[{"publication_status":"published","oa_version":"Published Version","corr_author":"1","volume":6,"type":"conference","main_file_link":[{"url":"https://proceedings.mlsys.org/paper_files/paper/2024/hash/9069a8976ff06f6443e7f4172990a580-Abstract-Conference.html","open_access":"1"}],"publisher":"Association for Computing Machinery","abstract":[{"lang":"eng","text":"Data-parallel distributed training of deep neural networks (DNN) has gained very widespread adoption, but can still experience communication bottlenecks. To address this issue, entire families of compression mechanisms have been developed, including quantization, sparsification, and low-rank approximation, some of which are seeing significant practical adoption. Despite this progress, almost all known compression schemes apply compression uniformly across DNN layers, although layers are heterogeneous in terms of parameter count and their impact on model accuracy.In this work, we provide a general framework for adapting the degree of compression across the model's layers dynamically during training, improving the overall compression, while leading to substantial speedups, without sacrificing accuracy. Our framework, called L-GreCo, is based on an adaptive algorithm, which automatically picks the optimal compression parameters for model layers guaranteeing the best compression ratio while satisfying an error constraint. Extensive experiments over image classification and language modeling tasks shows that L-GreCo is effective across all existing families of compression methods, and achieves up to 2.5\r\n×\r\n training speedup and up to 5\r\n×\r\n compression improvement over efficient implementations of existing approaches, while recovering full accuracy. Moreover, L-GreCo is complementary to existing adaptive algorithms, improving their compression ratio by 50\\% and practical throughput by 66\\%. An anonymized implementation is available at https://github.com/LGrCo/L-GreCo."}],"researchdata_availability":"no","publication":"Proceedings of Machine Learning and Systems ","article_processing_charge":"No","quality_controlled":"1","related_material":{"record":[{"id":"17490","relation":"dissertation_contains","status":"public"}]},"editor":[{"full_name":"Gibbons, P.","last_name":"Gibbons","first_name":"P."},{"full_name":"Pekhimenko, G.","first_name":"G.","last_name":"Pekhimenko"},{"last_name":"De Sa","first_name":"C.","full_name":"De Sa, C."}],"day":"01","_id":"17456","language":[{"iso":"eng"}],"arxiv":1,"title":"L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning","date_updated":"2026-10-02T11:20:05Z","ddc":["000"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-04-01T00:00:00Z","supplementarymaterial":"no","intvolume":"         6","das_tickbox":"0","conference":{"end_date":"2024-04-22","name":"MLSys: Machine Learning and Systems","location":"Athens, Greece","start_date":"2024-04-22"},"author":[{"last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","first_name":"Ilia","full_name":"Markov, Ilia"},{"full_name":"Alimohammadi, Kaveh","last_name":"Alimohammadi","first_name":"Kaveh"},{"first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar","full_name":"Frantar, Elias"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"oa":1,"month":"04","external_id":{"arxiv":["2210.17357"]},"department":[{"_id":"DaAl"}],"date_created":"2024-08-22T08:29:25Z","citation":{"mla":"Markov, Ilia, et al. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons et al., vol. 6, Association for Computing Machinery, 2024.","ama":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In: Gibbons P, Pekhimenko G, De Sa C, eds. <i>Proceedings of Machine Learning and Systems </i>. Vol 6. Association for Computing Machinery; 2024.","short":"I. Markov, K. Alimohammadi, E. Frantar, D.-A. Alistarh, in:, P. Gibbons, G. Pekhimenko, C. De Sa (Eds.), Proceedings of Machine Learning and Systems , Association for Computing Machinery, 2024.","apa":"Markov, I., Alimohammadi, K., Frantar, E., &#38; Alistarh, D.-A. (2024). L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In P. Gibbons, G. Pekhimenko, &#38; C. De Sa (Eds.), <i>Proceedings of Machine Learning and Systems </i> (Vol. 6). Athens, Greece: Association for Computing Machinery.","ista":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. 2024. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. Proceedings of Machine Learning and Systems . MLSys: Machine Learning and Systems vol. 6.","chicago":"Markov, Ilia, Kaveh Alimohammadi, Elias Frantar, and Dan-Adrian Alistarh. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” In <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons, G. Pekhimenko, and C. De Sa, Vol. 6. Association for Computing Machinery, 2024.","ieee":"I. Markov, K. Alimohammadi, E. Frantar, and D.-A. Alistarh, “L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning,” in <i>Proceedings of Machine Learning and Systems </i>, Athens, Greece, 2024, vol. 6."},"year":"2024","status":"public"},{"month":"12","oa":1,"degree_awarded":"PhD","has_accepted_license":"1","author":[{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia"}],"status":"public","year":"2024","citation":{"mla":"Datler, Julia. <i>Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>.","apa":"Datler, J. (2024). <i>Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>","ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria.","chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>."},"date_created":"2025-01-07T10:23:12Z","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","doi_confirm":"1","keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"_id":"18766","language":[{"iso":"eng"}],"day":"30","OA_place":"publisher","das_tickbox":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-049-7"]},"supplementarymaterial":"no","file_date_updated":"2025-01-07T12:15:14Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_published":"2024-12-30T00:00:00Z","date_updated":"2026-10-02T11:21:19Z","article_processing_charge":"No","researchdata_availability":"yes","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses."}],"file":[{"date_updated":"2025-01-07T12:15:11Z","date_created":"2025-01-07T12:15:11Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18769","file_name":"PhD_thesis_Julia_Datler.docx","file_size":38814932,"checksum":"3e51cab327c754045c3d29c1a50cc9a9","creator":"jstanger","relation":"source_file"},{"access_level":"open_access","content_type":"application/pdf","date_updated":"2025-01-07T12:15:14Z","date_created":"2025-01-07T12:15:14Z","relation":"main_file","success":1,"file_id":"18770","file_size":12044865,"checksum":"22fabe5b97950bf852212f6edb555173","file_name":"PhD_thesis_Julia_Datler.pdf","creator":"jstanger"}],"supervisor":[{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"doi":"10.15479/at:ista:18766","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample.","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12334"},{"id":"14979","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA thesis"],"page":"106","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","publisher":"Institute of Science and Technology Austria","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"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:18766"},{"doi":"10.1038/s41594-023-01201-6","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","related_material":{"link":[{"url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"id":"18766","relation":"dissertation_contains","status":"public"}]},"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2024-07-22T11:27:22Z","date_created":"2024-07-22T11:27:22Z","relation":"main_file","file_id":"17307","success":1,"file_size":17485494,"file_name":"2024_NatureStrucBio_Datler.pdf","creator":"dernst","checksum":"bda7bf65d81455480efaed8ca293b0db"}],"publication":"Nature Structural & Molecular Biology","researchdata_availability":"yes","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","call_identifier":"FWF"}],"article_type":"original","abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","dataavailabilitystatement":"The electron microscopy density maps of the A10 trimer and the hexameric flower-shaped pore, the subtomogram average of the palisade layer and representative tomograms for complete viruses as well as isolated cores have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410, EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB 8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1), orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1) were used for protein sequence alignment. Source data for MS experiments are provided as Supplementary Information accompanying this manuscript.","license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","fulldoi":"https://doi.org/10.1038/s41594-023-01201-6","publisher":"Springer Nature","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"},"scopus_import":"1","corr_author":"1","oa_version":"Published Version","publication_status":"published","volume":31,"page":"1114-1123","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"year":"2024","OA_type":"hybrid","date_created":"2024-02-12T09:59:45Z","citation":{"ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>."