--- APC_amount: 3145,39 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17890' abstract: - lang: eng 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. acknowledged_ssus: - _id: ScienComp 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. " article_number: e1011376 article_processing_charge: Yes article_type: original author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 2024;20(8). doi:10.1371/journal.pgen.1011376 apa: Elkrewi, M. N., & Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1011376 chicago: Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” PLoS Genetics. Public Library of Science, 2024. https://doi.org/10.1371/journal.pgen.1011376. ieee: M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” PLoS Genetics, vol. 20, no. 8. Public Library of Science, 2024. 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. mla: Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” PLoS Genetics, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:10.1371/journal.pgen.1011376. short: M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024). corr_author: '1' das_tickbox: '1' 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' date_created: 2024-09-08T22:01:11Z date_published: 2024-08-30T00:00:00Z date_updated: 2026-10-26T23:30:56Z day: '30' ddc: - '570' department: - _id: BeVi doi: 10.1371/journal.pgen.1011376 external_id: isi: - '001304090200001' pmid: - '39213449' file: - access_level: open_access checksum: f5d96b9af57126fc1063e951440477d6 content_type: application/pdf creator: dernst date_created: 2024-09-11T07:54:12Z date_updated: 2024-09-11T07:54:12Z file_id: '18056' file_name: 2024_PloSGenetics_Elkrewi.pdf file_size: 8962687 relation: main_file success: 1 file_date_updated: 2024-09-11T07:54:12Z fulldoi: https://doi.org/10.1371/journal.pgen.1011376 has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/Melkrewi/Artemia-snRNAseq-Project record: - id: '17362' relation: research_data status: public - id: '19386' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- OA_place: publisher _id: '18101' 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." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dario J full_name: Porley, Dario J id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87 last_name: Porley citation: ama: Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:10.15479/at:ista:18101 apa: Porley Esteves, D. (2024). Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18101 chicago: Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18101. 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. mla: Porley Esteves, Darío. Structural Characterization of Spumavirus Capsid Assemblies. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18101. short: D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-20T10:21:03Z date_published: 2024-09-26T00:00:00Z date_updated: 2026-10-02T11:20:53Z day: '26' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:18101 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 3b8b0bacfe61112f3852744f3170e468 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dporley date_created: 2024-09-26T13:40:33Z date_updated: 2025-03-25T23:30:03Z embargo_to: open_access file_id: '18149' file_name: PhD_thesis_DPorley_final_20240919.docx file_size: 14213128 relation: source_file - access_level: open_access checksum: 6c3a652a8eede874118e11d66a63652f content_type: application/pdf creator: dporley date_created: 2024-09-26T13:41:39Z date_updated: 2025-03-25T23:30:03Z embargo: 2025-03-25 file_id: '18150' file_name: PhD_thesis_DPorley_final_20240926_pdfa1.pdf file_size: 18583031 relation: main_file file_date_updated: 2025-03-25T23:30:03Z fulldoi: https://doi.org/10.15479/at:ista:18101 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '131' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A grant_number: '25762' name: Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms publication_identifier: isbn: - 978-3-99078-041-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: unclear status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 supplementarymaterial: unclear title: Structural characterization of spumavirus capsid assemblies type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- APC_amount: 3062,93 EUR OA_place: publisher OA_type: hybrid _id: '18525' 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. 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. article_number: e2402340121 article_processing_charge: Yes article_type: original author: - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2402340121 apa: 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. National Academy of Sciences. https://doi.org/10.1073/pnas.2402340121 chicago: Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2402340121. ieee: N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024. 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. mla: Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:10.1073/pnas.2402340121. short: N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). corr_author: '1' das_tickbox: '1' 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)." date_created: 2024-11-10T23:01:59Z date_published: 2024-10-29T00:00:00Z date_updated: 2026-10-26T23:30:58Z day: '29' ddc: - '570' department: - _id: GaTk - _id: NiBa doi: 10.1073/pnas.2402340121 external_id: isi: - '001349462600001' pmid: - '39441639' file: - access_level: open_access checksum: d930e2ccf9ec900c7d7509a78cfb3564 content_type: application/pdf creator: dernst date_created: 2024-11-11T09:31:00Z date_updated: 2024-11-11T09:31:00Z file_id: '18536' file_name: 2024_PNAS_Ruzickova.pdf file_size: 25529709 relation: main_file success: 1 file_date_updated: 2024-11-11T09:31:00Z fulldoi: https://doi.org/10.1073/pnas.2402340121 has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '44' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e name: Collective behaviour of cells in pancreatic Islets of Langerhans - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: record: - id: '20357' relation: dissertation_contains status: public researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: yes title: Quantitative omnigenic model discovers interpretable genome-wide associations tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- OA_place: publisher _id: '17881' 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." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 citation: ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881 apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881 chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881. ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024. ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881. short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-08T10:23:25Z date_published: 2024-09-10T00:00:00Z date_updated: 2026-10-02T11:12:07Z day: '10' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/at:ista:17881 doi_confirm: '1' file: - access_level: open_access checksum: ed7763c3bbd59e1d7e1b664de3a26f3c content_type: application/pdf creator: smukhopa date_created: 2024-09-12T10:46:04Z date_updated: 2025-03-13T23:30:04Z embargo: 2025-03-13 file_id: '18059' file_name: PhD_Thesis_Soham_Mukhopadhyay.pdf file_size: 10297052 relation: main_file - access_level: closed checksum: e352667482701dd18a9a0e7418aef465 content_type: application/zip creator: smukhopa date_created: 2024-09-12T10:50:58Z date_updated: 2025-03-13T23:30:04Z embargo_to: open_access file_id: '18060' file_name: PhD_Thesis_Soham_Mukhopadhyay_source.zip file_size: 29178634 relation: source_file file_date_updated: 2025-03-13T23:30:04Z fulldoi: https://doi.org/10.15479/at:ista:17881 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '82' project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition publication_identifier: isbn: - 978-3-99078-043-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14032' relation: part_of_dissertation status: public - id: '18057' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 supplementarymaterial: unclear title: Thermal effects in one dimensional Josephson chains type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '15009' 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. article_number: evae006 article_processing_charge: Yes article_type: original author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006 apa: Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006 chicago: Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006. ieee: V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024. 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.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006. short: V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024). corr_author: '1' das_tickbox: '1' 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. date_created: 2024-02-18T23:01:02Z date_published: 2024-01-20T00:00:00Z date_updated: 2026-10-26T23:30:57Z day: '20' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evae006 external_id: isi: - '001153952800001' pmid: - '38245839' file: - access_level: open_access checksum: 106a40f10443b2e7ba66749844ebbdf1 content_type: application/pdf creator: dernst date_created: 2024-02-26T09:54:59Z date_updated: 2024-02-26T09:54:59Z file_id: '15029' file_name: 2024_GBE_Bett.pdf file_size: 5213306 relation: main_file success: 1 file_date_updated: 2024-02-26T09:54:59Z fulldoi: https://doi.org/10.1093/gbe/evae006 has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology and Evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '14705' relation: research_data status: public - id: '19386' relation: dissertation_contains status: public - id: '20449' relation: dissertation_contains status: public - id: '20444' relation: dissertation_contains status: deleted researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 16 year: '2024' ... --- OA_place: repository _id: '18057' 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." acknowledged_ssus: - _id: NanoFab - _id: M-Shop 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" article_number: '2408.07829' article_processing_charge: No arxiv: 1 author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 - first_name: Diego A full_name: Lancheros Naranjo, Diego A id: 6c55e976-15b2-11ec-abd3-d790e8937fde last_name: Lancheros Naranjo - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829 apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv. https://doi.org/10.48550/arXiv.2408.07829 chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829. ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” arXiv. . ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829. mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829. short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-09-11T09:25:22Z date_published: 2024-08-14T00:00:00Z date_updated: 2026-10-26T23:30:57Z day: '14' department: - _id: AnHi - _id: GradSch doi: 10.48550/arXiv.2408.07829 ec_funded: 1 external_id: arxiv: - '2408.07829' fulldoi: https://doi.org/10.48550/arXiv.2408.07829 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.07829 month: '08' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication: arXiv publication_status: draft related_material: record: - id: '20324' relation: later_version status: public - id: '17881' relation: dissertation_contains status: public researchdata_availability: no status: public supplementarymaterial: no title: Dual relaxation oscillations in a Josephson junction array type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '17119' abstract: - lang: eng 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 citation: ama: Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:10.15479/at:ista:17119 apa: Kelemen, R. K. (2024). Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17119 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. https://doi.org/10.15479/at:ista:17119. ieee: R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024. ista: Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria. mla: Kelemen, Réka K. Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17119. short: R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-06-07T16:14:13Z date_published: 2024-06-20T00:00:00Z date_updated: 2026-10-02T11:14:33Z day: '20' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:17119 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: fab59146e3b3dc2e5d214576984a2a63 content_type: application/zip creator: rkelemen date_created: 2024-06-07T16:09:17Z date_updated: 2025-01-10T23:30:10Z embargo_to: open_access file_id: '17121' file_name: thesis.zip file_size: 180557931 relation: source_file - access_level: open_access checksum: 91cc4c25a792239e8a7688e8aec7c62a content_type: application/pdf creator: rkelemen date_created: 2024-07-10T08:00:20Z date_updated: 2025-01-10T23:30:10Z embargo: 2025-01-10 file_id: '17213' file_name: thesis_to_archive.pdf file_size: 19405484 relation: main_file file_date_updated: 2025-01-10T23:30:10Z fulldoi: https://doi.org/10.15479/at:ista:17119 has_accepted_license: '1' keyword: - meiotic driver - neofunctionalization - single nucleus sequencing language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '06' oa: 1 oa_version: Published Version page: '105' project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: isbn: - 978-3-99078-039-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '542' relation: part_of_dissertation status: public - id: '10767' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 supplementarymaterial: unclear title: Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_embargo: '6' OA_place: publisher _id: '18531' abstract: - lang: eng 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. " acknowledged_ssus: - _id: ScienComp - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac citation: ama: Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:10.15479/at:ista:18531 apa: Mrnjavac, A. (2024). Early stages of sex chromosome evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18531 chicago: Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18531. ieee: A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024. ista: Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria. mla: Mrnjavac, Andrea. Early Stages of Sex Chromosome Evolution. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18531. short: A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-11T08:40:45Z date_published: 2024-11-11T00:00:00Z date_updated: 2026-10-02T11:14:08Z day: '11' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:18531 doi_confirm: '1' file: - access_level: closed checksum: 3e48b163c22114ef5d5371f758668289 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amrnjava date_created: 2024-11-13T12:15:28Z date_updated: 2025-05-11T22:30:04Z embargo_to: open_access file_id: '18551' file_name: AMrnjavac_thesis_library.docx file_size: 26870629 relation: source_file title: Early stages of sex chromosome evolution - access_level: open_access checksum: 3ead60c1b678e7dcf018043aef3b5db2 content_type: application/pdf creator: amrnjava date_created: 2024-11-13T12:15:54Z date_updated: 2025-05-11T22:30:04Z embargo: 2025-05-11 file_id: '18552' file_name: AMrnjavac_thesis_library.pdf file_size: 4228766 relation: main_file title: Early stages of sex chromosome evolution file_date_updated: 2025-05-11T22:30:04Z fulldoi: https://doi.org/10.15479/at:ista:18531 has_accepted_license: '1' keyword: - Sex chromosomes - evolution - selection - sheltering language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '181' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12521' relation: part_of_dissertation status: public - id: '18549' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 supplementarymaterial: unclear title: Early stages of sex chromosome evolution tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '18661' 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral citation: ama: 'Santana de Freitas Amaral M. Archaeal membranes: In silico modelling and design. 2024. doi:10.15479/at:ista:18661' apa: 'Santana de Freitas Amaral, M. (2024). Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661' chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal Membranes: In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.' ieee: 'M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.' ista: 'Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.' mla: 'Santana de Freitas Amaral, Miguel. Archaeal Membranes: In Silico Modelling and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.' short: 'M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-12-16T10:53:39Z date_published: 2024-12-17T00:00:00Z date_updated: 2026-10-02T11:12:49Z day: '17' ddc: - '572' - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnSa doi: 10.15479/at:ista:18661 doi_confirm: '1' file: - access_level: closed checksum: eca06497a29078558395455c890a32d9 content_type: application/zip creator: mamaral date_created: 2024-12-18T12:27:01Z date_updated: 2025-06-18T22:30:03Z embargo_to: open_access file_id: '18671' file_name: 2024_msfa_thesis.zip file_size: 19161387 relation: source_file - access_level: open_access checksum: 2dc30ea46c5daf48d07e4cccb3c3de00 content_type: application/pdf creator: mamaral date_created: 2024-12-18T12:26:30Z date_updated: 2025-06-18T22:30:03Z embargo: 2025-06-18 file_id: '18672' file_name: 2024_msfa_thesis.pdf file_size: 16530084 relation: main_file file_date_updated: 2025-06-18T22:30:03Z fulldoi: https://doi.org/10.15479/at:ista:18661 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '12' oa: 1 oa_version: Published Version page: '57' publication_identifier: isbn: - 978-3-99078-046-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18670' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 supplementarymaterial: unclear title: 'Archaeal membranes: In silico modelling and design' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository _id: '18549' abstract: - lang: eng 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" article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 biorxivid: 1 citation: ama: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. doi:10.1101/2024.07.02.601697 apa: Mrnjavac, A., & Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. https://doi.org/10.1101/2024.07.02.601697 chicago: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, n.d. https://doi.org/10.1101/2024.07.02.601697. ieee: A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” bioRxiv. . ista: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, 10.1101/2024.07.02.601697. mla: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, doi:10.1101/2024.07.02.601697. short: A. Mrnjavac, B. Vicoso, BioRxiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-11-13T09:12:08Z date_published: 2024-07-04T00:00:00Z date_updated: 2026-10-26T23:30:59Z day: '04' department: - _id: BeVi doi: 10.1101/2024.07.02.601697 external_id: biorxivid: - 10.1101/2024.07.02.601697 fulldoi: https://doi.org/10.1101/2024.07.02.601697 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.07.02.601697 month: '07' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: draft related_material: record: - id: '19370' relation: later_version status: public - id: '18531' relation: dissertation_contains status: public researchdata_availability: no status: public supplementarymaterial: yes title: Evidence of a Slower-Z effect in Schistosoma japonicum tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository _id: '18670' 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. 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." article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Xiuyun full_name: Jiang, Xiuyun last_name: Jiang - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. doi:10.1101/2024.10.18.619072' apa: 'Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. https://doi.org/10.1101/2024.10.18.619072' chicago: 'Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.18.619072.' ieee: 'M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” bioRxiv. .' ista: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, 10.1101/2024.10.18.619072.' mla: 'Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, doi:10.1101/2024.10.18.619072.' short: M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.). corr_author: '1' date_created: 2024-12-18T10:07:45Z date_published: 2024-11-27T00:00:00Z date_updated: 2026-10-26T23:30:59Z day: '27' department: - _id: AnSa doi: 10.1101/2024.10.18.619072 ec_funded: 1 fulldoi: https://doi.org/10.1101/2024.10.18.619072 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.10.18.619072 month: '11' oa: 1 oa_version: Preprint project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: bioRxiv publication_status: draft related_material: record: - id: '18661' relation: dissertation_contains status: public status: public title: 'Stability vs flexibility: Reshaping archaeal membranes in silico' tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository _id: '17465' 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" acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko citation: ama: Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:10.15479/at:ista:17465 apa: Shevchenko, A. (2024). High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17465 chicago: Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17465. ieee: A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024. ista: Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. mla: Shevchenko, Alexander. High-Dimensional Limits in Artificial Neural Networks. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17465. short: A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024. corr_author: '1' das_tickbox: '0' date_created: 2024-08-28T15:14:25Z date_published: 2024-08-29T00:00:00Z date_updated: 2026-10-02T11:20:32Z day: '29' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: MaMo doi: 10.15479/at:ista:17465 doi_confirm: '1' file: - access_level: open_access checksum: da6dd3166078934577f6af93d27000e2 content_type: application/pdf creator: ashevche date_created: 2024-09-02T09:23:32Z date_updated: 2024-10-05T22:30:05Z embargo: 2024-10-04 file_id: '17482' file_name: thesis_a2b.pdf file_size: 4468610 relation: main_file - access_level: closed checksum: 76a39ef252239560923cdda4ce0a31a4 content_type: application/zip creator: ashevche date_created: 2024-09-02T09:23:46Z date_updated: 2024-10-05T22:30:05Z embargo_to: open_access file_id: '17483' file_name: Thesis Alex - ISTA.zip file_size: 15930999 relation: source_file