[{"day":"24","ddc":["500"],"type":"dissertation","year":"2023","supervisor":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert"}],"file":[{"relation":"source_file","date_created":"2023-08-24T13:02:49Z","access_level":"closed","creator":"cchlebak","file_size":15501411,"content_type":"application/x-zip-compressed","embargo_to":"open_access","date_updated":"2024-02-26T23:30:03Z","checksum":"453caf851d75c3478c10ed09bd242a91","file_name":"documents-export-2023-08-24.zip","file_id":"14227"},{"relation":"main_file","date_created":"2023-08-24T13:03:42Z","access_level":"open_access","creator":"cchlebak","file_size":6854783,"content_type":"application/pdf","date_updated":"2024-02-26T23:30:03Z","embargo":"2024-02-25","file_name":"thesis_pdf_a.pdf","checksum":"7349d29963d6695e555e171748648d9a","file_id":"14228"}],"date_published":"2023-08-24T00:00:00Z","month":"08","title":"Generalizing medial axes with homology switches","citation":{"short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226."},"file_date_updated":"2024-02-26T23:30:03Z","author":[{"orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R"}],"abstract":[{"lang":"eng","text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes."}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"MS","publication_status":"published","oa":1,"publication_identifier":{"issn":["2791-4585"]},"date_created":"2023-08-24T13:01:18Z","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/at:ista:14226","alternative_title":["ISTA Master's Thesis"],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"OA_place":"publisher","status":"public","page":"43","date_updated":"2026-04-07T14:02:30Z","article_processing_charge":"No","_id":"14226","doi":"10.15479/at:ista:14226"},{"ddc":["570"],"issue":"6","day":"01","publication":"Molecular Ecology","intvolume":" 32","article_type":"original","type":"journal_article","year":"2023","month":"03","title":"On the origin and structure of haplotype blocks","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","date_published":"2023-03-01T00:00:00Z","file":[{"success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2023-08-16T08:15:41Z","content_type":"application/pdf","file_size":7144607,"date_updated":"2023-08-16T08:15:41Z","file_id":"14062","file_name":"2023_MolecularEcology_Shipilina.pdf","checksum":"b10e0f8fa3dc4d72aaf77a557200978a"}],"corr_author":"1","pmid":1,"abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"author":[{"full_name":"Shipilina, Daria","last_name":"Shipilina","first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226"},{"last_name":"Pal","full_name":"Pal, Arka","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"file_date_updated":"2023-08-16T08:15:41Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20694"}]},"citation":{"ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793"},"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"oa":1,"isi":1,"has_accepted_license":"1","date_created":"2023-01-12T12:09:17Z","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":32,"fulldoi":"https://doi.org/10.1111/mec.16793","external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"department":[{"_id":"NiBa"}],"status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-10-01T22:30:39Z","scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"page":"1441-1457","_id":"12159","doi":"10.1111/mec.16793","article_processing_charge":"Yes (via OA deal)"},{"supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose"}],"year":"2023","file":[{"relation":"source_file","date_created":"2023-11-20T09:18:51Z","access_level":"closed","creator":"ngnyliuk","embargo_to":"open_access","file_size":20824903,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_id":"14567","date_updated":"2024-11-23T23:30:38Z"},{"date_created":"2023-11-20T09:23:11Z","access_level":"open_access","creator":"ngnyliuk","relation":"main_file","date_updated":"2024-11-23T23:30:38Z","embargo":"2024-11-23","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","file_id":"14568","file_size":24871844,"content_type":"application/pdf"}],"date_published":"2023-11-10T00:00:00Z","month":"11","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","day":"10","ddc":["570"],"type":"dissertation","publication_status":"published","oa":1,"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"citation":{"ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510."},"file_date_updated":"2024-11-23T23:30:38Z","related_material":{"record":[{"status":"public","id":"14591","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9887","status":"public"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh"}],"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. "}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/at:ista:14510","alternative_title":["ISTA Thesis"],"date_created":"2023-11-10T09:10:06Z","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"page":"180","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"date_updated":"2026-10-01T22:30:51Z","ec_funded":1,"article_processing_charge":"No","_id":"14510","doi":"10.15479/at:ista:14510","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"OA_place":"publisher","status":"public"},{"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","month":"10","date_published":"2023-10-10T00:00:00Z","year":"2023","fulldoi":"https://doi.org/10.1101/2023.10.09.561523","language":[{"iso":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.09.561523","open_access":"1"}],"type":"preprint","day":"10","publication":"bioRxiv","date_created":"2023-11-22T10:17:49Z","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"_id":"14591","doi":"10.1101/2023.10.09.561523","article_processing_charge":"No","ec_funded":1,"oa":1,"date_updated":"2026-10-01T22:30:50Z","publication_status":"draft","status":"public","OA_place":"repository","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh"},{"full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843"},{"last_name":"Nagel","full_name":"Nagel, Marie-Kristin","first_name":"Marie-Kristin"},{"last_name":"Monzer","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline"},{"last_name":"Hlavata","full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria"},{"first_name":"Erika","full_name":"Isono, Erika","last_name":"Isono"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"15330","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"14510","status":"public"}]},"citation":{"mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.)."}},{"citation":{"apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"11943","status":"public"},{"relation":"part_of_dissertation","id":"11950","status":"public"}]},"file_date_updated":"2023-07-27T22:30:54Z","author":[{"last_name":"Michalska","full_name":"Michalska, Julia M","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"}],"abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_status":"published","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-026-8"]},"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"day":"09","ddc":["610"],"type":"dissertation","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl"}],"year":"2023","file":[{"relation":"main_file","creator":"cchlebak","access_level":"open_access","date_created":"2023-01-31T15:11:42Z","content_type":"application/pdf","file_size":41771714,"file_id":"12471","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_name":"20230109_PhD_thesis_JM_final.pdf","embargo":"2023-07-09","date_updated":"2023-07-27T22:30:54Z"},{"date_updated":"2023-07-10T22:30:04Z","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_name":"20230109_PhD_thesis_JM_final.docx","file_id":"12472","file_size":66983464,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2023-01-31T15:11:51Z","access_level":"closed","creator":"cchlebak","relation":"source_file"}],"date_published":"2023-01-09T00:00:00Z","month":"01","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"status":"public","page":"201","date_updated":"2026-07-06T12:50:45Z","ec_funded":1,"article_processing_charge":"No","_id":"12470","doi":"10.15479/at:ista:12470","date_created":"2023-01-31T15:10:53Z","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/at:ista:12470","alternative_title":["ISTA Thesis"]},{"type":"journal_article","article_type":"original","intvolume":" 14","ddc":["530"],"publication":"Nature Communications","day":"24","month":"05","title":"Tunable directional photon scattering from a pair of superconducting qubits","date_published":"2023-05-24T00:00:00Z","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","file":[{"file_size":1654389,"content_type":"application/pdf","date_updated":"2023-06-06T07:31:20Z","file_name":"2023_NaturePhysics_Redchenko.pdf","checksum":"a857df40f0882859c48a1ff1e2001ec2","file_id":"13123","relation":"main_file","success":1,"date_created":"2023-06-06T07:31:20Z","creator":"dernst","access_level":"open_access"}],"year":"2023","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"corr_author":"1","pmid":1,"file_date_updated":"2023-06-06T07:31:20Z","citation":{"ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023.","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6."},"related_material":{"record":[{"status":"public","id":"13124","relation":"research_data"},{"status":"public","id":"19533","relation":"dissertation_contains"}]},"author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"first_name":"Alexander V.","full_name":"Poshakinskiy, Alexander V.","last_name":"Poshakinskiy"},{"full_name":"Sett, Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7641-8348","first_name":"Riya"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0009-0005-0878-3032","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"full_name":"Poddubny, Alexander N.","last_name":"Poddubny","first_name":"Alexander N."},{"last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"publication_identifier":{"eissn":["2041-1723"]},"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"arxiv":1,"oa":1,"quality_controlled":"1","publication_status":"published","oa_version":"Published Version","language":[{"iso":"eng"}],"has_accepted_license":"1","isi":1,"date_created":"2023-06-04T22:01:02Z","volume":14,"external_id":{"pmid":["37225689"],"isi":["001001099700002"],"arxiv":["2205.03293"]},"fulldoi":"https://doi.org/10.1038/s41467-023-38761-6","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"2998","department":[{"_id":"JoFi"}],"_id":"13117","doi":"10.1038/s41467-023-38761-6","ec_funded":1,"article_processing_charge":"No","date_updated":"2026-10-01T22:31:05Z","scopus_import":"1"},{"page":"142","date_updated":"2026-09-14T08:36:32Z","article_processing_charge":"No","ec_funded":1,"_id":"14622","doi":"10.15479/at:ista:14622","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"OA_place":"publisher","status":"public","fulldoi":"https://doi.org/10.15479/at:ista:14622","alternative_title":["ISTA Thesis"],"date_created":"2023-11-28T10:58:13Z","has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"publication_status":"published","oa":1,"project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IBM PhD Nomination Fellowship - Stefan Sack"},{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"13125"},{"relation":"part_of_dissertation","status":"public","id":"11471"},{"id":"9760","status":"public","relation":"part_of_dissertation"}]},"citation":{"apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria."},"file_date_updated":"2024-11-30T23:30:03Z","author":[{"full_name":"Sack, Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan"}],"abstract":[{"text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation.","lang":"eng"}],"corr_author":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","doi_confirm":"1","supervisor":[{"full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"year":"2023","file":[{"creator":"ssack","access_level":"open_access","date_created":"2023-11-30T15:53:10Z","relation":"main_file","embargo":"2024-11-30","date_updated":"2024-11-30T23:30:03Z","file_id":"14635","file_name":"PhD_Thesis.pdf","checksum":"068fd3570506ec42b2faa390de784bc4","content_type":"application/pdf","file_size":11947523},{"content_type":"application/zip","file_size":18422964,"embargo_to":"open_access","date_updated":"2024-11-30T23:30:03Z","file_id":"14636","file_name":"PhD Thesis (1).zip","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","relation":"source_file","access_level":"closed","creator":"ssack","date_created":"2023-11-30T15:54:11Z"}],"date_published":"2023-11-30T00:00:00Z","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","month":"11","day":"30","ddc":["530"],"type":"dissertation"},{"year":"2023","file":[{"date_updated":"2024-01-29T11:06:45Z","file_id":"14896","checksum":"8a75c4e29fd9b62e3c50663c2265b173","file_name":"2023_CurrOpSystBioloy_Minchington.pdf","content_type":"application/pdf","file_size":598842,"access_level":"open_access","creator":"dernst","date_created":"2024-01-29T11:06:45Z","success":1,"relation":"main_file"}],"date_published":"2023-09-01T00:00:00Z","acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","title":"Control of tissue dimensions in the developing neural tube and somites","month":"09","day":"01","publication":"Current Opinion in Systems Biology","ddc":["570"],"intvolume":" 35","article_type":"original","type":"journal_article","publication_status":"published","quality_controlled":"1","oa":1,"publication_identifier":{"eissn":["2452-3100"]},"project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"author":[{"last_name":"Minchington","full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","full_name":"Rus, Stefanie","last_name":"Rus"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"citation":{"ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","apa":"Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2023.100459","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.","mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35, 100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” Current Opinion in Systems Biology, vol. 35. Elsevier, 2023."},"file_date_updated":"2024-01-29T11:06:45Z","corr_author":"1","abstract":[{"lang":"eng","text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.coisb.2023.100459","volume":35,"date_created":"2023-06-18T22:00:46Z","has_accepted_license":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","date_updated":"2026-10-01T22:31:10Z","article_processing_charge":"Yes (via OA deal)","_id":"13136","doi":"10.1016/j.coisb.2023.100459","department":[{"_id":"AnKi"}],"article_number":"100459","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Oxford University Press","author":[{"last_name":"Lasne","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"},{"last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"file_date_updated":"2024-01-02T11:39:38Z","citation":{"apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., & Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:10.1093/molbev/msad245.","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution, vol. 40, no. 12. Oxford University Press, 2023.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245."},"related_material":{"record":[{"relation":"research_data","id":"14614","status":"public"},{"relation":"dissertation_contains","status":"public","id":"19386"}],"link":[{"relation":"press_release","description":"News on ISTA webpage","url":"https://ista.ac.at/en/news/on-the-hunt/"}]},"pmid":1,"corr_author":"1","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"oa":1,"project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","grant_number":"ESP39 49461","name":"Mechanisms and Evolution of Reproductive Plasticity"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication_status":"published","quality_controlled":"1","article_type":"original","intvolume":" 40","type":"journal_article","day":"01","publication":"Molecular Biology and Evolution","ddc":["570"],"issue":"12","file":[{"date_updated":"2024-01-02T11:39:38Z","file_id":"14727","file_name":"2023_MolecularBioEvo_Lasne.pdf","checksum":"47c1c72fb499f26ea52d216b242208c8","content_type":"application/pdf","file_size":8623505,"creator":"dernst","access_level":"open_access","date_created":"2024-01-02T11:39:38Z","success":1,"relation":"main_file"}],"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","date_published":"2023-12-01T00:00:00Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","month":"12","year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"BeVi"}],"article_number":"msad245","article_processing_charge":"Yes","doi":"10.1093/molbev/msad245","_id":"14613","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","date_updated":"2026-10-01T22:31:12Z","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-11-27T16:14:37Z","isi":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1093/molbev/msad245","external_id":{"pmid":["37988296"],"isi":["001122489000003"]},"volume":40},{"year":"2023","title":"Modeling Leidenfrost levitation of soft elastic solids","month":"10","date_published":"2023-10-20T00:00:00Z","file":[{"success":1,"relation":"main_file","access_level":"open_access","creator":"dernst","date_created":"2023-11-13T09:12:58Z","content_type":"application/pdf","file_size":724098,"file_id":"14524","checksum":"1a419e25b762aadffbcc8eb2e609bd97","file_name":"2023_PhysRevLetters_Binysh.pdf","date_updated":"2023-11-13T09:12:58Z"}],"acknowledgement":"We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) through New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1, EP/S022848/1, EP/S029966/1, and EP/P031684/1.","ddc":["530"],"issue":"16","day":"20","publication":"Physical Review Letters","article_type":"original","intvolume":" 131","type":"journal_article","quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"oa":1,"pmid":1,"abstract":[{"lang":"eng","text":"The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines."}],"author":[{"first_name":"Jack","full_name":"Binysh, Jack","last_name":"Binysh"},{"first_name":"Indrajit","full_name":"Chakraborty, Indrajit","last_name":"Chakraborty"},{"first_name":"Mykyta V.","full_name":"Chubynsky, Mykyta V.","last_name":"Chubynsky"},{"first_name":"Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","full_name":"Diaz Melian, Vicente L","last_name":"Diaz Melian"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"},{"full_name":"Sprittles, James E.","last_name":"Sprittles","first_name":"James E."},{"first_name":"Anton","full_name":"Souslov, Anton","last_name":"Souslov"}],"related_material":{"record":[{"relation":"research_data","id":"14523","status":"public"},{"id":"23005","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2023-11-13T09:12:58Z","citation":{"apa":"Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.168201","ieee":"J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society, 2023.","mla":"Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.168201.","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201.","ama":"Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201","short":"J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023).","ista":"Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 131(16), 168201."},"publisher":"American Physical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":131,"fulldoi":"https://doi.org/10.1103/PhysRevLett.131.168201","external_id":{"isi":["001164388300007"],"pmid":["37925690"]},"isi":1,"has_accepted_license":"1","date_created":"2023-11-12T23:00:55Z","language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","date_updated":"2026-10-02T08:44:47Z","_id":"14514","doi":"10.1103/PhysRevLett.131.168201","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"ScWa"}],"article_number":"168201","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"article_processing_charge":"No","oa":1,"doi":"10.5281/ZENODO.8277285","_id":"14919","date_updated":"2026-10-02T08:57:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","department":[{"_id":"FrPe"}],"author":[{"first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas","last_name":"Shaw"},{"first_name":"Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba","full_name":"Buri, Pascal","last_name":"Buri"},{"first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca","orcid":"0000-0002-5554-8087","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"citation":{"ista":"Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. 2023. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, 10.5281/ZENODO.8277285.","ama":"Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:10.5281/ZENODO.8277285","short":"T. Shaw, P. Buri, M. McCarthy, E. Miles, F. Pellicciotti, (2023).","mla":"Shaw, Thomas, et al. Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer. Zenodo, 2023, doi:10.5281/ZENODO.8277285.","chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan Miles, and Francesca Pellicciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8277285.","ieee":"T. Shaw, P. Buri, M. McCarthy, E. Miles, and F. Pellicciotti, “Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.” Zenodo, 2023.","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E., & Pellicciotti, F. (2023). Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. Zenodo. https://doi.org/10.5281/ZENODO.8277285"},"related_material":{"record":[{"status":"public","id":"14885","relation":"used_in_publication"}]},"corr_author":"1","abstract":[{"text":"GLACIER METEOROLOGICAL DATA SWISS ALPS -2022\r\n","lang":"eng"}],"date_published":"2023-08-23T00:00:00Z","title":"Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer","month":"08","year":"2023","fulldoi":"https://doi.org/10.5281/ZENODO.8277285","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8277285"}],"type":"research_data_reference","oa_version":"Published Version","day":"23","date_created":"2024-01-31T12:08:26Z","ddc":["550"]},{"doi":"10.5281/zenodo.8277284","_id":"23030","article_processing_charge":"No","oa":1,"date_updated":"2026-10-02T08:59:03Z","OA_place":"repository","publisher":"Zenodo","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\r\n GLACIER METEOROLOGICAL DATA\r\n SWISS ALPS -2022\r\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\r\nData gathered and structured by Thomas Shaw (WSL, Switzerland (until Oct 2022)).\r\n\r\nOn and off-glacier meteorological data were gathered and analysed as part of a Marie-Curie project 'TEMPEST' (tempestglacier.com).\r\nThe dataset consists of hourly low-cost AWS (Davis Vantage Pro2) and simple temperature ('T-')logger (Onset TidBitv2) sensor records on three glaciers in the Swiss Alps (Canton Valais).\r\n\r\nThe glaciers are:\r\nHaut Glacier d'Arolla (45.967°N, 7.526°E)\r\nGlacier d'Otemma (45.956°N, 7.454°E)\r\nGlacier du Corbassière (45.975°N, 7.303°E)\r\n\r\nData are provided in individual Excel files per glacier that contain all hourly data for the sub-period of comparison (11 August-18 September, 2022).\r\nData are quality controlled and checked for obvious errors. Any uncertain values are set to NaN.\r\nAir temperature data at 'T-Logger' stations were corrected for heating errors using the comparison of measurements in artificially (AWS) and naturally ventilated (T-Logger) radiation shields on Arolla and Corbassiere glaciers.\r\nA multiple linear regression model was applied to estimate these differences at all T-Loggers on all glaciers as a function of incoming shortwave radiation (MeteoSwiss station-derived) and wind speed (measured at AWS).\r\n\r\nEach Excel file contains a 'META' tab for simple metadata related to station locations (latitude 'LAT' (°), longitude 'LON' (°), elevation 'ELE' (m a.s.l.) and flowpath length 'FPL' (m)) and a 'DATA' tab for the hourly data. \r\nSuffixes to the station names in each column provide the variable measured at that site:\r\n'TA' - 2m air temperature (°C)\r\n'TA_Hi' - Maximum air temperature for timestep (°C)\r\n'TA_Lo' - Minimum air temperature for timestep (°C)\r\n'RH' - 2m relative humiditiy (%)\r\n'FF' - Wind speed (m s^-1)\r\n'FF_Hi' - Maximum wind speed for timestep (m s^-1)\r\n'FF_Lo' - Minimum wind speed for timestep (m s^-1)\r\n'DIR' - Wind direction (°)\r\n'DEW' - Dewpoint temperature (°C)\r\n'PRESS' - Air pressure (mbar)\r\n'CHILL' - Calculated wind chill temperature (°C)\r\n'Heat_idx' - Calculated heat index (°C)\r\n'THSW' - A calculated index that uses humidity and temperature like for the Heat Index, but also includes the heating effects of sunshine and the cooling effects of wind (like Wind Chill) to calculate an apparent temperature of what it \"feels\" like out in the shade\r\n\r\nWind speeds and direction measured at off-glacier sites 'OG' are for the lower off-glacier station ('OG_Low'). ","lang":"eng"}],"citation":{"ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Pelliciotti F. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:10.5281/zenodo.8277284","short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pelliciotti, (2023).","ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Pelliciotti F. 2023. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, 10.5281/zenodo.8277284.","apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., & Pelliciotti, F. (2023). Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. Zenodo. https://doi.org/10.5281/zenodo.8277284","mla":"Shaw, Thomas E., et al. Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer. Zenodo, 2023, doi:10.5281/zenodo.8277284.","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pelliciotti, “Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.” Zenodo, 2023.","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca Pelliciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. https://doi.org/10.5281/zenodo.8277284."},"related_material":{"record":[{"id":"14885","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"FrPe"}],"author":[{"full_name":"Shaw, Thomas E.","last_name":"Shaw","first_name":"Thomas E."},{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal"},{"first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"full_name":"Pelliciotti, Francesca","last_name":"Pelliciotti","first_name":"Francesca"}],"month":"08","title":"Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer","acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058.","date_published":"2023-08-23T00:00:00Z","fulldoi":"https://doi.org/10.5281/zenodo.8277284","year":"2023","oa_version":"None","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8277284"}],"ddc":["550"],"OA_type":"green","date_created":"2026-10-02T08:58:12Z","day":"23"},{"fulldoi":"https://doi.org/10.5281/zenodo.8005257","year":"2023","date_published":"2023-06-05T00:00:00Z","month":"06","title":"A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen","date_created":"2026-10-02T09:16:51Z","day":"05","ddc":["550"],"OA_type":"green","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8005257"}],"oa_version":"None","contributor":[{"last_name":"Muñoz Hermosilla","first_name":"José M","contributor_type":"contact_person"}],"date_updated":"2026-10-02T09:16:55Z","article_processing_charge":"No","oa":1,"doi":"10.5281/zenodo.8005257","_id":"23031","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"18628"}]},"citation":{"mla":"Muñoz Hermosilla, José M. A 3D Glacier Dynamics-Line Plume Model to Estimate the Frontal Ablation of Hansbreen. Zenodo, 2023, doi:10.5281/zenodo.8005257.","ieee":"J. M. Muñoz Hermosilla, “A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen.” Zenodo, 2023.","chicago":"Muñoz Hermosilla, José M. “A 3D Glacier Dynamics-Line Plume Model to Estimate the Frontal Ablation of Hansbreen.” Zenodo, 2023. https://doi.org/10.5281/zenodo.8005257.","apa":"Muñoz Hermosilla, J. M. (2023). A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen. Zenodo. https://doi.org/10.5281/zenodo.8005257","ista":"Muñoz Hermosilla JM. 2023. A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Zenodo, 10.5281/zenodo.8005257.","ama":"Muñoz Hermosilla JM. A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen. 2023. doi:10.5281/zenodo.8005257","short":"J.M. Muñoz Hermosilla, (2023)."},"department":[{"_id":"FrPe"}],"author":[{"first_name":"José M","full_name":"Muñoz Hermosilla, José M","last_name":"Muñoz Hermosilla"}],"abstract":[{"text":"There are 4 tar.xz files with the result of the model for the paper: A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. These archives can be unzipped on Linux using the tar command, or on other systems using a specific software.\r\n\r\nFrontPositions includes data files with the coordinates of the nodes of the front positons.\r\n\r\nCalvingStats includes txt files with some characteristics of the calving events.\r\n\r\nHydrologyOutput includes csv files with the main results of the hydrological model.\r\n\r\nModelOutput include output and visualization files of the model results. The .vtu and .pvtu files are best viewed in the software Paraview.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","publisher":"Zenodo","status":"public"},{"article_processing_charge":"No","oa":1,"doi":"10.5281/ZENODO.8005257","_id":"18634","date_updated":"2026-10-02T09:16:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Zenodo","OA_place":"repository","department":[{"_id":"FrPe"}],"author":[{"last_name":"Muñoz Hermosilla","full_name":"Muñoz Hermosilla, José M","orcid":"0000-0002-1990-8508","id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","first_name":"José M"}],"related_material":{"record":[{"id":"18628","status":"public","relation":"research_data"}]},"citation":{"short":"J.M. Muñoz Hermosilla, (2023).","ama":"Muñoz Hermosilla JM. A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen. 2023. doi:10.5281/ZENODO.8005257","ista":"Muñoz Hermosilla JM. 2023. A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Zenodo, 10.5281/ZENODO.8005257.","apa":"Muñoz Hermosilla, J. M. (2023). A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen. Zenodo. https://doi.org/10.5281/ZENODO.8005257","ieee":"J. M. Muñoz Hermosilla, “A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen.” Zenodo, 2023.","mla":"Muñoz Hermosilla, José M. A 3D Glacier Dynamics-Line Plume Model to Estimate the Frontal Ablation of Hansbreen. Zenodo, 2023, doi:10.5281/ZENODO.8005257.","chicago":"Muñoz Hermosilla, José M. “A 3D Glacier Dynamics-Line Plume Model to Estimate the Frontal Ablation of Hansbreen.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8005257."},"corr_author":"1","abstract":[{"text":"There are 4 tar.xz files with the result of the model for the paper: A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. ","lang":"eng"}],"date_published":"2023-06-05T00:00:00Z","month":"06","title":"A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen","fulldoi":"https://doi.org/10.5281/ZENODO.8005257","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8005258"}],"type":"research_data_reference","oa_version":"Published Version","day":"05","date_created":"2024-12-09T09:33:07Z","ddc":["550"]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","publisher":"Figshare","status":"public","citation":{"ieee":"K. Sarkisyan, “A hybrid pathway for self-sustained luminescence - Raw data.” Figshare, 2023.","mla":"Sarkisyan, Karen. A Hybrid Pathway for Self-Sustained Luminescence - Raw Data. Figshare, 2023, doi:10.6084/m9.figshare.24772872.","chicago":"Sarkisyan, Karen. “A Hybrid Pathway for Self-Sustained Luminescence - Raw Data.” Figshare, 2023. https://doi.org/10.6084/m9.figshare.24772872.","apa":"Sarkisyan, K. (2023). A hybrid pathway for self-sustained luminescence - Raw data. Figshare. https://doi.org/10.6084/m9.figshare.24772872","ista":"Sarkisyan K. 2023. A hybrid pathway for self-sustained luminescence - Raw data, Figshare, 10.6084/m9.figshare.24772872.","ama":"Sarkisyan K. A hybrid pathway for self-sustained luminescence - Raw data. 2023. doi:10.6084/m9.figshare.24772872","short":"K. Sarkisyan, (2023)."