[{"status":"public","citation":{"ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","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."},"date_created":"2024-06-07T16:14:13Z","year":"2024","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"month":"06","degree_awarded":"PhD","has_accepted_license":"1","oa":1,"author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K"}],"OA_place":"publisher","file_date_updated":"2025-01-10T23:30:10Z","publication_identifier":{"isbn":["978-3-99078-039-8"],"issn":["2663-337X"]},"supplementarymaterial":"unclear","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-06-20T00:00:00Z","ddc":["576"],"date_updated":"2026-10-02T11:14:33Z","doi_confirm":"1","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"language":[{"iso":"eng"}],"_id":"17119","day":"20","file":[{"date_created":"2024-06-07T16:09:17Z","date_updated":"2025-01-10T23:30:10Z","embargo_to":"open_access","content_type":"application/zip","access_level":"closed","file_size":180557931,"creator":"rkelemen","file_name":"thesis.zip","checksum":"fab59146e3b3dc2e5d214576984a2a63","file_id":"17121","relation":"source_file"},{"file_id":"17213","file_name":"thesis_to_archive.pdf","checksum":"91cc4c25a792239e8a7688e8aec7c62a","creator":"rkelemen","file_size":19405484,"relation":"main_file","date_created":"2024-07-10T08:00:20Z","date_updated":"2025-01-10T23:30:10Z","access_level":"open_access","content_type":"application/pdf","embargo":"2025-01-10"}],"supervisor":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"doi":"10.15479/at:ista:17119","related_material":{"record":[{"id":"542","relation":"part_of_dissertation","status":"public"},{"id":"10767","status":"public","relation":"part_of_dissertation"}]},"article_processing_charge":"No","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"researchdata_availability":"unclear","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."}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:17119","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","type":"dissertation","page":"105","alternative_title":["ISTA Thesis"],"corr_author":"1","publication_status":"published","oa_version":"Published Version"},{"doi_confirm":"1","title":"Early stages of sex chromosome evolution","keyword":["Sex chromosomes","evolution","selection","sheltering"],"_id":"18531","language":[{"iso":"eng"}],"day":"11","OA_place":"publisher","file_date_updated":"2025-05-11T22:30:04Z","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"unclear","date_updated":"2026-10-02T11:14:08Z","date_published":"2024-11-11T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["576"],"month":"11","has_accepted_license":"1","degree_awarded":"PhD","oa":1,"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"}],"status":"public","citation":{"chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024."},"date_created":"2024-11-11T08:40:45Z","year":"2024","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"page":"181","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Institute of Science and Technology Austria","OA_embargo":"6","fulldoi":"https://doi.org/10.15479/at:ista:18531","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"dissertation","article_processing_charge":"No","researchdata_availability":"unclear","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. "}],"file":[{"relation":"source_file","title":"Early stages of sex chromosome evolution","checksum":"3e48b163c22114ef5d5371f758668289","file_size":26870629,"creator":"amrnjava","file_name":"AMrnjavac_thesis_library.docx","file_id":"18551","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","date_updated":"2025-05-11T22:30:04Z","date_created":"2024-11-13T12:15:28Z"},{"file_id":"18552","file_name":"AMrnjavac_thesis_library.pdf","file_size":4228766,"checksum":"3ead60c1b678e7dcf018043aef3b5db2","creator":"amrnjava","relation":"main_file","title":"Early stages of sex chromosome evolution","date_created":"2024-11-13T12:15:54Z","date_updated":"2025-05-11T22:30:04Z","access_level":"open_access","embargo":"2025-05-11","content_type":"application/pdf"}],"doi":"10.15479/at:ista:18531","supervisor":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"id":"12521","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18549"}]}},{"publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:18661","alternative_title":["ISTA Thesis"],"page":"57","corr_author":"1","oa_version":"Published Version","publication_status":"published","file":[{"content_type":"application/zip","embargo_to":"open_access","access_level":"closed","date_created":"2024-12-18T12:27:01Z","date_updated":"2025-06-18T22:30:03Z","relation":"source_file","creator":"mamaral","file_name":"2024_msfa_thesis.zip","checksum":"eca06497a29078558395455c890a32d9","file_size":19161387,"file_id":"18671"},{"relation":"main_file","creator":"mamaral","file_name":"2024_msfa_thesis.pdf","file_size":16530084,"checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","file_id":"18672","embargo":"2025-06-18","content_type":"application/pdf","access_level":"open_access","date_created":"2024-12-18T12:26:30Z","date_updated":"2025-06-18T22:30:03Z"}],"supervisor":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"doi":"10.15479/at:ista:18661","related_material":{"record":[{"id":"18670","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","researchdata_availability":"unclear","abstract":[{"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","lang":"eng"}],"OA_place":"publisher","publication_identifier":{"isbn":["978-3-99078-046-6"],"issn":["2663-337X"]},"supplementarymaterial":"unclear","file_date_updated":"2025-06-18T22:30:03Z","date_updated":"2026-10-02T11:12:49Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["572","530"],"date_published":"2024-12-17T00:00:00Z","title":"Archaeal membranes: In silico modelling and design","doi_confirm":"1","_id":"18661","language":[{"iso":"eng"}],"day":"17","status":"public","year":"2024","citation":{"apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes: In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>","short":"M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","ama":"Santana de Freitas Amaral M. Archaeal membranes: In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes: In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","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.