file_date_updated: 2024-10-05T22:30:05Z fulldoi: https://doi.org/10.15479/at:ista:17465 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '232' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11420' relation: part_of_dissertation status: public - id: '14459' relation: part_of_dissertation status: public - id: '9198' relation: part_of_dissertation status: public - id: '17469' relation: part_of_dissertation status: public researchdata_availability: no status: public supervisor: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X supplementarymaterial: no title: High-dimensional limits in artificial neural networks type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '18477' 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 alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Beata M full_name: Kaczmarek, Beata M id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarek citation: ama: Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:10.15479/at:ista:18477 apa: Kaczmarek, B. M. (2024). Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18477 chicago: Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18477. ieee: B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024. ista: Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria. mla: Kaczmarek, Beata M. Biochemical and Structural Insights into ADAR1 RNA Editing. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18477. short: B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-27T07:35:13Z date_published: 2024-10-29T00:00:00Z date_updated: 2026-10-02T11:14:50Z day: '29' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: CaBe doi: 10.15479/at:ista:18477 doi_confirm: '1' file: - access_level: closed checksum: 2053294ea4d770c495e4cc501e2a218b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: bkaczmar date_created: 2024-10-29T11:56:36Z date_updated: 2025-10-29T23:30:02Z embargo_to: open_access file_id: '18485' file_name: 20241029_PhD_thesis_BKaczmarek.docx file_size: 23136626 relation: source_file - access_level: open_access checksum: 8ce857a4cd44b776791eaf180ac9dbb3 content_type: application/pdf creator: bkaczmar date_created: 2024-10-29T11:56:44Z date_updated: 2025-10-29T23:30:02Z embargo: 2025-10-29 file_id: '18486' file_name: 20241029_PhD_thesis_BKaczmarek.pdf file_size: 11707360 relation: main_file file_date_updated: 2025-10-29T23:30:02Z fulldoi: https://doi.org/10.15479/at:ista:18477 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '124' publication_identifier: isbn: - 978-3-99078-045-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: unclear status: public supervisor: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 supplementarymaterial: unclear title: Biochemical and structural insights into ADAR1 RNA editing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '17346' abstract: - lang: eng 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lars full_name: Bollmann, Lars id: 47AD3038-F248-11E8-B48F-1D18A9856A87 last_name: Bollmann citation: ama: Bollmann L. Stability and change in the memory system during rest. 2024. doi:10.15479/at:ista:17346 apa: Bollmann, L. (2024). Stability and change in the memory system during rest. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17346 chicago: Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17346. ieee: L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024. ista: Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria. mla: Bollmann, Lars. Stability and Change in the Memory System during Rest. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17346. short: L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024. corr_author: '1' das_tickbox: '0' date_created: 2024-07-29T15:08:42Z date_published: 2024-07-31T00:00:00Z date_updated: 2026-10-02T11:26:02Z day: '31' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:17346 doi_confirm: '1' file: - access_level: open_access checksum: 12c76297cc27449da80c60d79127770d content_type: application/pdf creator: lbollman date_created: 2024-07-31T18:37:19Z date_updated: 2025-01-31T23:30:03Z embargo: 2025-01-31 file_id: '17359' file_name: PhD_Thesis_Lars_Bollmann.pdf file_size: 12920169 relation: main_file - access_level: closed checksum: 19a0265079dec8038830ad6e35c5106e content_type: application/zip creator: lbollman date_created: 2024-07-31T18:38:39Z date_updated: 2025-01-31T23:30:03Z embargo_to: open_access file_id: '17360' file_name: Latex_source.zip file_size: 27568807 relation: source_file file_date_updated: 2025-01-31T23:30:03Z fulldoi: https://doi.org/10.15479/at:ista:17346 has_accepted_license: '1' keyword: - Memory - Hippocampus - Consolidation language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '103' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: no status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 supplementarymaterial: no title: Stability and change in the memory system during rest type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '14821' abstract: - lang: eng text: "The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Heloisa full_name: Chiossi, Heloisa id: 2BBA502C-F248-11E8-B48F-1D18A9856A87 last_name: Chiossi orcid: 0009-0004-2973-278X citation: ama: Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821 apa: Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821 chicago: Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821. ieee: H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024. ista: Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. mla: Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821. short: H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024. corr_author: '1' das_tickbox: '0' date_created: 2024-01-16T14:25:21Z date_published: 2024-01-19T00:00:00Z date_updated: 2026-10-02T11:26:27Z day: '19' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:14821 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: d3fa3de1abd5af5204c13e9d55375615 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hchiossi date_created: 2024-01-19T11:04:05Z date_updated: 2025-01-19T23:30:04Z embargo_to: open_access file_id: '14838' file_name: PhD_Thesis_190124.docx file_size: 8656268 relation: source_file - access_level: open_access checksum: 13adc8dcfb5b6b18107f89f0a98fa8bd content_type: application/pdf creator: hchiossi date_created: 2024-01-19T11:03:59Z date_updated: 2025-01-19T23:30:04Z embargo: 2025-01-19 file_id: '14839' file_name: PhD_Thesis_190124.pdf file_size: 6567275 relation: main_file file_date_updated: 2025-01-19T23:30:04Z fulldoi: https://doi.org/10.15479/at:ista:14821 has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: no status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 supplementarymaterial: no title: Adaptive hierarchical representations in the hippocampus type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '17368' abstract: - lang: eng 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" alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Ariadna full_name: Villanueva Marijuan, Ariadna id: e0ae4864-133f-11ed-8f02-adaa8dd27540 last_name: Villanueva Marijuan citation: ama: Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:10.15479/at:ista:17368 apa: Villanueva Marijuan, A. (2024). Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17368 chicago: Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17368. ieee: A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024. ista: Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. mla: Villanueva Marijuan, Ariadna. Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17368. short: A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024. corr_author: '1' das_tickbox: '0' date_created: 2024-08-02T10:52:40Z date_published: 2024-08-13T00:00:00Z date_updated: 2026-10-02T11:35:19Z day: '13' ddc: - '610' degree_awarded: MS department: - _id: GradSch - _id: MaRo doi: 10.15479/at:ista:17368 doi_confirm: '1' file: - access_level: open_access checksum: 0c2daa174609f0c00919dccc5701d375 content_type: application/pdf creator: avillanu date_created: 2024-08-14T11:51:24Z date_updated: 2025-02-14T23:30:03Z embargo: 2025-02-14 file_id: '17433' file_name: Masters_thesis_AriadnaVillanueva.pdf file_size: 13052436 relation: main_file - access_level: closed checksum: e9ed4465dfa539ac4c3a8d4d0b6271a1 content_type: application/zip creator: avillanu date_created: 2024-08-14T11:51:57Z date_updated: 2025-02-14T23:30:03Z embargo_to: open_access file_id: '17434' file_name: Masters thesis-AriadnaVillanueva.zip file_size: 45642547 relation: source_file file_date_updated: 2025-02-14T23:30:03Z fulldoi: https://doi.org/10.15479/at:ista:17368 has_accepted_license: '1' keyword: - Epigenetics - Multi-omics - Bayesian regression language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '60' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: no status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 supplementarymaterial: no title: Bayesian linear regression for analyzing general omics data with time-to-event phenotypes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '17469' abstract: - lang: eng text: 'Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.' 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)." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Kevin full_name: Kögler, Kevin id: 94ec913c-dc85-11ea-9058-e5051ab2428b last_name: Kögler - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:24964-25015.' apa: 'Kögler, K., Shevchenko, A., Hassani, H., & Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.' chicago: 'Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In Proceedings of the 41st International Conference on Machine Learning, 235:24964–15. ML Research Press, 2024.' ieee: 'K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 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.' mla: 'Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 24964–5015.' 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. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' das_tickbox: '0' date_created: 2024-08-29T11:47:57Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-10-26T23:31:00Z day: '01' ddc: - '000' department: - _id: DaAl - _id: MaMo external_id: arxiv: - '2402.05013' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.mlr.press/v235/kogler24a.html month: '07' oa: 1 oa_version: Published Version page: 24964-25015 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 41st International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '23072' relation: dissertation_contains status: public - id: '17465' relation: dissertation_contains status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 235 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '14843' abstract: - lang: eng text: The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission. acknowledged_ssus: - _id: EM-Fac - _id: PreCl - _id: M-Shop 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: JingJing full_name: Chen, JingJing id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Itaru full_name: Arai, Itaru id: 32A73F6C-F248-11E8-B48F-1D18A9856A87 last_name: Arai - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim orcid: 0000-0003-2344-1039 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 2024;112(5):755-771.e9. doi:10.1016/j.neuron.2023.12.002 apa: Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002 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.