},"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"status":"public","APC_amount":"11700 EUR","has_accepted_license":"1","oa":1,"author":[{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia"},{"first_name":"Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","full_name":"Hansen, Jesse","orcid":"0000-0001-7967-2085"},{"id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","first_name":"Andreas","full_name":"Thader, Andreas"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","last_name":"Bauer","full_name":"Bauer, Lukas W"},{"orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"month":"07","ddc":["570"],"date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:21:19Z","das_tickbox":"1","OA_place":"publisher","intvolume":"        31","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"supplementarymaterial":"yes","file_date_updated":"2024-07-22T11:27:22Z","_id":"14979","language":[{"iso":"eng"}],"isi":1,"pmid":1,"day":"01","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","keyword":["Molecular Biology","Structural Biology"]},{"file":[{"relation":"main_file","file_id":"18151","file_size":11219837,"checksum":"d3303724e8d3c91321d71bbad4062048","creator":"lgonzale","file_name":"louisa_thesis_draft__240904b.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-09-27T10:32:33Z","date_updated":"2024-09-27T10:32:33Z"},{"file_name":"louisa_thesis_draft__240904b.docx","checksum":"22e63f7f9014dffde2af7a47e7d1d014","file_size":43338677,"creator":"lgonzale","file_id":"18152","relation":"source_file","date_created":"2024-09-27T10:34:34Z","date_updated":"2024-09-27T10:34:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"}],"doi":"10.15479/at:ista:17850","supervisor":[{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"}],"related_material":{"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}],"record":[{"relation":"part_of_dissertation","status":"public","id":"11448"}]},"article_processing_charge":"No","researchdata_availability":"no","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"abstract":[{"lang":"eng","text":"Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design."}],"publisher":"Institute of Science and Technology Austria","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"},"type":"dissertation","ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:17850","alternative_title":["ISTA Thesis"],"page":"89","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","status":"public","year":"2024","citation":{"chicago":"Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>.","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria.","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024.","mla":"Gonzalez Somermeyer, Louisa. <i>Fitness Landscapes of Orthologous Green Fluorescent Proteins</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>.","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>","short":"L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024.","apa":"Gonzalez Somermeyer, L. (2024). <i>Fitness landscapes of orthologous green fluorescent proteins</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>"},"date_created":"2024-09-06T12:57:44Z","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"month":"09","has_accepted_license":"1","oa":1,"degree_awarded":"PhD","author":[{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383"}],"das_tickbox":"0","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","file_date_updated":"2024-09-27T10:34:34Z","ddc":["570"],"date_published":"2024-09-06T00:00:00Z","date_updated":"2026-10-02T11:21:41Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Fitness landscapes of orthologous green fluorescent proteins","doi_confirm":"1","language":[{"iso":"eng"}],"_id":"17850","day":"06"},{"title":"Tipping points of space debris in low earth orbit","keyword":["Sociology and Political Science"],"language":[{"iso":"eng"}],"_id":"14901","day":"11","issue":"1","das_tickbox":"0","file_date_updated":"2024-02-05T10:06:35Z","intvolume":"        18","publication_identifier":{"issn":["1875-0281"]},"supplementarymaterial":"yes","ddc":["550"],"date_published":"2024-01-11T00:00:00Z","date_updated":"2026-10-02T11:22:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"01","oa":1,"has_accepted_license":"1","author":[{"first_name":"Keiko","last_name":"Nomura","full_name":"Nomura, Keiko"},{"full_name":"Rella, Simon","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","last_name":"Rella"},{"full_name":"Merritt, Haily","first_name":"Haily","last_name":"Merritt"},{"first_name":"Mathieu","last_name":"Baltussen","full_name":"Baltussen, Mathieu"},{"last_name":"Bird","first_name":"Darcy","full_name":"Bird, Darcy"},{"full_name":"Tjuka, Annika","last_name":"Tjuka","first_name":"Annika"},{"last_name":"Falk","first_name":"Dan","full_name":"Falk, Dan"}],"status":"public","citation":{"chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” <i>International Journal of the Commons</i>. Ubiquity Press, 2024. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>.","ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","ieee":"K. Nomura <i>et al.</i>, “Tipping points of space debris in low earth orbit,” <i>International Journal of the Commons</i>, vol. 18, no. 1. Ubiquity Press, 2024.","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. 2024;18(1). doi:<a href=\"https://doi.org/10.5334/ijc.1275\">10.5334/ijc.1275</a>","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., &#38; Falk, D. (2024). Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. Ubiquity Press. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” <i>International Journal of the Commons</i>, vol. 18, no. 1, Ubiquity Press, 2024, doi:<a href=\"https://doi.org/10.5334/ijc.1275\">10.5334/ijc.1275</a>."},"date_created":"2024-01-30T11:58:02Z","year":"2024","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"volume":18,"publication_status":"published","oa_version":"Published Version","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":"Ubiquity Press","scopus_import":"1","fulldoi":"https://doi.org/10.5334/ijc.1275","type":"journal_article","quality_controlled":"1","article_processing_charge":"Yes","publication":"International Journal of the Commons","researchdata_availability":"no","article_type":"original","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"file":[{"date_created":"2024-02-05T10:06:35Z","date_updated":"2024-02-05T10:06:35Z","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14939","checksum":"b80ebc889033c365d8f8c05a0c655382","file_size":1305786,"file_name":"2023_IntJourCommons_Nomura.pdf","creator":"dernst","relation":"main_file"}],"doi":"10.5334/ijc.1275","acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study."