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes: In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>."},"date_created":"2024-12-16T10:53:39Z","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"month":"12","has_accepted_license":"1","oa":1,"degree_awarded":"PhD","author":[{"full_name":"Santana de Freitas Amaral, Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","last_name":"Santana de Freitas Amaral","first_name":"Miguel"}]},{"status":"public","department":[{"_id":"BeVi"}],"citation":{"mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","apa":"Mrnjavac, A., &#38; Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>.","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, <a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>."},"date_created":"2024-11-13T09:12:08Z","year":"2024","month":"07","external_id":{"biorxivid":["10.1101/2024.07.02.601697"]},"author":[{"first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"oa":1,"supplementarymaterial":"yes","das_tickbox":"0","OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-25T23:31:16Z","date_published":"2024-07-04T00:00:00Z","title":"Evidence of a Slower-Z effect in Schistosoma japonicum","day":"04","_id":"18549","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"19370","status":"public","relation":"later_version"},{"id":"18531","status":"public","relation":"dissertation_contains"}]},"doi":"10.1101/2024.07.02.601697","article_processing_charge":"No","abstract":[{"text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n","lang":"eng"}],"publication":"bioRxiv","researchdata_availability":"no","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.07.02.601697"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"biorxivid":1,"fulldoi":"https://doi.org/10.1101/2024.07.02.601697","type":"preprint","publication_status":"draft","oa_version":"Preprint","corr_author":"1"},{"related_material":{"record":[{"id":"18661","relation":"dissertation_contains","status":"public"}]},"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.","doi":"10.1101/2024.10.18.619072","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."}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"}],"publication":"bioRxiv","article_processing_charge":"No","fulldoi":"https://doi.org/10.1101/2024.10.18.619072","ec_funded":1,"type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2024.10.18.619072","open_access":"1"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_status":"draft","oa_version":"Preprint","corr_author":"1","department":[{"_id":"AnSa"}],"citation":{"ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>.","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.).","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>"},"date_created":"2024-12-18T10:07:45Z","year":"2024","status":"public","author":[{"full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","last_name":"Frey","first_name":"Felix F","orcid":"0000-0001-8501-6017","full_name":"Frey, Felix F"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"oa":1,"month":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-25T23:31:16Z","date_published":"2024-11-27T00:00:00Z","OA_place":"repository","day":"27","_id":"18670","language":[{"iso":"eng"}],"title":"Stability vs flexibility: Reshaping archaeal membranes in silico"},{"fulldoi":"https://doi.org/10.15479/at:ista:17465","type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"page":"232","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11420"},{"status":"public","relation":"part_of_dissertation","id":"14459"},{"status":"public","relation":"part_of_dissertation","id":"9198"},{"id":"17469","status":"public","relation":"part_of_dissertation"}]},"supervisor":[{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"doi":"10.15479/at:ista:17465","file":[{"creator":"ashevche","file_size":4468610,"checksum":"da6dd3166078934577f6af93d27000e2","file_name":"thesis_a2b.pdf","file_id":"17482","relation":"main_file","date_updated":"2024-10-05T22:30:05Z","date_created":"2024-09-02T09:23:32Z","embargo":"2024-10-04","content_type":"application/pdf","access_level":"open_access"},{"content_type":"application/zip","embargo_to":"open_access","access_level":"closed","date_created":"2024-09-02T09:23:46Z","date_updated":"2024-10-05T22:30:05Z","relation":"source_file","file_size":15930999,"file_name":"Thesis Alex - ISTA.zip","checksum":"76a39ef252239560923cdda4ce0a31a4","creator":"ashevche","file_id":"17483"}],"abstract":[{"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","lang":"eng"}],"researchdata_availability":"no","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"article_processing_charge":"No","date_updated":"2026-10-02T11:20:32Z","ddc":["519"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-08-29T00:00:00Z","file_date_updated":"2024-10-05T22:30:05Z","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","OA_place":"repository","das_tickbox":"0","day":"29","_id":"17465","language":[{"iso":"eng"}],"doi_confirm":"1","title":"High-dimensional limits in artificial neural