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.12.002. ieee: J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron, 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. mla: Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:10.1016/j.neuron.2023.12.002. short: J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9. corr_author: '1' date_created: 2024-01-21T23:00:56Z date_published: 2024-03-06T00:00:00Z date_updated: 2026-10-26T23:31:02Z day: '06' ddc: - '570' department: - _id: PeJo - _id: EM-Fac - _id: RySh doi: 10.1016/j.neuron.2023.12.002 ec_funded: 1 external_id: isi: - '001202925700001' pmid: - '38215739' file: - access_level: open_access checksum: 30098b4f0209556ddfb3540a23d07ca5 content_type: application/pdf creator: dernst date_created: 2025-04-23T14:02:08Z date_updated: 2025-04-23T14:02:08Z file_id: '19614' file_name: 2024_Neuron_Chen.pdf file_size: 8192355 relation: main_file success: 1 file_date_updated: 2025-04-23T14:02:08Z fulldoi: https://doi.org/10.1016/j.neuron.2023.12.002 has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 755-771.e9 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: 26B66A3E-B435-11E9-9278-68D0E5697425 grant_number: '25383' name: Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse publication: Neuron publication_identifier: eissn: - 1097-4199 issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/synapses-brought-to-the-point/ record: - id: '15101' relation: dissertation_contains status: public scopus_import: '1' status: public title: Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2024' ... --- OA_place: publisher _id: '18129' abstract: - lang: eng 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" acknowledged_ssus: - _id: M-Shop - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 citation: ama: Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:10.15479/at:ista:18129 apa: Janik, M. (2024). Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18129 chicago: Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18129. ieee: M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024. ista: Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria. mla: Janik, Marian. Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18129. short: M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-23T17:25:43Z date_published: 2024-09-24T00:00:00Z date_updated: 2026-10-02T11:22:53Z day: '24' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:18129 doi_confirm: '1' file: - access_level: closed checksum: dc15958f6400b5bdaa28bf58fc7a4056 content_type: application/x-zip-compressed creator: mjanik date_created: 2024-09-23T17:15:09Z date_updated: 2025-05-23T22:30:09Z embargo_to: open_access file_id: '18130' file_name: janik_thesis.zip file_size: 156207943 relation: source_file - access_level: open_access checksum: 74737aee285dc1f491643327350efe9c content_type: application/pdf creator: mjanik date_created: 2024-09-23T17:15:30Z date_updated: 2025-05-23T22:30:09Z embargo: 2025-05-23 file_id: '18131' file_name: janik_thesis_pdfa.pdf file_size: 96195684 relation: main_file file_date_updated: 2025-05-23T22:30:09Z fulldoi: https://doi.org/10.15479/at:ista:18129 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '164' project: - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18144' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X supplementarymaterial: unclear title: Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '15101' 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." acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: JingJing full_name: Chen, JingJing id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101 apa: 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. https://doi.org/10.15479/at:ista:15101 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. https://doi.org/10.15479/at:ista:15101. 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. 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. mla: 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, doi:10.15479/at:ista:15101. 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. corr_author: '1' das_tickbox: '0' date_created: 2024-03-11T10:09:54Z date_published: 2024-03-11T00:00:00Z date_updated: 2026-10-02T11:42:02Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: PeJo doi: 10.15479/at:ista:15101 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: db4947474ffa271e66c254b6fe876a55 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jchen date_created: 2024-03-11T14:10:58Z date_updated: 2024-04-02T22:30:03Z embargo_to: open_access file_id: '15104' file_name: Thesis_Jingjing CHEN.docx file_size: 11271363 relation: source_file - access_level: open_access checksum: a5eeae8b5702cd540f5d03469bc33dde content_type: application/pdf creator: jchen date_created: 2024-03-11T14:11:06Z date_updated: 2024-04-02T22:30:03Z embargo: 2024-04-01 file_id: '15105' file_name: Thesis_Jingjing CHEN_merged.pdf file_size: 16627311 relation: main_file file_date_updated: 2024-04-02T22:30:03Z fulldoi: https://doi.org/10.15479/at:ista:15101 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '84' project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: 26B66A3E-B435-11E9-9278-68D0E5697425 grant_number: '25383' name: Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14843' relation: part_of_dissertation status: public researchdata_availability: no status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 supplementarymaterial: no title: Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ...