchdata_availability":"unclear","oa_version":"Published Version","OA_place":"publisher","has_accepted_license":"1","date_published":"2024-12-17T00:00:00Z","ddc":["572","530"],"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"fulldoi":"https://doi.org/10.15479/at:ista:18661","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n"}],"file_date_updated":"2025-06-18T22:30:03Z","date_updated":"2026-10-02T11:12:49Z","alternative_title":["ISTA Thesis"]},{"main_file_link":[{"url":"https://doi.org/10.1101/2024.07.02.601697","open_access":"1"}],"doi":"10.1101/2024.07.02.601697","type":"preprint","oa":1,"title":"Evidence of a Slower-Z effect in Schistosoma japonicum","author":[{"first_name":"Andrea","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication":"bioRxiv","corr_author":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"19370"},{"status":"public","relation":"dissertation_contains","id":"18531"}]},"date_created":"2024-11-13T09:12:08Z","supplementarymaterial":"yes","article_processing_charge":"No","month":"07","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"publication_status":"draft","OA_place":"repository","fulldoi":"https://doi.org/10.1101/2024.07.02.601697","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2024-07-04T00:00:00Z","abstract":[{"text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-26T23:30:59Z","external_id":{"biorxivid":["10.1101/2024.07.02.601697"]},"biorxivid":1,"year":"2024","citation":{"short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>.","apa":"Mrnjavac, A., &#38; Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, <a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>"},"das_tickbox":"0","day":"04","oa_version":"Preprint","status":"public","_id":"18549","researchdata_availability":"no"},{"date_created":"2024-12-18T10:07:45Z","article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","id":"18661","status":"public"}]},"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"publication_status":"draft","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.10.18.619072"}],"doi":"10.1101/2024.10.18.619072","type":"preprint","title":"Stability vs flexibility: Reshaping archaeal membranes in silico","oa":1,"corr_author":"1","author":[{"last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel"},{"first_name":"Felix F","orcid":"0000-0001-8501-6017","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"last_name":"Baum","full_name":"Baum, Buzz","first_name":"Buzz"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"}],"publication":"bioRxiv","oa_version":"Preprint","status":"public","_id":"18670","year":"2024","citation":{"ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.).","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>."},"acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","day":"27","fulldoi":"https://doi.org/10.1101/2024.10.18.619072","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2024-11-27T00:00:00Z","OA_place":"repository","date_updated":"2026-10-26T23:30:59Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"OA_place":"repository","fulldoi":"https://doi.org/10.15479/at:ista:17465","ddc":["519"],"date_published":"2024-08-29T00:00:00Z","has_accepted_license":"1","file_date_updated":"2024-10-05T22:30:05Z","abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:20:32Z","alternative_title":["ISTA Thesis"],"file":[{"relation":"main_file","access_level":"open_access","checksum":"da6dd3166078934577f6af93d27000e2","date_updated":"2024-10-05T22:30:05Z","content_type":"application/pdf","creator":"ashevche","file_id":"17482","file_name":"thesis_a2b.pdf","file_size":4468610,"date_created":"2024-09-02T09:23:32Z","embargo":"2024-10-04"},{"checksum":"76a39ef252239560923cdda4ce0a31a4","access_level":"closed","relation":"source_file","date_updated":"2024-10-05T22:30:05Z","content_type":"application/zip","creator":"ashevche","embargo_to":"open_access","file_id":"17483","file_name":"Thesis Alex - ISTA.zip","date_created":"2024-09-02T09:23:46Z","file_size":15930999}],"acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2024","citation":{"mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>"},"publisher":"Institute of Science and Technology Austria","day":"29","das_tickbox":"0","supervisor":[{"full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"oa_version":"Published Version","status":"public","_id":"17465","researchdata_availability":"no","doi_confirm":"1","doi":"10.15479/at:ista:17465","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"High-dimensional limits in artificial neural networks","oa":1,"author":[{"first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"}],"corr_author":"1","related_material":{"record":[{"id":"11420","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"14459","status":"public"},{"relation":"part_of_dissertation","id":"9198","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17469"}]},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"degree_awarded":"PhD","date_created":"2024-08-28T15:14:25Z","supplementarymaterial":"no","article_processing_charge":"No","month":"08","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"publication_status":"published","page":"232"},{"date_published":"2024-10-29T00:00:00Z","has_accepted_license":"1","ddc":["572"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/at:ista:18477","OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T11:14:50Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-10-29T23:30:02Z","abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"file":[{"date_created":"2024-10-29T11:56:36Z","file_size":23136626,"file_name":"20241029_PhD_thesis_BKaczmarek.docx","embargo_to":"open_access","file_id":"18485","creator":"bkaczmar","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-10-29T23:30:02Z","checksum":"2053294ea4d770c495e4cc501e2a218b","access_level":"closed","relation":"source_file"},{"relation":"main_file","access_level":"open_access","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","creator":"bkaczmar","content_type":"application/pdf","date_updated":"2025-10-29T23:30:02Z","file_id":"18486","file_size":11707360,"date_created":"2024-10-29T11:56:44Z","embargo":"2025-10-29","file_name":"20241029_PhD_thesis_BKaczmarek.pdf"}],"status":"public","_id":"18477","researchdata_availability":"unclear","oa_version":"Published Version","supervisor":[{"orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"day":"29","publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>"},"title":"Biochemical and structural insights into ADAR1 RNA editing","oa":1,"publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/at:ista:18477","doi_confirm":"1","corr_author":"1","author":[{"id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M","first_name":"Beata M"}],"article_processing_charge":"No","supplementarymaterial":"unclear","date_created":"2024-10-27T07:35:13Z","degree_awarded":"PhD","page":"124","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"language":[{"iso":"eng"}],"month":"10"},{"author":[{"first_name":"Lars","last_name":"Bollmann","id":"47AD3038-F248-11E8-B48F-1D18A9856A87","full_name":"Bollmann, Lars"}],"corr_author":"1","doi_confirm":"1","title":"Stability and change in the memory system during rest","oa":1,"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/at:ista:17346","month":"07","page":"103","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"degree_awarded":"PhD","article_processing_charge":"No","supplementarymaterial":"no","date_created":"2024-07-29T15:08:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-01-31T23:30:03Z","abstract":[{"text":"Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas.","lang":"eng"}],"date_updated":"2026-10-02T11:26:02Z","alternative_title":["ISTA Thesis"],"OA_place":"publisher","has_accepted_license":"1","date_published":"2024-07-31T00:00:00Z","ddc":["573"],"keyword":["Memory","Hippocampus","Consolidation"],"fulldoi":"https://doi.org/10.15479/at:ista:17346","supervisor":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"das_tickbox":"0","day":"31","publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"short":"L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024.","mla":"Bollmann, Lars. <i>Stability and Change in the Memory System during Rest</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>.","chicago":"Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>.","ieee":"L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024.","apa":"Bollmann, L. (2024). <i>Stability and change in the memory system during rest</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>","ista":"Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria.","ama":"Bollmann L. Stability and change in the memory system during rest. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>"},"_id":"17346","researchdata_availability":"no","status":"public","oa_version":"Published Version","file":[{"file_name":"PhD_Thesis_Lars_Bollmann.pdf","embargo":"2025-01-31","date_created":"2024-07-31T18:37:19Z","file_size":12920169,"file_id":"17359","date_updated":"2025-01-31T23:30:03Z","content_type":"application/pdf","creator":"lbollman","relation":"main_file","access_level":"open_access","checksum":"12c76297cc27449da80c60d79127770d"},{"file_name":"Latex_source.zip","file_size":27568807,"date_created":"2024-07-31T18:38:39Z","file_id":"17360","embargo_to":"open_access","date_updated":"2025-01-31T23:30:03Z","content_type":"application/zip","creator":"lbollman","relation":"source_file","checksum":"19a0265079dec8038830ad6e35c5106e","access_level":"closed"}]},{"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"degree_awarded":"PhD","date_created":"2024-01-16T14:25:21Z","supplementarymaterial":"no","article_processing_charge":"No","month":"01","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"89","doi_confirm":"1","doi":"10.15479/at:ista:14821","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"oa":1,"title":"Adaptive hierarchical representations in the hippocampus","author":[{"id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","last_name":"Chiossi","full_name":"Chiossi, Heloisa","orcid":"0009-0004-2973-278X","first_name":"Heloisa"}],"corr_author":"1","file":[{"access_level":"closed","checksum":"d3fa3de1abd5af5204c13e9d55375615","relation":"source_file","creator":"hchiossi","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-01-19T23:30:04Z","embargo_to":"open_access","file_id":"14838","file_size":8656268,"date_created":"2024-01-19T11:04:05Z","file_name":"PhD_Thesis_190124.docx"},{"file_name":"PhD_Thesis_190124.pdf","embargo":"2025-01-19","date_created":"2024-01-19T11:03:59Z","file_size":6567275,"file_id":"14839","date_updated":"2025-01-19T23:30:04Z","content_type":"application/pdf","creator":"hchiossi","access_level":"open_access","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","relation":"main_file"}],"year":"2024","citation":{"chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024."},"publisher":"Institute of Science and Technology Austria","das_tickbox":"0","day":"19","supervisor":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"oa_version":"Published Version","status":"public","_id":"14821","researchdata_availability":"no","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/at:ista:14821","ddc":["570"],"has_accepted_license":"1","date_published":"2024-01-19T00:00:00Z","ec_funded":1,"file_date_updated":"2025-01-19T23:30:04Z","abstract":[{"text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:26:27Z","alternative_title":["ISTA Thesis"]},{"doi_confirm":"1","type":"dissertation","doi":"10.15479/at:ista:17368","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","oa":1,"publication_identifier":{"issn":["2791-4585"]},"author":[{"full_name":"Villanueva Marijuan, Ariadna","id":"e0ae4864-133f-11ed-8f02-adaa8dd27540","last_name":"Villanueva