networks","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"date_created":"2024-08-28T15:14:25Z","citation":{"ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>"},"year":"2024","status":"public","author":[{"full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr"}],"degree_awarded":"PhD","has_accepted_license":"1","oa":1,"month":"08"},{"license":"https://creativecommons.org/licenses/by/4.0/","type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:18477","publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","publication_status":"published","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"page":"124","doi":"10.15479/at:ista:18477","supervisor":[{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A"}],"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2024-10-29T11:56:36Z","date_updated":"2025-10-29T23:30:02Z","relation":"source_file","checksum":"2053294ea4d770c495e4cc501e2a218b","creator":"bkaczmar","file_name":"20241029_PhD_thesis_BKaczmarek.docx","file_size":23136626,"file_id":"18485"},{"relation":"main_file","creator":"bkaczmar","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","file_size":11707360,"file_id":"18486","embargo":"2025-10-29","content_type":"application/pdf","access_level":"open_access","date_created":"2024-10-29T11:56:44Z","date_updated":"2025-10-29T23:30:02Z"}],"abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"researchdata_availability":"unclear","article_processing_charge":"No","date_published":"2024-10-29T00:00:00Z","date_updated":"2026-10-02T11:14:50Z","ddc":["572"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"unclear","publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"file_date_updated":"2025-10-29T23:30:02Z","OA_place":"publisher","day":"29","_id":"18477","language":[{"iso":"eng"}],"title":"Biochemical and structural insights into ADAR1 RNA editing","doi_confirm":"1","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"year":"2024","citation":{"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.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>"},"date_created":"2024-10-27T07:35:13Z","status":"public","author":[{"full_name":"Kaczmarek, Beata M","first_name":"Beata M","last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","degree_awarded":"PhD","oa":1,"month":"10"},{"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/at:ista:17346","type":"dissertation","page":"103","alternative_title":["ISTA Thesis"],"corr_author":"1","publication_status":"published","oa_version":"Published Version","file":[{"date_updated":"2025-01-31T23:30:03Z","date_created":"2024-07-31T18:37:19Z","access_level":"open_access","content_type":"application/pdf","embargo":"2025-01-31","file_id":"17359","checksum":"12c76297cc27449da80c60d79127770d","file_size":12920169,"file_name":"PhD_Thesis_Lars_Bollmann.pdf","creator":"lbollman","relation":"main_file"},{"file_size":27568807,"file_name":"Latex_source.zip","checksum":"19a0265079dec8038830ad6e35c5106e","creator":"lbollman","file_id":"17360","relation":"source_file","date_updated":"2025-01-31T23:30:03Z","date_created":"2024-07-31T18:38:39Z","content_type":"application/zip","embargo_to":"open_access","access_level":"closed"}],"supervisor":[{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"doi":"10.15479/at:ista:17346","article_processing_charge":"No","researchdata_availability":"no","abstract":[{"text":"Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas.","lang":"eng"}],"OA_place":"publisher","das_tickbox":"0","file_date_updated":"2025-01-31T23:30:03Z","supplementarymaterial":"no","publication_identifier":{"issn":["2663-337X"]},"date_published":"2024-07-31T00:00:00Z","ddc":["573"],"date_updated":"2026-10-02T11:26:02Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi_confirm":"1","title":"Stability and change in the memory system during rest","keyword":["Memory","Hippocampus","Consolidation"],"_id":"17346","language":[{"iso":"eng"}],"day":"31","status":"public","date_created":"2024-07-29T15:08:42Z","citation":{"mla":"Bollmann, Lars. <i>Stability and Change in the Memory System during Rest</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>.","short":"L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024.","apa":"Bollmann, L. (2024). <i>Stability and change in the memory system during rest</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>","ama":"Bollmann L. Stability and change in the memory system during rest. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>","ieee":"L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024.","chicago":"Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>.","ista":"Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria."},"year":"2024","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"month":"07","degree_awarded":"PhD","has_accepted_license":"1","oa":1,"author":[{"id":"47AD3038-F248-11E8-B48F-1D18A9856A87","last_name":"Bollmann","first_name":"Lars","full_name":"Bollmann, Lars"}]},{"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"researchdata_availability":"no","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."}],"article_processing_charge":"No","doi":"10.15479/at:ista:14821","supervisor":[{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"file":[{"file_id":"14838","checksum":"d3fa3de1abd5af5204c13e9d55375615","file_size":8656268,"creator":"hchiossi","file_name":"PhD_Thesis_190124.docx","relation":"source_file","date_updated":"2025-01-19T23:30:04Z","date_created":"2024-01-19T11:04:05Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"date_updated":"2025-01-19T23:30:04Z","date_created":"2024-01-19T11:03:59Z","access_level":"open_access","embargo":"2025-01-19","content_type":"application/pdf","file_id":"14839","file_size":6567275,"file_name":"PhD_Thesis_190124.pdf","creator":"hchiossi","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","relation":"main_file"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"],"page":"89","type":"dissertation","ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:14821","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa":1,"degree_awarded":"PhD","author":[{"last_name":"Chiossi","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","first_name":"Heloisa","orcid":"0009-0004-2973-278X","full_name":"Chiossi, Heloisa"}],"month":"01","year":"2024","citation":{"apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria."},"date_created":"2024-01-16T14:25:21Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"status":"public","language":[{"iso":"eng"}],"_id":"14821","day":"19","title":"Adaptive hierarchical representations in the hippocampus","doi_confirm":"1","date_published":"2024-01-19T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_updated":"2026-10-02T11:26:27Z","OA_place":"publisher","das_tickbox":"0","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","file_date_updated":"2025-01-19T23:30:04Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-08-13T00:00:00Z","date_updated":"2026-10-02T11:35:19Z","ddc":["610"],"OA_place":"publisher","das_tickbox":"0","supplementarymaterial":"no","publication_identifier":{"issn":["2791-4585"]},"file_date_updated":"2025-02-14T23:30:03Z","_id":"17368","language":[{"iso":"eng"}],"day":"13","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","doi_confirm":"1","keyword":["Epigenetics","Multi-omics","Bayesian regression"],"year":"2024","date_created":"2024-08-02T10:52:40Z","citation":{"apa":"Villanueva Marijuan, A. (2024). <i>Bayesian linear regression for analyzing general omics data with time-to-event phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>","short":"A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024.","ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>","mla":"Villanueva Marijuan, Ariadna. <i>Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>.","ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","chicago":"Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>.","ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"status":"public","has_accepted_license":"1","degree_awarded":"MS","oa":1,"author":[{"first_name":"Ariadna","id":"e0ae4864-133f-11ed-8f02-adaa8dd27540","last_name":"Villanueva Marijuan","full_name":"Villanueva Marijuan, Ariadna"}],"month":"08","type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:17368","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"corr_author":"1","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Master's Thesis"],"page":"60","supervisor":[{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"}],"doi":"10.15479/at:ista:17368","file":[{"file_name":"Masters_thesis_AriadnaVillanueva.pdf","creator":"avillanu","file_size":13052436,"checksum":"0c2daa174609f0c00919dccc5701d375","file_id":"17433","relation":"main_file","date_created":"2024-08-14T11:51:24Z","date_updated":"2025-02-14T23:30:03Z","embargo":"2025-02-14","content_type":"application/pdf","access_level":"open_access"},{"access_level":"closed","content_type":"application/zip","embargo_to":"open_access","date_updated":"2025-02-14T23:30:03Z","date_created":"2024-08-14T11:51:57Z","relation":"source_file","file_id":"17434","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1","creator":"avillanu","file_name":"Masters thesis-AriadnaVillanueva.zip","file_size":45642547}],"researchdata_availability":"no","abstract":[{"text":"Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n","lang":"eng"}],"article_processing_charge":"No"},{"publication_status":"published","oa_version":"Published Version","corr_author":"1","page":"24964-25015","volume":235,"alternative_title":["PMLR"],"type":"conference","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v235/kogler24a.html"}],"scopus_import":"1","publisher":"ML Research Press","abstract":[{"text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.","lang":"eng"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","researchdata_availability":"no","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"article_processing_charge":"No","quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"23072"},{"status":"public","relation":"dissertation_contains","id":"17465"}]},"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).","day":"01","language":[{"iso":"eng"}],"_id":"17469","arxiv":1,"title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-25T23:31:17Z","ddc":["000"],"supplementarymaterial":"no","intvolume":"       235","das_tickbox":"0","conference":{"location":"Vienna, Austria","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27","start_date":"2024-07-21"},"author":[{"last_name":"Kögler","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","first_name":"Kevin","full_name":"Kögler, Kevin"},{"last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"oa":1,"month":"07","external_id":{"arxiv":["2402.05013"]},"department":[{"_id":"DaAl"},{"_id":"MaMo"}],"citation":{"mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015.","apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024.","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.","ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015."},"date_created":"2024-08-29T11:47:57Z","year":"2024","status":"public"},{"month":"03","external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"author":[{"last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","full_name":"Chen, JingJing"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"full_name":"Chen, Chong","first_name":"Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arai, Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","first_name":"Itaru"},{"last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","orcid":"0000-0003-2344-1039","full_name":"Kim, Olena"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"date_created":"2024-01-21T23:00:56Z","citation":{"ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","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.","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>."