},"related_material":{"record":[{"relation":"used_in_publication","id":"15179","status":"public"}]},"department":[{"_id":"FyKo"}],"author":[{"first_name":"Karen","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen"}],"abstract":[{"text":"Datasets in .csv or .xlsx format sorted into folders by figures. In some cases additional files with roi/well-to-sample mapping were provided.\r\n\r\nFor more details contact authors.","lang":"eng"}],"article_processing_charge":"No","oa":1,"doi":"10.6084/m9.figshare.24772872","_id":"23032","date_updated":"2026-10-02T09:22:30Z","type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.24772872","open_access":"1"}],"oa_version":"None","date_created":"2026-10-02T09:22:23Z","day":"08","ddc":["580"],"OA_type":"green","date_published":"2023-12-08T00:00:00Z","title":"A hybrid pathway for self-sustained luminescence - Raw data","month":"12","year":"2023","fulldoi":"https://doi.org/10.6084/m9.figshare.24772872"},{"year":"2023","date_published":"2023-10-01T00:00:00Z","file":[{"file_size":71057,"content_type":"application/pdf","date_updated":"2024-01-24T11:12:33Z","file_name":"2023_EurJourPublicHealth_Rella.pdf","checksum":"98706755bb4cc5d553818ade7660a7d2","file_id":"14882","success":1,"relation":"main_file","date_created":"2024-01-24T11:12:33Z","creator":"dernst","access_level":"open_access"}],"title":"Complex vaccination strategies prevent the emergence of vaccine resistance","month":"10","day":"01","publication":"European Journal of Public Health","issue":"Supplement_2","ddc":["570"],"intvolume":" 33","type":"conference_abstract","publication_status":"published","quality_controlled":"1","oa":1,"publication_identifier":{"eissn":["1464-360X"],"issn":["1101-1262"]},"author":[{"full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"first_name":"Y","last_name":"Kulikova","full_name":"Kulikova, Y"},{"first_name":"Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","full_name":"Minnegalieva, Aygul","last_name":"Minnegalieva"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"}],"citation":{"ista":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597.","short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: European Journal of Public Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. 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Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"corr_author":"1","citation":{"ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109.","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.)."},"related_material":{"record":[{"id":"13286","status":"public","relation":"dissertation_contains"},{"id":"14793","status":"public","relation":"later_version"}]},"author":[{"last_name":"Valentini","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"full_name":"Sagi, Oliver","last_name":"Sagi","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"first_name":"Thijs de","full_name":"Gijsel, Thijs de","last_name":"Gijsel"},{"first_name":"Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","full_name":"Jung, Jason","last_name":"Jung"},{"first_name":"Stefano","full_name":"Calcaterra, Stefano","last_name":"Calcaterra"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"first_name":"Juan Aguilera","last_name":"Servin","full_name":"Servin, Juan Aguilera"},{"full_name":"Aggarwal, Kushagra","last_name":"Aggarwal","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra"},{"full_name":"Janik, Marian","last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","orcid":"0009-0003-9037-8831"},{"full_name":"Adletzberger, Thomas","last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Rubén Seoane","last_name":"Souto","full_name":"Souto, Rubén Seoane"},{"last_name":"Leijnse","full_name":"Leijnse, Martin","first_name":"Martin"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"last_name":"Schrade","full_name":"Schrade, Constantin","first_name":"Constantin"},{"last_name":"Bakkers","full_name":"Bakkers, Erik","first_name":"Erik"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","project":[{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"},{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"arxiv":1,"oa":1,"ddc":["530"],"publication":"arXiv","day":"13","type":"preprint","year":"2023","title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","month":"06","acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","date_published":"2023-06-13T00:00:00Z","article_number":"2306.07109","department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"OA_place":"repository","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-10-02T10:23:31Z","keyword":["Mesoscale and Nanoscale Physics"],"doi":"10.48550/arXiv.2306.07109","_id":"13312","ec_funded":1,"article_processing_charge":"No","date_created":"2023-07-26T11:17:20Z","oa_version":"Preprint","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"external_id":{"arxiv":["2306.07109"]},"fulldoi":"https://doi.org/10.48550/arXiv.2306.07109"},{"status":"public","publisher":"Zenodo","OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"GeKa"}],"author":[{"last_name":"Valentini","full_name":"Valentini, Marco","first_name":"Marco"}],"citation":{"mla":"Valentini, Marco. Data Repository for “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” Zenodo, 2023, doi:10.5281/zenodo.10119345.","ieee":"M. Valentini, “Data repository for ‘Parity-conserving Cooper-pair transport and ideal superconducting diode in planar Germanium.’” Zenodo, 2023.","chicago":"Valentini, Marco. “Data Repository for ‘Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.’” Zenodo, 2023. https://doi.org/10.5281/zenodo.10119345.","apa":"Valentini, M. (2023). Data repository for “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar Germanium.” Zenodo. https://doi.org/10.5281/zenodo.10119345","ista":"Valentini M. 2023. Data repository for ‘Parity-conserving Cooper-pair transport and ideal superconducting diode in planar Germanium’, Zenodo, 10.5281/zenodo.10119345.","short":"M. Valentini, (2023).","ama":"Valentini M. Data repository for “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar Germanium.” 2023. doi:10.5281/zenodo.10119345"},"related_material":{"record":[{"id":"14793","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/zenodo.10119345","_id":"23036","article_processing_charge":"No","oa":1,"date_updated":"2026-10-02T10:23:54Z","oa_version":"None","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10119345","open_access":"1"}],"type":"research_data_reference","OA_type":"green","ddc":["530"],"day":"13","date_created":"2026-10-02T10:23:47Z","month":"11","title":"Data repository for 'Parity-conserving Cooper-pair transport and ideal superconducting diode in planar Germanium'","date_published":"2023-11-13T00:00:00Z","fulldoi":"https://doi.org/10.5281/zenodo.10119345","year":"2023"},{"corr_author":"1","abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"author":[{"last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","first_name":"Soham"},{"first_name":"Jorden L","orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","last_name":"Senior"},{"full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime"},{"full_name":"Puglia, Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0003-1144-2763","first_name":"Denise"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M"},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"}],"file_date_updated":"2024-01-29T11:25:38Z","citation":{"ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023.","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17881"}]},"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"oa":1,"ddc":["530"],"day":"01","publication":"Nature Physics","article_type":"original","intvolume":" 19","type":"journal_article","year":"2023","title":"Superconductivity from a melted insulator in Josephson junction arrays","month":"11","file":[{"date_updated":"2024-01-29T11:25:38Z","file_id":"14899","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","checksum":"1fc86d71bfbf836e221c1e925343adc5","content_type":"application/pdf","file_size":1977706,"creator":"dernst","access_level":"open_access","date_created":"2024-01-29T11:25:38Z","relation":"main_file","success":1}],"acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","date_published":"2023-11-01T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"status":"public","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","date_updated":"2026-10-02T11:12:07Z","keyword":["General Physics and Astronomy"],"page":"1630-1635","_id":"14032","doi":"10.1038/s41567-023-02161-w","article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"isi":1,"has_accepted_license":"1","date_created":"2023-08-11T07:41:17Z","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":19,"fulldoi":"https://doi.org/10.1038/s41567-023-02161-w","external_id":{"isi":["001054563800006"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","author":[{"last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023)."},"file_date_updated":"2023-08-16T11:43:33Z","related_material":{"record":[{"status":"public","id":"18531","relation":"dissertation_contains"}]},"pmid":1,"corr_author":"1","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"oa":1,"project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"publication_identifier":{"issn":["2056-3744"]},"publication_status":"published","quality_controlled":"1","article_type":"original","intvolume":" 7","type":"journal_article","day":"01","publication":"Evolution Letters","issue":"1","ddc":["570"],"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","date_published":"2023-02-01T00:00:00Z","file":[{"relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","date_created":"2023-08-16T11:43:33Z","content_type":"application/pdf","file_size":2592189,"date_updated":"2023-08-16T11:43:33Z","file_id":"14068","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_name":"2023_EvLetters_Mrnjavac.pdf"}],"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","month":"02","year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"article_number":"qrac004","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","doi":"10.1093/evlett/qrac004","_id":"12521","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","date_updated":"2026-10-02T11:14:08Z","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-02-06T13:59:12Z","isi":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1093/evlett/qrac004","external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"volume":7}]