Marijuan","first_name":"Ariadna"}],"corr_author":"1","degree_awarded":"MS","article_processing_charge":"No","date_created":"2024-08-02T10:52:40Z","supplementarymaterial":"no","month":"08","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"page":"60","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"keyword":["Epigenetics","Multi-omics","Bayesian regression"],"fulldoi":"https://doi.org/10.15479/at:ista:17368","date_published":"2024-08-13T00:00:00Z","has_accepted_license":"1","ddc":["610"],"file_date_updated":"2025-02-14T23:30:03Z","abstract":[{"text":"Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","alternative_title":["ISTA Master's Thesis"],"date_updated":"2026-10-02T11:35:19Z","file":[{"file_id":"17433","file_name":"Masters_thesis_AriadnaVillanueva.pdf","embargo":"2025-02-14","date_created":"2024-08-14T11:51:24Z","file_size":13052436,"relation":"main_file","checksum":"0c2daa174609f0c00919dccc5701d375","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-02-14T23:30:03Z","creator":"avillanu"},{"file_size":45642547,"date_created":"2024-08-14T11:51:57Z","file_name":"Masters thesis-AriadnaVillanueva.zip","embargo_to":"open_access","file_id":"17434","creator":"avillanu","date_updated":"2025-02-14T23:30:03Z","content_type":"application/zip","access_level":"closed","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1","relation":"source_file"}],"publisher":"Institute of Science and Technology Austria","year":"2024","citation":{"short":"A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024.","mla":"Villanueva Marijuan, Ariadna. <i>Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>.","chicago":"Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>.","apa":"Villanueva Marijuan, A. (2024). <i>Bayesian linear regression for analyzing general omics data with time-to-event phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>","ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>","ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria."},"supervisor":[{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"}],"das_tickbox":"0","day":"13","oa_version":"Published Version","status":"public","_id":"17368","researchdata_availability":"no"},{"ddc":["000"],"date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.","lang":"eng"}],"date_updated":"2026-10-26T23:31:00Z","alternative_title":["PMLR"],"external_id":{"arxiv":["2402.05013"]},"intvolume":"       235","das_tickbox":"0","day":"01","arxiv":1,"citation":{"ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015.","apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015.","ista":"Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015.","mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024."},"acknowledgement":"Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","year":"2024","publisher":"ML Research Press","_id":"17469","researchdata_availability":"no","status":"public","oa_version":"Published Version","title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","oa":1,"main_file_link":[{"url":"https://proceedings.mlr.press/v235/kogler24a.html","open_access":"1"}],"type":"conference","publication":"Proceedings of the 41st International Conference on Machine Learning","author":[{"full_name":"Kögler, Kevin","last_name":"Kögler","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","first_name":"Kevin"},{"first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"corr_author":"1","conference":{"location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21"},"scopus_import":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"23072","status":"public"},{"id":"17465","relation":"dissertation_contains","status":"public"}]},"quality_controlled":"1","date_created":"2024-08-29T11:47:57Z","supplementarymaterial":"no","article_processing_charge":"No","month":"07","page":"24964-25015","department":[{"_id":"DaAl"},{"_id":"MaMo"}],"language":[{"iso":"eng"}],"volume":235,"publication_status":"published"},{"PlanS_conform":"1","has_accepted_license":"1","date_published":"2024-03-06T00:00:00Z","OA_type":"hybrid","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1016/j.neuron.2023.12.002","article_type":"original","OA_place":"publisher","date_updated":"2026-10-26T23:31:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-04-23T14:02:08Z","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"issue":"5","external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"intvolume":"       112","file":[{"content_type":"application/pdf","date_updated":"2025-04-23T14:02:08Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"30098b4f0209556ddfb3540a23d07ca5","file_name":"2024_Neuron_Chen.pdf","date_created":"2025-04-23T14:02:08Z","file_size":8192355,"file_id":"19614","success":1}],"status":"public","_id":"14843","oa_version":"Published Version","isi":1,"day":"06","publisher":"Elsevier","citation":{"short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>"},"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","year":"2024","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","oa":1,"publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"pmid":1,"type":"journal_article","doi":"10.1016/j.neuron.2023.12.002","corr_author":"1","scopus_import":"1","publication":"Neuron","author":[{"full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing"},{"orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann"},{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chong"},{"last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Arai, Itaru","first_name":"Itaru"},{"orcid":"0000-0003-2344-1039","first_name":"Olena","full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2024-01-21T23:00:56Z","project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"},{"grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"related_material":{"record":[{"id":"15101","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}]},"quality_controlled":"1","page":"755-771.e9","publication_status":"published","volume":112,"department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"language":[{"iso":"eng"}],"month":"03"},{"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publication_status":"published","page":"164","month":"09","supplementarymaterial":"unclear","date_created":"2024-09-23T17:25:43Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18144"}]},"project":[{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"},{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"degree_awarded":"PhD","corr_author":"1","author":[{"first_name":"Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","full_name":"Janik, Marian"}],"doi":"10.15479/at:ista:18129","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors","oa":1,"doi_confirm":"1","oa_version":"Published Version","_id":"18129","status":"public","researchdata_availability":"unclear","citation":{"ama":"Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>","ista":"Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria.","apa":"Janik, M. (2024). <i>Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>","ieee":"M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024.","chicago":"Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>.","mla":"Janik, Marian. <i>Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>.","short":"M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024."},"year":"2024","publisher":"Institute of Science and Technology Austria","day":"24","supervisor":[{"orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"file":[{"embargo_to":"open_access","file_id":"18130","date_created":"2024-09-23T17:15:09Z","file_size":156207943,"file_name":"janik_thesis.zip","checksum":"dc15958f6400b5bdaa28bf58fc7a4056","access_level":"closed","relation":"source_file","creator":"mjanik","content_type":"application/x-zip-compressed","date_updated":"2025-05-23T22:30:09Z"},{"file_name":"janik_thesis_pdfa.pdf","embargo":"2025-05-23","file_size":96195684,"date_created":"2024-09-23T17:15:30Z","file_id":"18131","date_updated":"2025-05-23T22:30:09Z","content_type":"application/pdf","creator":"mjanik","relation":"main_file","checksum":"74737aee285dc1f491643327350efe9c","access_level":"open_access"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T11:22:53Z","file_date_updated":"2025-05-23T22:30:09Z","abstract":[{"text":"State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate\r\nfor qubits due to their long coherence, tunability, control, and readout. However, their natural\r\ncoupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.\r\nLong-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a\r\ncoherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of\r\nhigh-impedance resonators to compensate for this has gained significant attention in the past\r\ndecade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not\r\nexceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The\r\nlarge kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude\r\nenhancement. However, fully exploiting the potential of disordered or granular superconductors\r\nis challenging as their impedances close to the superconductor-to-insulator transition are\r\ndifficult to control reproducibly. We report on the realization of a wireless ohmmeter which\r\nallows in situ resistance measurements during film deposition and, therefore, indirect control\r\nof the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators\r\nwith characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due\r\nto the large sheet kinetic inductance of up to 3 nH □−1\r\n. By integrating an 8 kW resonator\r\nwith a germanium double QD, we demonstrate a strong charge-photon coupling with the\r\nhighest rate reported, 566 MHz. The demonstrated method and grAl properties make these\r\nresonators suitable for boosting the spin-photon coupling strength, a crucial requirement for\r\nfast, high-fidelity, long-distance two-qubit gates.\r\n","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.15479/at:ista:18129","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["539"],"date_published":"2024-09-24T00:00:00Z","has_accepted_license":"1","OA_place":"publisher"},{"type":"dissertation","doi":"10.15479/at:ista:15101","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","oa":1,"publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","corr_author":"1","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"}],"article_processing_charge":"No","supplementarymaterial":"no","date_created":"2024-03-11T10:09:54Z","related_material":{"record":[{"status":"public","id":"14843","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"language":[{"iso":"eng"}],"page":"84","month":"03","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.15479/at:ista:15101","has_accepted_license":"1","date_published":"2024-03-11T00:00:00Z","ddc":["570"],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-10-02T11:42:02Z","ec_funded":1,"file_date_updated":"2024-04-02T22:30:03Z","abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"EM-Fac"}],"file":[{"file_name":"Thesis_Jingjing CHEN.docx","date_created":"2024-03-11T14:10:58Z","file_size":11271363,"file_id":"15104","embargo_to":"open_access","date_updated":"2024-04-02T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jchen","relation":"source_file","access_level":"closed","checksum":"db4947474ffa271e66c254b6fe876a55"},{"relation":"main_file","checksum":"a5eeae8b5702cd540f5d03469bc33dde","access_level":"open_access","creator":"jchen","date_updated":"2024-04-02T22:30:03Z","content_type":"application/pdf","file_id":"15105","date_created":"2024-03-11T14:11:06Z","file_size":16627311,"embargo":"2024-04-01","file_name":"Thesis_Jingjing CHEN_merged.pdf"}],"oa_version":"Published Version","_id":"15101","researchdata_availability":"no","status":"public","publisher":"Institute of Science and Technology Austria","citation":{"mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>"},"year":"2024","supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"day":"11","das_tickbox":"0"}]