},"OA_type":"hybrid","year":"2024","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","day":"06","PlanS_conform":"1","pmid":1,"isi":1,"issue":"5","_id":"14843","language":[{"iso":"eng"}],"file_date_updated":"2025-04-23T14:02:08Z","intvolume":"       112","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"OA_place":"publisher","ddc":["570"],"date_updated":"2026-10-25T23:31:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-03-06T00:00:00Z","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","article_type":"original","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"publication":"Neuron","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":8192355,"creator":"dernst","file_name":"2024_Neuron_Chen.pdf","checksum":"30098b4f0209556ddfb3540a23d07ca5","file_id":"19614","success":1,"relation":"main_file","date_created":"2025-04-23T14:02:08Z","date_updated":"2025-04-23T14:02:08Z","content_type":"application/pdf","access_level":"open_access"}],"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"}]},"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.","doi":"10.1016/j.neuron.2023.12.002","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"page":"755-771.e9","volume":112,"publication_status":"published","oa_version":"Published Version","corr_author":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.neuron.2023.12.002","ec_funded":1,"type":"journal_article"},{"_id":"18129","language":[{"iso":"eng"}],"day":"24","title":"Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors","doi_confirm":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-24T00:00:00Z","ddc":["539"],"date_updated":"2026-10-02T11:22:53Z","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"unclear","file_date_updated":"2025-05-23T22:30:09Z","has_accepted_license":"1","oa":1,"degree_awarded":"PhD","author":[{"last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","full_name":"Janik, Marian","orcid":"0009-0003-9037-8831"}],"month":"09","year":"2024","date_created":"2024-09-23T17:25:43Z","citation":{"ieee":"M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024.","chicago":"Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>.","ista":"Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria.","mla":"Janik, Marian. <i>Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>.","apa":"Janik, M. (2024). <i>Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>","short":"M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024.","ama":"Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>"},"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"status":"public","corr_author":"1","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"],"page":"164","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:18129","publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"researchdata_availability":"unclear","project":[{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology","grant_number":"101069515"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"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"}],"article_processing_charge":"No","doi":"10.15479/at:ista:18129","supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"18144"}]},"file":[{"relation":"source_file","file_id":"18130","file_name":"janik_thesis.zip","checksum":"dc15958f6400b5bdaa28bf58fc7a4056","creator":"mjanik","file_size":156207943,"access_level":"closed","content_type":"application/x-zip-compressed","embargo_to":"open_access","date_updated":"2025-05-23T22:30:09Z","date_created":"2024-09-23T17:15:09Z"},{"date_updated":"2025-05-23T22:30:09Z","date_created":"2024-09-23T17:15:30Z","access_level":"open_access","content_type":"application/pdf","embargo":"2025-05-23","file_id":"18131","checksum":"74737aee285dc1f491643327350efe9c","file_name":"janik_thesis_pdfa.pdf","file_size":96195684,"creator":"mjanik","relation":"main_file"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/at:ista:15101","ec_funded":1,"type":"dissertation","acknowledged_ssus":[{"_id":"EM-Fac"}],"page":"84","alternative_title":["ISTA Thesis"],"publication_status":"published","oa_version":"Published Version","corr_author":"1","file":[{"date_updated":"2024-04-02T22:30:03Z","date_created":"2024-03-11T14:10:58Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","checksum":"db4947474ffa271e66c254b6fe876a55","file_name":"Thesis_Jingjing CHEN.docx","file_size":11271363,"creator":"jchen","file_id":"15104","relation":"source_file"},{"relation":"main_file","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_size":16627311,"creator":"jchen","file_name":"Thesis_Jingjing CHEN_merged.pdf","file_id":"15105","embargo":"2024-04-01","content_type":"application/pdf","access_level":"open_access","date_created":"2024-03-11T14:11:06Z","date_updated":"2024-04-02T22:30:03Z"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14843"}]},"supervisor":[{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"doi":"10.15479/at:ista:15101","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","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"}],"researchdata_availability":"no","file_date_updated":"2024-04-02T22:30:03Z","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","das_tickbox":"0","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_updated":"2026-10-02T11:42:02Z","date_published":"2024-03-11T00:00:00Z","doi_confirm":"1","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","day":"11","language":[{"iso":"eng"}],"_id":"15101","status":"public","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"date_created":"2024-03-11T10:09:54Z","citation":{"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.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","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. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","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.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>"},"year":"2024","month":"03","author":[{"full_name":"Chen, JingJing","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"}],"has_accepted_license":"1","degree_awarded":"PhD","oa":1},{"doi":"10.48550/arXiv.2407.03079","acknowledgement":"We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project, the FWF Projects with DOI:10.55776/P32235, DOI:10.55776/I5060 and DOI:10.55776/P36507. IMP acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG – German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC’s\r\nQuantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors\r\nacknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development\r\nFund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM [60].","related_material":{"record":[{"id":"18886","relation":"research_data","status":"public"},{"id":"19401","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"18129"}]},"article_processing_charge":"No","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology","grant_number":"101069515"},{"call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235","name":"Towards scalable hut wire quantum devices"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"}],"researchdata_availability":"yes","publication":"arXiv","abstract":[{"lang":"eng","text":"High kinetic inductance superconductors are gaining increasing interest for\r\nthe realisation of qubits, amplifiers and detectors. Moreover, thanks to their\r\nhigh impedance, quantum buses made of such materials enable large zero-point\r\nfluctuations of the voltage, boosting the coupling rates to spin and charge\r\nqubits. However, fully exploiting the potential of disordered or granular\r\nsuperconductors is challenging, as their inductance and, therefore, impedance\r\nat high values are difficult to control. Here we have integrated a granular\r\naluminium resonator, having a characteristic impedance exceeding the resistance\r\nquantum, with a germanium double quantum dot and demonstrate strong\r\ncharge-photon coupling with a rate of $g_\\text{c}/2\\pi= (566 \\pm 2)$ MHz. This\r\nwas achieved due to the realisation of a wireless ohmmeter, which allows\r\n\\emph{in situ} measurements during film deposition and, therefore, control of\r\nthe kinetic inductance of granular aluminium films. Reproducible fabrication of\r\ncircuits with impedances (inductances) exceeding 13 k$\\Omega$ (1 nH per square)\r\nis now possible. This broadly applicable method opens the path for novel qubits\r\nand high-fidelity, long-distance two-qubit gates."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.03079"}],"type":"preprint","fulldoi":"https://doi.org/10.48550/arXiv.2407.03079","article_number":"2407.03079","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"corr_author":"1","oa_version":"Preprint","publication_status":"draft","status":"public","year":"2024","citation":{"chicago":"Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular  Aluminium Superinductors.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2407.03079\">https://doi.org/10.48550/arXiv.2407.03079</a>.","ista":"Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Manjón AG, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors. arXiv, 2407.03079.","ieee":"M. Janik <i>et al.</i>, “Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors,” <i>arXiv</i>. .","mla":"Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular  Aluminium Superinductors.” <i>ArXiv</i>, 2407.03079, doi:<a href=\"https://doi.org/10.48550/arXiv.2407.03079\">10.48550/arXiv.2407.03079</a>.","ama":"Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2407.03079\">10.48550/arXiv.2407.03079</a>","short":"M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A.G. Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, ArXiv (n.d.).","apa":"Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (n.d.). Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2407.03079\">https://doi.org/10.48550/arXiv.2407.03079</a>"},"date_created":"2024-09-26T09:50:43Z","department":[{"_id":"GeKa"},{"_id":"GradSch"},{"_id":"JoFi"}],"external_id":{"arxiv":["2407.03079"]},"month":"07","oa":1,"author":[{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian","orcid":"0009-0003-9037-8831","full_name":"Janik, Marian"},{"full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","id":"53f93ea2-803f-11ed-ab7e-b283135794ef","first_name":"Kevin Etienne Robert"},{"last_name":"Borja Espinosa","id":"18777c01-896a-11ed-bdf8-e4851dc07d16","first_name":"Carla N","full_name":"Borja Espinosa, Carla N"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","full_name":"Sagi, Oliver"},{"full_name":"Baghdadi, Abdulhamid","first_name":"Abdulhamid","last_name":"Baghdadi","id":"160D87FA-96B5-11E9-BF77-7626E6697425"},{"first_name":"Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","last_name":"Adletzberger","full_name":"Adletzberger, Thomas"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"full_name":"Manjón, Alba Garzón","last_name":"Manjón","first_name":"Alba Garzón"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"last_name":"Pop","first_name":"Ioan M.","full_name":"Pop, Ioan M."},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"OA_place":"repository","das_tickbox":"1","supplementarymaterial":"unclear","date_published":"2024-07-03T00:00:00Z","date_updated":"2026-10-25T23:31:19Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors","arxiv":1,"_id":"18144","language":[{"iso":"eng"}],"day":"03"},{"fulldoi":"https://doi.org/10.48550/arXiv.2403.07803","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.07803"}],"corr_author":"1","publication_status":"draft","oa_version":"Preprint","article_number":"2403.07803","doi":"10.48550/arXiv.2403.07803","related_material":{"record":[{"id":"20865","status":"public","relation":"later_version"},{"id":"20563","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n","publication":"arXiv","project":[{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":"F06504","name":"Taming Complexity in Partial Differential Systems","call_identifier":"FWF"}],"abstract":[{"text":"We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum.   In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. ","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-25T23:31:21Z","date_published":"2024-04-09T00:00:00Z","OA_place":"repository","_id":"20571","language":[{"iso":"eng"}],"day":"09","title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","arxiv":1,"keyword":["gradient flows","Jordan–Kinderlehrer–Otto scheme","curves of maximal slope","optimal transport","Dirichlet boundary conditions","Fokker–Planck equation"],"citation":{"ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>","short":"F. Quattrocchi, ArXiv (n.d.).","apa":"Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, 2403.07803, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>.","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>.","ista":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803.","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” <i>arXiv</i>. ."},"date_created":"2025-10-28T13:12:56Z","year":"2024","OA_type":"green","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"status":"public","oa":1,"author":[{"first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo","orcid":"0009-0000-9773-1931"}],"external_id":{"arxiv":["2403.07803"]},"month":"04"},{"OA_type":"green","year":"2024","date_created":"2025-10-28T13:12:22Z","citation":{"ieee":"F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” <i>arXiv</i>. .","ista":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924.","chicago":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>.","mla":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, 2408.12924, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>.","apa":"Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>","short":"F. Quattrocchi, ArXiv (n.d.).","ama":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>"},"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"status":"public","oa":1,"author":[{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","first_name":"Filippo","full_name":"Quattrocchi, Filippo","orcid":"0009-0000-9773-1931"}],"external_id":{"arxiv":["2408.12924"]},"month":"08","date_published":"2024-08-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-25T23:31:21Z","OA_place":"repository","language":[{"iso":"eng"}],"_id":"20570","day":"23","title":"Asymptotics for optimal empirical quantization of measures","keyword":["optimal empirical quantization","vector quantization","Wasserstein distance","semidiscrete optimal transport","Zador’s Theorem","Pierce’s Lemma"],"arxiv":1,"doi":"10.48550/arXiv.2408.12924","related_material":{"record":[{"id":"20563","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"The author is thankful to Nicolas Clozeau, Lorenzo Dello Schiavo, Jan Maas, Dejan Slepčev,\r\nand Dario Trevisan for many fruitful discussions and comments. The author gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","publication":"arXiv","project":[{"call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems","grant_number":"F06504"}],"abstract":[{"text":"We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le p<d$, we establish asymptotic upper and\r\nlower bounds as $n \\to \\infty$ on the rescaled minimal error that have the\r\nsame, explicit dependency on $\\mu$.\r\n  In some instances, we prove that the rescaled minimal error has a limit.\r\nThese include general measures in dimension $d = 2$ with $1 \\le p < 2$, and\r\nuniform measures in arbitrary dimension with $1 \\le p < d$. For some uniform\r\nmeasures, we prove the limit existence for $p \\ge d$ as well.\r\n  For a class of compactly supported measures with H\\\"older densities, we\r\ndetermine the convergence speed of the minimal error for every $p \\ge 1$.\r\n  Furthermore, we establish a new Pierce-type (i.e., nonasymptotic) upper\r\nestimate of the minimal error when $1 \\le p < d$.\r\n  In the initial sections, we survey the state of the art and draw connections\r\nwith similar problems, such as classical and random quantization.","lang":"eng"}],"article_processing_charge":"No","type":"preprint","fulldoi":"https://doi.org/10.48550/arXiv.2408.12924","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.12924","open_access":"1"}],"corr_author":"1","oa_version":"Preprint","publication_status":"draft","article_number":"2408.12924"},{"_id":"17183","language":[{"iso":"eng"}],"day":"16","isi":1,"issue":"1","title":"Emergent macroscopic bistability induced by a single superconducting qubit","arxiv":1,"ddc":["530"],"date_updated":"2026-10-25T23:31:22Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-02-16T00:00:00Z","OA_place":"publisher","das_tickbox":"0","file_date_updated":"2024-06-28T12:04:43Z","publication_identifier":{"eissn":["2691-3399"]},"supplementarymaterial":"yes","intvolume":"         5","oa":1,"has_accepted_license":"1","author":[{"last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya","orcid":"0000-0001-7641-8348","full_name":"Sett, Riya"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"first_name":"Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"first_name":"Andras","last_name":"Vukics","full_name":"Vukics, Andras"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"external_id":{"arxiv":["2210.14182"],"isi":["001171652500001"]},"month":"02","date_created":"2024-06-27T10:58:06Z","citation":{"ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” <i>PRX Quantum</i>, vol. 5, no. 1. American Physical Society, 2024.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327.","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>."},"OA_type":"gold","year":"2024","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"status":"public","APC_amount":"3782,54","corr_author":"1","publication_status":"published","oa_version":"Published Version","article_number":"010327","volume":5,"acknowledged_ssus":[{"_id":"M-Shop"}],"ec_funded":1,"fulldoi":"https://doi.org/10.1103/prxquantum.5.010327","DOAJ_listed":"1","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Physical Society","scopus_import":"1","researchdata_availability":"yes","publication":"PRX Quantum","project":[{"call_identifier":"H2020","grant_number":"862644","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"article_type":"original","abstract":[{"text":"The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes","doi":"10.1103/prxquantum.5.010327","acknowledgement":"This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations.","related_material":{"record":[{"id":"18978","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"19533"}]},"file":[{"success":1,"file_id":"17185","creator":"cchlebak","file_size":1443351,"file_name":"2024_PRXQuantum_Sett.pdf","checksum":"0833880d47f74ad1deda93a1d8ffa5a7","relation":"main_file","date_updated":"2024-06-28T12:04:43Z","date_created":"2024-06-28T12:04:43Z","access_level":"open_access","content_type":"application/pdf"}]},{"doi_confirm":"1","title":"Visualizing the neuronal transcriptional landscape with tissue context","day":"28","_id":"18471","language":[{"iso":"eng"}],"file_date_updated":"2025-05-05T22:30:04Z","publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"supplementarymaterial":"unclear","OA_place":"publisher","date_published":"2024-10-28T00:00:00Z","date_updated":"2026-10-02T11:26:48Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","author":[{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"}],"degree_awarded":"PhD","has_accepted_license":"1","oa":1,"status":"public","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_created":"2024-10-26T20:02:42Z","citation":{"chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024."},"year":"2024","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"page":"97","alternative_title":["ISTA Thesis"],"publication_status":"published","oa_version":"Published Version","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/at:ista:18471","ec_funded":1,"type":"dissertation","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. "}],"researchdata_availability":"unclear","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"file":[{"date_created":"2024-10-26T22:29:06Z","date_updated":"2025-05-05T22:30:04Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"18475","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","checksum":"6d7c7725d040d8debc070dcb35ac965d","creator":"nagudelo","file_size":183077763,"relation":"source_file"},{"relation":"main_file","file_id":"18476","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","creator":"nagudelo","file_size":47027710,"access_level":"open_access","content_type":"application/pdf","embargo":"2025-05-05","date_created":"2024-10-26T23:13:33Z","date_updated":"2025-05-05T22:30:04Z"}],"doi":"10.15479/at:ista:18471","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}]},{"publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"type":"dissertation","ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:18574","OA_embargo":"12","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"alternative_title":["ISTA Thesis"],"page":"86","oa_version":"Published Version","publication_status":"published","corr_author":"1","file":[{"file_id":"18589","file_size":75512262,"file_name":"PhD Thesis - Divyansh Gupta.zip","checksum":"ebb000d361c36b22ed6e639a931c6b7c","creator":"dgupta","relation":"source_file","date_created":"2024-11-25T14:44:03Z","date_updated":"2025-11-11T23:30:02Z","access_level":"closed","embargo_to":"open_access","content_type":"application/zip"},{"file_id":"18591","creator":"dgupta","checksum":"1282401eb71598bc311058b0fcefc6a1","file_size":6412619,"file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","relation":"main_file","date_updated":"2025-11-11T23:30:02Z","date_created":"2024-11-26T11:43:19Z","access_level":"open_access","embargo":"2025-11-11","content_type":"application/pdf"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12349"},{"status":"public","relation":"research_data","id":"12370"}]},"acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","supervisor":[{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:18574","article_processing_charge":"No","abstract":[{"text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n","lang":"eng"}],"project":[{"_id":"bdaf81a8-d553-11ed-ba76-c95961984540","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","grant_number":"101086580"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","grant_number":"756502"}],"researchdata_availability":"unclear","supplementarymaterial":"unclear","publication_identifier":{"isbn":["978-3-99078-050-3"],"issn":["2663-337X"]},"file_date_updated":"2025-11-11T23:30:02Z","OA_place":"publisher","date_updated":"2026-10-02T11:33:52Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["573"],"date_published":"2024-11-22T00:00:00Z","title":"Visual adaptations to natural statistics","doi_confirm":"1","day":"22","language":[{"iso":"eng"}],"_id":"18574","status":"public","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"year":"2024","citation":{"ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>."},"date_created":"2024-11-20T21:30:44Z","month":"11","author":[{"last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","first_name":"Divyansh","orcid":"0000-0001-7400-6665","full_name":"Gupta, Divyansh"}],"has_accepted_license":"1","oa":1,"degree_awarded":"PhD"}]