},{"publication_status":"published","oa_version":"Published Version","corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"page":"111","alternative_title":["ISTA Thesis"],"ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:18076","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","type":"dissertation","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","abstract":[{"text":"The new era of Ge has opened up new possibilities in quantum computing. The maturity of Ge\r\nspin qubits is unquestioned, while hybrid semiconductor-superconductor Ge circuits are on track\r\nto enter the game. Gate-tunable transmons (gatemons) employing semiconductor Josephson\r\njunctions have recently emerged as building blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor from the Ge quantum well. The Josephson junction is then integrated\r\ninto an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults, combined with the recent advances in the spin qubit field, pave the way towards novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material.","lang":"eng"}],"project":[{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"researchdata_availability":"no","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17202"}]},"supervisor":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"doi":"10.15479/at:ista:18076","file":[{"date_created":"2024-09-18T14:13:01Z","date_updated":"2024-09-18T14:13:01Z","content_type":"application/pdf","access_level":"open_access","creator":"osagi","file_name":"OliverSagi_Thesis_pdfa.pdf","file_size":86679095,"checksum":"d01d0e2846c2f3ac5bb14d321554a4cd","success":1,"file_id":"18093","relation":"main_file"},{"content_type":"application/x-zip-compressed","access_level":"local","date_updated":"2024-09-19T09:20:33Z","date_created":"2024-09-18T14:14:02Z","relation":"source_file","checksum":"0543f473d509ee545f4ed3a56f742f4b","creator":"osagi","file_name":"Thesis_OliverSagi.zip","file_size":172098524,"file_id":"18094"}],"day":"18","language":[{"iso":"eng"}],"_id":"18076","doi_confirm":"1","title":"Hybrid circuits on planar Germanium","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-18T00:00:00Z","ddc":["539"],"date_updated":"2026-10-02T11:22:29Z","file_date_updated":"2024-09-19T09:20:33Z","supplementarymaterial":"yes","publication_identifier":{"issn":["2663-337X"]},"das_tickbox":"0","OA_place":"publisher","author":[{"full_name":"Sagi, Oliver","first_name":"Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"}],"has_accepted_license":"1","degree_awarded":"PhD","oa":1,"month":"09","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_created":"2024-09-16T12:58:36Z","citation":{"ama":"Sagi O. Hybrid circuits on planar Germanium. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18076\">10.15479/at:ista:18076</a>","short":"O. Sagi, Hybrid Circuits on Planar Germanium, Institute of Science and Technology Austria, 2024.","apa":"Sagi, O. (2024). <i>Hybrid circuits on planar Germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18076\">https://doi.org/10.15479/at:ista:18076</a>","mla":"Sagi, Oliver. <i>Hybrid Circuits on Planar Germanium</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18076\">10.15479/at:ista:18076</a>.","chicago":"Sagi, Oliver. “Hybrid Circuits on Planar Germanium.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18076\">https://doi.org/10.15479/at:ista:18076</a>.","ista":"Sagi O. 2024. Hybrid circuits on planar Germanium. Institute of Science and Technology Austria.","ieee":"O. Sagi, “Hybrid circuits on planar Germanium,” Institute of Science and Technology Austria, 2024."},"year":"2024","status":"public"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","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"},"scopus_import":"1","type":"conference","ec_funded":1,"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2024.11","alternative_title":["LIPIcs"],"volume":293,"page":"11:1-11:19","oa_version":"Published Version","publication_status":"published","file":[{"date_created":"2024-06-25T11:47:26Z","date_updated":"2024-06-25T11:47:26Z","content_type":"application/pdf","access_level":"open_access","creator":"cfillmor","file_name":"LIPIcs.SoCG.2024.11.pdf","checksum":"6a2ddc8b51aa58f197a8b294750f1f8d","file_size":20886142,"success":1,"file_id":"17171","relation":"main_file"}],"doi":"10.4230/LIPIcs.SoCG.2024.11","acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur.","quality_controlled":"1","article_processing_charge":"No","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"researchdata_availability":"no","publication":"40th International Symposium on Computational Geometry","abstract":[{"text":"In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately.","lang":"eng"}],"das_tickbox":"0","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773164"]},"supplementarymaterial":"no","intvolume":"       293","file_date_updated":"2024-06-25T11:47:26Z","ddc":["516"],"date_updated":"2026-10-02T11:23:43Z","date_published":"2024-06-06T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds","arxiv":1,"_id":"17170","language":[{"iso":"eng"}],"day":"06","status":"public","year":"2024","date_created":"2024-06-25T11:45:58Z","citation":{"chicago":"Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh, André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” In <i>40th International Symposium on Computational Geometry</i>, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>.","ista":"Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 11:1-11:19.","ieee":"D. Attali <i>et al.</i>, “Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 11:1-11:19.","ama":"Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>","short":"D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.","apa":"Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson, E. R., &#38; Wintraecken, M. (2024). Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">https://doi.org/10.4230/LIPIcs.SoCG.2024.11</a>","mla":"Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.11\">10.4230/LIPIcs.SoCG.2024.11</a>."},"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"external_id":{"arxiv":["2206.10485"]},"month":"06","oa":1,"has_accepted_license":"1","author":[{"full_name":"Attali, Dominique","last_name":"Attali","first_name":"Dominique"},{"full_name":"Kourimska, Hana","orcid":"0000-0001-7841-0091","first_name":"Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","last_name":"Kourimska"},{"full_name":"Fillmore, Christopher D","first_name":"Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore"},{"id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff","last_name":"Ghosh","first_name":"Ishika","full_name":"Ghosh, Ishika"},{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","first_name":"Elizabeth R"},{"last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs"}],"conference":{"start_date":"2024-06-11","location":"Athens, Greece","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry"}},{"status":"public","APC_amount":"6828 EUR","year":"2024","OA_type":"gold","citation":{"ieee":"O. Sagi <i>et al.</i>, “A gate tunable transmon qubit in planar Ge,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ista":"Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400.","chicago":"Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>.","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>","short":"O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>, vol. 15, 6400, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>."},"date_created":"2024-07-04T11:40:45Z","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"external_id":{"arxiv":["2403.16774"],"pmid":["39080279"],"isi":["001281271000022"]},"month":"07","has_accepted_license":"1","oa":1,"author":[{"full_name":"Sagi, Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver"},{"full_name":"Crippa, Alessandro","orcid":"0000-0002-2968-611X","first_name":"Alessandro","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco"},{"full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","first_name":"Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik"},{"first_name":"Levon","last_name":"Baghumyan","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","full_name":"Baghumyan, Levon"},{"first_name":"Giorgio","last_name":"Fabris","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","full_name":"Fabris, Giorgio"},{"orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","first_name":"Lucky"},{"orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"first_name":"Stefano","last_name":"Calcaterra","full_name":"Calcaterra, Stefano"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"OA_place":"publisher","das_tickbox":"1","publication_identifier":{"eissn":["2041-1723"]},"intvolume":"        15","supplementarymaterial":"yes","file_date_updated":"2024-08-05T08:38:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-30T00:00:00Z","ddc":["530"],"date_updated":"2026-10-02T11:23:23Z","title":"A gate tunable transmon qubit in planar Ge","arxiv":1,"language":[{"iso":"eng"}],"_id":"17202","pmid":1,"isi":1,"day":"30","file":[{"date_created":"2024-08-05T08:38:01Z","date_updated":"2024-08-05T08:38:01Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":1928001,"checksum":"ddf5361dcb6c543e2cea818501c09910","file_name":"2024_NatureComm_Sagi.pdf","success":1,"file_id":"17388","relation":"main_file"}],"doi":"10.1038/s41467-024-50763-6","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-024-53910-1"}],"record":[{"status":"public","relation":"dissertation_contains","id":"18076"},{"id":"17196","relation":"research_data","status":"public"}]},"acknowledgement":"We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support.","quality_controlled":"1","article_processing_charge":"Yes","publication":"Nature Communications","researchdata_availability":"yes","project":[{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"article_type":"original","abstract":[{"lang":"eng","text":"Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material."}],"publisher":"Springer Nature","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"},"scopus_import":"1","dataavailabilitystatement":"All experimental data included in this work will be available at the ISTA Research Data Repository","type":"journal_article","DOAJ_listed":"1","fulldoi":"https://doi.org/10.1038/s41467-024-50763-6","volume":15,"article_number":"6400","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published"},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"contributor":[{"orcid":"0000-0002-2968-611X","contributor_type":"project_member","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","last_name":"Crippa","first_name":"Alessandro"},{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","first_name":"Marco","contributor_type":"project_member"},{"contributor_type":"project_member","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian"},{"contributor_type":"project_member","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","last_name":"Baghumyan","first_name":"Levon"},{"last_name":"Fabris","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","first_name":"Giorgio","contributor_type":"project_member"},{"contributor_type":"project_member","id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","first_name":"Lucky"},{"first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","contributor_type":"project_member"},{"orcid":"0000-0001-8112-028X","contributor_type":"project_member","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"contributor_type":"project_member","last_name":"Calcaterra","first_name":"Stefano"},{"contributor_type":"project_member","last_name":"Chrastina","first_name":"Daniel"},{"last_name":"Isella","first_name":"Giovanni","contributor_type":"project_member"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","contributor_type":"supervisor"}],"oa_version":"Published Version","corr_author":"1","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"},"type":"research_data","fulldoi":"https://doi.org/10.15479/AT:ISTA:17196","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This .zip File contains the data for the figures presented in the main text and supplementary material of \"A gate tunable transmon qubit in planar Ge\" by O.Sagi et al. The measurements were done using Qcodes. The description of the files and the instructions on opening the data can be found in the Readme. An additional Jupyter Notebook is attached that walks through the data analysis."}],"project":[{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"}],"file":[{"date_updated":"2024-07-04T10:01:51Z","date_created":"2024-07-04T10:01:51Z","content_type":"application/octet-stream","access_level":"open_access","creator":"osagi","file_size":1960182,"file_name":"GeGatemon_DataAnalysis.ipynb","checksum":"a9f640a0b72a92171353f3ea14406f0b","file_id":"17197","success":1,"relation":"main_file"},{"date_created":"2024-07-04T10:01:50Z","date_updated":"2024-07-04T10:01:50Z","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","success":1,"file_id":"17198","creator":"osagi","file_name":"OlSa_Readme.pptx","checksum":"f0feec931233e8e845ade56165c1588f","file_size":34194,"relation":"main_file"},{"creator":"osagi","file_size":72939292,"checksum":"92bb11e3a508d736d01ff0738a1172c7","file_name":"Al_Transmon.zip","file_id":"17199","success":1,"relation":"main_file","date_created":"2024-07-04T10:11:16Z","date_updated":"2024-07-04T10:11:16Z","content_type":"application/x-zip-compressed","access_level":"open_access"},{"date_updated":"2024-07-04T10:11:40Z","date_created":"2024-07-04T10:11:40Z","content_type":"application/x-zip-compressed","access_level":"open_access","file_name":"Gatemon_RT_5nm_1.zip","file_size":465618029,"checksum":"871e96fe0ecc97581196e883045cd516","creator":"osagi","success":1,"file_id":"17200","relation":"main_file"},{"relation":"main_file","success":1,"file_id":"17201","file_size":281503513,"file_name":"Gatemon_RT_5nm_2.zip","creator":"osagi","checksum":"a3e141af90f0104b7269c8a72370848a","access_level":"open_access","content_type":"application/x-zip-compressed","date_updated":"2024-07-04T10:11:35Z","date_created":"2024-07-04T10:11:35Z"}],"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. 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Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and Technology Austria, 2024.","chicago":"Sagi, Oliver. “A Gate-Tunable Transmon in Planar Ge.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>.","ista":"Sagi O. 2024. A gate-tunable transmon in planar Ge, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>.","apa":"Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>","short":"O. Sagi, (2024).","ama":"Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>","mla":"Sagi, Oliver. <i>A Gate-Tunable Transmon in Planar Ge</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>."},"date_created":"2024-07-04T10:14:34Z"},{"doi":"10.1093/jxb/erae246","acknowledgement":"We thank other lab members for their critical comments on this manuscript. We also thank the editor and reviewers for their constructive comments to improve our manuscript. We apologize to authors whose important work we could not include due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural University (9232308314) and the Science and Technology Department of Jiangxi Province (20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province (20202ACB215002) to SYP.","file":[{"date_created":"2025-01-02T10:26:22Z","date_updated":"2025-01-02T10:26:22Z","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"18720","file_size":763097,"creator":"dernst","file_name":"2024_JourExperimentalBotany_Zhang.pdf","checksum":"91b9435ed0f6640809c7588df19abf2f","relation":"main_file"}],"publication":"Journal of Experimental Botany","researchdata_availability":"no","article_type":"original","abstract":[{"text":"The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted to (de)active transcriptional regulation, thus controlling auxin-associated developmental processes. 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Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erae246\">https://doi.org/10.1093/jxb/erae246</a>","mla":"Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 75, no. 18, erae246, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/jxb/erae246\">10.1093/jxb/erae246</a>."},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"status":"public","oa":1,"has_accepted_license":"1","author":[{"last_name":"Zhang","first_name":"Zilin","full_name":"Zhang, Zilin"},{"last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"last_name":"Peng","first_name":"Shuaiying","full_name":"Peng, Shuaiying"},{"first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"}],"external_id":{"pmid":["38794966"],"isi":["001270051200001"]},"month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:25:38Z","ddc":["580"],"date_published":"2024-09-27T00:00:00Z","OA_place":"publisher","das_tickbox":"0","supplementarymaterial":"no","intvolume":"        75","publication_identifier":{"issn":["0022-0957"]},"file_date_updated":"2025-01-02T10:26:22Z","_id":"17141","language":[{"iso":"eng"}],"issue":"18","isi":1,"pmid":1,"day":"27","title":"Slow and rapid auxin responses in Arabidopsis"},{"title":"Super-resolution expansion microscopy in plant roots","_id":"18689","language":[{"iso":"eng"}],"day":"21","OA_place":"repository","das_tickbox":"0","supplementarymaterial":"no","date_published":"2024-02-21T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:27:43Z","month":"02","oa":1,"author":[{"last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline"},{"full_name":"Inumella, Syamala","orcid":"0009-0002-5890-120X","last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","first_name":"Vitali","full_name":"Vistunou, Vitali"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","first_name":"Mojtaba"},{"full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","first_name":"Nathalie"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","first_name":"Jakob"},{"full_name":"Jahr, Wiebke","orcid":"0000-0003-0201-2315","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"status":"public","citation":{"mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. ."},"date_created":"2024-12-19T12:28:00Z","year":"2024","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"corr_author":"1","publication_status":"draft","oa_version":"Preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.21.581330"}],"ec_funded":1,"fulldoi":"https://doi.org/10.1101/2024.02.21.581330","type":"preprint","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_processing_charge":"No","researchdata_availability":"no","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","_id":"269B5B22-B435-11E9-9278-68D0E5697425"}],"publication":"bioRxiv","abstract":[{"lang":"eng","text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores."}],"doi":"10.1101/2024.02.21.581330","related_material":{"record":[{"id":"19003","status":"public","relation":"later_version"},{"id":"18681","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript."},{"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"citation":{"ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>.","ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024.","apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>"},"date_created":"2024-12-19T02:30:39Z","year":"2024","status":"public","author":[{"orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","degree_awarded":"PhD","month":"12","date_updated":"2026-10-02T11:27:43Z","date_published":"2024-12-20T00:00:00Z","ddc":["600","570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2026-07-28T08:33:51Z","publication_identifier":{"isbn":["978-3-99078-048-0"],"issn":["2663-337X"]},"supplementarymaterial":"unclear","das_tickbox":"1","OA_place":"publisher","day":"20","language":[{"iso":"eng"}],"_id":"18681","doi_confirm":"1","title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11160"},{"id":"18688","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18689"},{"status":"public","relation":"part_of_dissertation","id":"18677"}]},"doi":"10.15479/at:ista:18681","supervisor":[{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G"}],"file":[{"date_created":"2024-12-20T10:23:17Z","date_updated":"2024-12-20T10:31:37Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18699","creator":"mtavakol","file_name":"Thesis_Mojtaba Tavakoli_.docx","checksum":"b61651d417cafddd740a8528f46068c5","file_size":118593521,"relation":"source_file"},{"date_updated":"2026-07-28T08:33:51Z","date_created":"2024-12-20T10:25:12Z","embargo":"2027-08-01","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","creator":"mtavakol","checksum":"c80bcfd1a34c23afc3538052325283e5","file_name":"Thesis_Mojtaba Tavakoli_.pdf","file_size":63885521,"file_id":"18700","relation":"main_file"}],"project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"researchdata_availability":"unclear","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/at:ista:18681","type":"dissertation","OA_embargo":"20","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","publication_status":"published","oa_version":"Published Version","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"page":"230","alternative_title":["ISTA Thesis"]},{"year":"2024","date_created":"2024-12-18T14:48:24Z","citation":{"ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>.","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” <i>bioRxiv</i>. .","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.)."},"department":[{"_id":"GaNo"},{"_id":"JoDa"}],"status":"public","oa":1,"author":[{"first_name":"Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"},{"last_name":"Januszewski","first_name":"Michał","full_name":"Januszewski, Michał"},{"first_name":"Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","full_name":"Vistunou, Vitali"},{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","first_name":"Jakob"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"first_name":"Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira","full_name":"Oliveira, Bárbara"},{"last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","full_name":"Cenameri, Alban"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"last_name":"Jain","first_name":"Viren","full_name":"Jain, Viren"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-08T00:00:00Z","date_updated":"2026-10-02T11:27:43Z","das_tickbox":"0","OA_place":"repository","supplementarymaterial":"no","language":[{"iso":"eng"}],"_id":"18677","day":"08","title":"Light-microscopy based dense connectomic reconstruction of mammalian brain tissue","doi":"10.1101/2024.03.01.582884","acknowledgement":"We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n","related_material":{"record":[{"relation":"later_version","status":"public","id":"19704"},{"id":"18674","relation":"dissertation_contains","status":"public"},{"id":"18681","relation":"dissertation_contains","status":"public"}]},"project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF"}],"publication":"bioRxiv","researchdata_availability":"no","abstract":[{"text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner.","lang":"eng"}],"article_processing_charge":"No","type":"preprint","ec_funded":1,"fulldoi":"https://doi.org/10.1101/2024.03.01.582884","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.03.01.582884"}],"corr_author":"1","oa_version":"Preprint","publication_status":"draft","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"}]},{"corr_author":"1","publication_status":"published","oa_version":"Published Version","page":"161","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"fulldoi":"https://doi.org/10.15479/at:ista:17133","type":"dissertation","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","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"researchdata_availability":"no","abstract":[{"text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing.","lang":"eng"}],"article_processing_charge":"No","supervisor":[{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"doi":"10.15479/at:ista:17133","related_material":{"record":[{"id":"13227","relation":"part_of_dissertation","status":"public"},{"id":"9928","relation":"part_of_dissertation","status":"public"},{"id":"8755","relation":"part_of_dissertation","status":"public"}]},"file":[{"relation":"main_file","file_id":"17137","file_size":28370759,"checksum":"258c353d47fa37ea63ea43b1e10a34a0","creator":"fhassani","file_name":"Thesis_main_final.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-06-12T07:53:19Z","date_updated":"2024-06-20T11:52:22Z"},{"relation":"source_file","checksum":"deffa5d0db88093f74812fa71520d5e1","file_size":445735,"file_name":"Thesis_main.tex","creator":"fhassani","file_id":"17138","content_type":"text/x-tex","access_level":"closed","date_updated":"2024-06-12T07:54:27Z","date_created":"2024-06-12T07:54:27Z"}],"_id":"17133","language":[{"iso":"eng"}],"day":"11","doi_confirm":"1","title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","keyword":["Quantum information","Qubits","Superconducting devices"],"date_published":"2024-06-11T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:28:17Z","ddc":["530"],"OA_place":"publisher","das_tickbox":"0","file_date_updated":"2024-06-20T11:52:22Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"supplementarymaterial":"no","oa":1,"has_accepted_license":"1","degree_awarded":"PhD","author":[{"orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"}],"month":"06","date_created":"2024-06-11T18:20:05Z","citation":{"ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>"},"year":"2024","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"status":"public"},{"article_type":"original","abstract":[{"lang":"eng","text":"The physical conditions giving rise to high escape fractions of ionizing radiation (LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization – are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α emitters at 2.9 &amp;lt; z &amp;lt; 6.7, we compare stacked rest-frame UV spectra of candidates for LyC leakers and non-leakers selected based on their Ly α profiles. We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666, [Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640 (∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533 emission, revealing substantial amounts of neutral hydrogen off the line of sight; (iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75) , signalling the presence of low column density channels in the ISM. In contrast, the stacks with broad, asymmetric Ly α profiles with large peak separation show weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen column densities. Our results suggest that C iv/C iii] might be sensitive to the physical conditions that govern LyC photon escape, providing a promising tool for identification of ionizing sources among star-forming galaxies in the epoch of reionization."}],"researchdata_availability":"upon request","publication":"Monthly Notices of the Royal Astronomical Society","article_processing_charge":"Yes","quality_controlled":"1","acknowledgement":"We thank the anonymous referee for the constructive feedback that helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions. We also thank the organizers and participants of the 24th MUSE Science Busy Week in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty of Science of the University of Geneva. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant number 200020_207349 and SNSF Professorship grant number 190079. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant number 140. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source software packages and we are thankful to the respective authors for sharing their work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB (Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).","doi":"10.1093/mnras/stad3853","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2024-01-23T12:30:45Z","date_created":"2024-01-23T12:30:45Z","relation":"main_file","file_name":"2024_MNAstronomSoc_Kramarenko.pdf","checksum":"9d02df4035c4951cf63dee0db1e462e9","file_size":4521738,"creator":"dernst","success":1,"file_id":"14879"}],"oa_version":"Published Version","publication_status":"published","corr_author":"1","volume":527,"page":"9853-9871","type":"journal_article","DOAJ_listed":"1","fulldoi":"https://doi.org/10.1093/mnras/stad3853","dataavailabilitystatement":"Raw MUSE data cubes are available from the ESO Science Archive Facility.2 The MUSE-Wide data from the first data release, which covers 44 fields in GOODS-S/CDFS, are available on the MUSE-Wide project page.3 The MUSE HUDF data from the second data release are available via the Advanced MUSE Data products (AMUSED) web interface.4 The stacked spectra in a machine-readable format and the spectral line measurements will be shared upon request to the corresponding author.","scopus_import":"1","publisher":"Oxford University Press","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"},"author":[{"last_name":"Kramarenko","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","first_name":"Ivan","orcid":"0000-0001-5346-6048","full_name":"Kramarenko, Ivan"},{"full_name":"Kerutt, J","first_name":"J","last_name":"Kerutt"},{"full_name":"Verhamme, A","last_name":"Verhamme","first_name":"A"},{"last_name":"Oesch","first_name":"P A","full_name":"Oesch, P A"},{"last_name":"Barrufet","first_name":"L","full_name":"Barrufet, L"},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"full_name":"Kusakabe, H","last_name":"Kusakabe","first_name":"H"},{"full_name":"Goovaerts, I","first_name":"I","last_name":"Goovaerts"},{"full_name":"Thai, T T","first_name":"T T","last_name":"Thai"}],"has_accepted_license":"1","oa":1,"month":"02","external_id":{"isi":["001133672400004"],"arxiv":["2305.07044"]},"department":[{"_id":"GradSch"},{"_id":"JoMa"}],"year":"2024","date_created":"2024-01-22T08:22:17Z","citation":{"ieee":"I. Kramarenko <i>et al.</i>, “Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024.","chicago":"Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties of MUSE Ly α Emitters at <i>z</i> ≳ 3 to Lyman Continuum Escape.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stad3853\">https://doi.org/10.1093/mnras/stad3853</a>.","ista":"Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871.","mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at <i>z</i> ≳ 3 to Lyman Continuum Escape.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:<a href=\"https://doi.org/10.1093/mnras/stad3853\">10.1093/mnras/stad3853</a>.","short":"I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee, H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical Society 527 (2024) 9853–9871.","apa":"Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee, J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stad3853\">https://doi.org/10.1093/mnras/stad3853</a>","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;527(4):9853-9871. doi:<a href=\"https://doi.org/10.1093/mnras/stad3853\">10.1093/mnras/stad3853</a>"},"status":"public","issue":"4","isi":1,"day":"01","_id":"14852","language":[{"iso":"eng"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"arxiv":1,"title":"Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape","ddc":["520"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-02-01T00:00:00Z","date_updated":"2026-10-02T11:29:18Z","intvolume":"       527","supplementarymaterial":"no","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"file_date_updated":"2024-01-23T12:30:45Z","das_tickbox":"1"},{"article_processing_charge":"No","quality_controlled":"1","article_type":"original","abstract":[{"text":"Matrix games are the most basic model in game theory, and yet robustness with respect to small perturbations of the matrix entries is not fully understood. In this paper, we introduce value positivity and uniform value positivity, two properties that refine the notion of optimality in the context of polynomially perturbed matrix games. The first concept captures how the value depends on the perturbation parameter, and the second consists of the existence of a fixed strategy that guarantees the value of the unperturbed matrix game for every sufficiently small positive parameter. We provide polynomial-time algorithms to check whether a polynomially perturbed matrix game satisfies these properties. We further provide the functional form for a parameterized optimal strategy and the value function. Finally, we translate our results to linear programming and stochastic games, where value positivity is related to the existence of robust solutions.","lang":"eng"}],"researchdata_availability":"unclear","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"publication":"Mathematics of Operations Research","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20234"}]},"acknowledgement":"This research was supported by Fondation CFM pour la Recherche, the H2020 European Research Council [Grant ERC-CoG-863818 (ForM-SMArt)], the Austrian Science Fund [Grant 10.55776/COE12], ANID Chile [Grant ACT210005], and Agence Nationale de la Recherche [Grant ANR-21-CE40-0020].","doi":"10.1287/moor.2022.0332","volume":50,"page":"2433-3282","oa_version":"None","publication_status":"published","corr_author":"1","scopus_import":"1","publisher":"Institute for Operations Research and the Management Sciences","type":"journal_article","ec_funded":1,"fulldoi":"https://doi.org/10.1287/moor.2022.0332","month":"10","external_id":{"isi":["001328875900001"]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Oliu-Barton, Miquel","first_name":"Miquel","last_name":"Oliu-Barton"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","first_name":"Raimundo J","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"}],"status":"public","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"OA_type":"closed access","year":"2024","citation":{"mla":"Chatterjee, Krishnendu, et al. “Value-Positivity for Matrix Games.” <i>Mathematics of Operations Research</i>, vol. 50, no. 4, Institute for Operations Research and the Management Sciences, 2024, pp. 2433–3282, doi:<a href=\"https://doi.org/10.1287/moor.2022.0332\">10.1287/moor.2022.0332</a>.","apa":"Chatterjee, K., Oliu-Barton, M., &#38; Saona Urmeneta, R. J. (2024). Value-positivity for matrix games. <i>Mathematics of Operations Research</i>. Institute for Operations Research and the Management Sciences. <a href=\"https://doi.org/10.1287/moor.2022.0332\">https://doi.org/10.1287/moor.2022.0332</a>","short":"K. Chatterjee, M. Oliu-Barton, R.J. Saona Urmeneta, Mathematics of Operations Research 50 (2024) 2433–3282.","ama":"Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. Value-positivity for matrix games. <i>Mathematics of Operations Research</i>. 2024;50(4):2433-3282. doi:<a href=\"https://doi.org/10.1287/moor.2022.0332\">10.1287/moor.2022.0332</a>","ieee":"K. Chatterjee, M. Oliu-Barton, and R. J. Saona Urmeneta, “Value-positivity for matrix games,” <i>Mathematics of Operations Research</i>, vol. 50, no. 4. Institute for Operations Research and the Management Sciences, pp. 2433–3282, 2024.","chicago":"Chatterjee, Krishnendu, Miquel Oliu-Barton, and Raimundo J Saona Urmeneta. “Value-Positivity for Matrix Games.” <i>Mathematics of Operations Research</i>. Institute for Operations Research and the Management Sciences, 2024. <a href=\"https://doi.org/10.1287/moor.2022.0332\">https://doi.org/10.1287/moor.2022.0332</a>.","ista":"Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. 2024. Value-positivity for matrix games. Mathematics of Operations Research. 50(4), 2433–3282."},"date_created":"2024-10-09T07:02:20Z","title":"Value-positivity for matrix games","issue":"4","isi":1,"day":"01","language":[{"iso":"eng"}],"_id":"18266","intvolume":"        50","publication_identifier":{"eissn":["1526-5471"],"issn":["0364-765X"]},"supplementarymaterial":"unclear","das_tickbox":"0","date_published":"2024-10-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:30:08Z"},{"article_processing_charge":"No","quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"We provide a dynamical study of a model of multiplicative perturbation of a unitary matrix introduced by Fyodorov. In particular, we identify a flow of deterministic domains that bound the spectrum with high probability, separating the outlier from the typical eigenvalues at all sub-critical timescales. These results are obtained under generic assumptions on U that hold for a variety of unitary random matrix models."}],"publication":"Random Matrices: Theory and Applications","project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"researchdata_availability":"unclear","related_material":{"record":[{"id":"17164","relation":"dissertation_contains","status":"public"}]},"doi":"10.1142/s2010326324500072","volume":13,"article_number":"2450007","oa_version":"Preprint","publication_status":"published","corr_author":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2212.14638"}],"publisher":"World Scientific Publishing","type":"journal_article","fulldoi":"https://doi.org/10.1142/s2010326324500072","ec_funded":1,"month":"04","external_id":{"isi":["001229295200002"],"arxiv":["2212.14638"]},"author":[{"orcid":"0000-0001-6892-8137","full_name":"Dubach, Guillaume","last_name":"Dubach","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume"},{"full_name":"Reker, Jana","first_name":"Jana","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","last_name":"Reker"}],"oa":1,"status":"public","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"year":"2024","OA_type":"green","date_created":"2024-05-23T08:31:57Z","citation":{"mla":"Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” <i>Random Matrices: Theory and Applications</i>, vol. 13, no. 2, 2450007, World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/s2010326324500072\">10.1142/s2010326324500072</a>.","ama":"Dubach G, Reker J. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. <i>Random Matrices: Theory and Applications</i>. 2024;13(2). doi:<a href=\"https://doi.org/10.1142/s2010326324500072\">10.1142/s2010326324500072</a>","apa":"Dubach, G., &#38; Reker, J. (2024). Dynamics of a rank-one multiplicative perturbation of a unitary matrix. <i>Random Matrices: Theory and Applications</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s2010326324500072\">https://doi.org/10.1142/s2010326324500072</a>","short":"G. Dubach, J. Reker, Random Matrices: Theory and Applications 13 (2024).","ista":"Dubach G, Reker J. 2024. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. Random Matrices: Theory and Applications. 13(2), 2450007.","chicago":"Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” <i>Random Matrices: Theory and Applications</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/s2010326324500072\">https://doi.org/10.1142/s2010326324500072</a>.","ieee":"G. Dubach and J. Reker, “Dynamics of a rank-one multiplicative perturbation of a unitary matrix,” <i>Random Matrices: Theory and Applications</i>, vol. 13, no. 2. World Scientific Publishing, 2024."},"arxiv":1,"title":"Dynamics of a rank-one multiplicative perturbation of a unitary matrix","issue":"2","isi":1,"day":"01","language":[{"iso":"eng"}],"_id":"17047","publication_identifier":{"eissn":["2010-3271"],"issn":["2010-3263"]},"supplementarymaterial":"unclear","intvolume":"        13","OA_place":"repository","das_tickbox":"0","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-04-01T00:00:00Z","date_updated":"2026-10-02T11:31:29Z"},{"day":"01","language":[{"iso":"eng"}],"_id":"18891","arxiv":1,"title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:34:35Z","ddc":["000"],"date_published":"2024-12-01T00:00:00Z","file_date_updated":"2025-02-04T08:11:25Z","supplementarymaterial":"no","intvolume":"        37","das_tickbox":"0","OA_place":"publisher","conference":{"start_date":"2024-12-16","location":"Vancouver, Canada","end_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems"},"author":[{"full_name":"Súkeník, Peter","first_name":"Peter","last_name":"Súkeník","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"oa":1,"has_accepted_license":"1","month":"12","external_id":{"arxiv":["2405.14468"]},"department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"date_created":"2025-01-27T11:15:18Z","citation":{"mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","apa":"Súkeník, P., Lampert, C., &#38; Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024."},"OA_type":"gold","year":"2024","status":"public","publication_status":"published","oa_version":"Published Version","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"alternative_title":["Advances in Neural Information Processing Systems"],"volume":37,"type":"conference","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":"Neural Information Processing Systems Foundation","abstract":[{"text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent.","lang":"eng"}],"publication":"38th Annual Conference on Neural Information Processing Systems","researchdata_availability":"no","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"article_processing_charge":"No","quality_controlled":"1","acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","file":[{"date_created":"2025-02-04T08:11:25Z","date_updated":"2025-02-04T08:11:25Z","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"18989","creator":"dernst","file_name":"2024_NeurIPS_Sukenik.pdf","file_size":1784118,"checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","relation":"main_file"}]},{"month":"11","oa":1,"degree_awarded":"PhD","has_accepted_license":"1","author":[{"full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"}],"status":"public","citation":{"chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>."},"date_created":"2024-11-06T21:25:37Z","year":"2024","OA_type":"gold","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"doi_confirm":"1","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","language":[{"iso":"eng"}],"_id":"18515","day":"07","das_tickbox":"1","OA_place":"publisher","file_date_updated":"2024-11-07T10:59:42Z","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-11-07T00:00:00Z","ddc":["576"],"date_updated":"2026-10-02T11:36:48Z","article_processing_charge":"No","project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"researchdata_availability":"yes","abstract":[{"text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations.","lang":"eng"}],"file":[{"relation":"main_file","success":1,"file_id":"18519","creator":"psurendr","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","checksum":"c32cf7bc75748d9c551d8eb70178bbec","file_size":37019760,"access_level":"open_access","content_type":"application/pdf","date_created":"2024-11-07T10:59:29Z","date_updated":"2024-11-07T10:59:29Z"},{"relation":"source_file","file_id":"18520","file_size":41198857,"creator":"psurendr","file_name":"PhD Thesis- Parvathy_071124.zip","checksum":"4417e02d54084d89e75734e18caaa96d","access_level":"closed","content_type":"application/zip","date_created":"2024-11-07T10:59:42Z","date_updated":"2024-11-07T10:59:42Z"}],"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"doi":"10.15479/at:ista:18515","acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","page":"219","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","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","fulldoi":"https://doi.org/10.15479/at:ista:18515","type":"dissertation"},{"das_tickbox":"0","OA_place":"publisher","supplementarymaterial":"yes","publication_identifier":{"eissn":["2643-1564"]},"intvolume":"         6","file_date_updated":"2024-09-23T09:46:20Z","date_published":"2024-09-10T00:00:00Z","date_updated":"2026-10-02T11:36:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["530"],"title":"Theory of angular momentum transfer from light to molecules","arxiv":1,"_id":"18087","language":[{"iso":"eng"}],"issue":"3","day":"10","status":"public","APC_amount":"3028,31 EUR","OA_type":"gold","year":"2024","citation":{"ieee":"M. Maslov, G. Koutentakis, M. Hrast, O. H. Heckl, and M. Lemeshko, “Theory of angular momentum transfer from light to molecules,” <i>Physical Review Research</i>, vol. 6, no. 3. American Physical Society, 2024.","chicago":"Maslov, Mikhail, Georgios Koutentakis, Mateja Hrast, Oliver H. Heckl, and Mikhail Lemeshko. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>.","ista":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. 2024. Theory of angular momentum transfer from light to molecules. Physical Review Research. 6(3), 033277.","mla":"Maslov, Mikhail, et al. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>, vol. 6, no. 3, 033277, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>.","short":"M. Maslov, G. Koutentakis, M. Hrast, O.H. Heckl, M. Lemeshko, Physical Review Research 6 (2024).","apa":"Maslov, M., Koutentakis, G., Hrast, M., Heckl, O. H., &#38; Lemeshko, M. (2024). Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>","ama":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. 2024;6(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>"},"date_created":"2024-09-18T11:43:16Z","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"external_id":{"arxiv":["2310.00095"]},"month":"09","has_accepted_license":"1","oa":1,"author":[{"last_name":"Maslov","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Maslov, Mikhail","orcid":"0000-0003-4074-2570"},{"full_name":"Koutentakis, Georgios","last_name":"Koutentakis","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios"},{"full_name":"Hrast, Mateja","last_name":"Hrast","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","first_name":"Mateja"},{"first_name":"Oliver H.","last_name":"Heckl","full_name":"Heckl, Oliver H."},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"publisher":"American Physical Society","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"},"scopus_import":"1","type":"journal_article","DOAJ_listed":"1","fulldoi":"https://doi.org/10.1103/physrevresearch.6.033277","ec_funded":1,"volume":6,"article_number":"033277","corr_author":"1","oa_version":"Published Version","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-09-23T09:46:20Z","date_updated":"2024-09-23T09:46:20Z","relation":"main_file","success":1,"file_id":"18125","checksum":"8f744d94956a1683b473b1cf9b411a37","file_name":"2024_PhysicalReviewResearch_Maslov.pdf","creator":"dernst","file_size":1563824}],"doi":"10.1103/physrevresearch.6.033277","acknowledgement":"We are grateful to Emilio Pisanty and Philipp Lunt for valuable discussions. This research was funded wholly or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). O.H.H. acknowledges support by the Austrian Science Fund (FWF) [10.55776/P36040]. Furthermore, the financial support by the Austrian Federal Ministry for Digital and Economic Affairs, the National Foundation for Research, Technology and Development, and the Christian Doppler Research Association is gratefully acknowledged.","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19048"}]},"quality_controlled":"1","article_processing_charge":"Yes","publication":"Physical Review Research","project":[{"_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3","name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"researchdata_availability":"no","article_type":"original","abstract":[{"lang":"eng","text":"We present a theory describing the interaction of structured light, such as light carrying orbital angular momentum, with molecules. The light-matter interaction Hamiltonian we derive is expressed through couplings between spherical gradients of the electric field and the (transition) electric multipole moments of a particle of any nontrivial rotation point group. Our model can therefore accommodate an arbitrary complexity of the molecular and electric field structure, and it can be straightforwardly extended to atoms or nanostructures. Applying this framework to rovibrational spectroscopy of molecules, we uncover the general mechanism of angular momentum exchange between the spin and orbital angular momenta of light, molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions that are considered forbidden in the case of nonhelical light. We discuss the experimental requirements for the observation of these forbidden transitions in state-of-the-art spatially resolved spectroscopy measurements."}]}]