[{"author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko"},{"last_name":"Ucar","first_name":"Mehmet C","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"last_name":"Canigova","id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola"},{"full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_type":"original","ddc":["570"],"oa":1,"year":"2023","article_processing_charge":"No","month":"09","issue":"87","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"intvolume":" 8","citation":{"mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584"},"corr_author":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"14279"},{"status":"public","relation":"dissertation_contains","id":"14697"},{"relation":"dissertation_contains","status":"public","id":"19745"}]},"date_created":"2023-09-06T08:07:51Z","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"scopus_import":"1","publication":"Science Immunology","article_number":"adc9584","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","volume":8,"ec_funded":1,"publication_identifier":{"issn":["2470-9468"]},"quality_controlled":"1","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1126/sciimmunol.adc9584","isi":1,"date_published":"2023-09-01T00:00:00Z","day":"01","keyword":["General Medicine","Immunology"],"pmid":1,"date_updated":"2026-09-30T22:30:39Z","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","doi":"10.1126/sciimmunol.adc9584","status":"public","_id":"14274","project":[{"name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"type":"journal_article"},{"publication_status":"published","author":[{"last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X"}],"ddc":["500"],"degree_awarded":"MS","article_processing_charge":"No","oa":1,"year":"2023","oa_version":"Published Version","month":"08","alternative_title":["ISTA Master's Thesis"],"has_accepted_license":"1","corr_author":"1","citation":{"mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","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.","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.","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.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_created":"2023-08-24T13:01:18Z","supervisor":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","publication_identifier":{"issn":["2791-4585"]},"file":[{"file_name":"documents-export-2023-08-24.zip","content_type":"application/x-zip-compressed","file_id":"14227","embargo_to":"open_access","access_level":"closed","creator":"cchlebak","relation":"source_file","date_created":"2023-08-24T13:02:49Z","checksum":"453caf851d75c3478c10ed09bd242a91","date_updated":"2024-02-26T23:30:03Z","file_size":15501411},{"file_id":"14228","access_level":"open_access","embargo":"2024-02-25","content_type":"application/pdf","file_name":"thesis_pdf_a.pdf","checksum":"7349d29963d6695e555e171748648d9a","date_updated":"2024-02-26T23:30:03Z","file_size":6854783,"creator":"cchlebak","date_created":"2023-08-24T13:03:42Z","relation":"main_file"}],"fulldoi":"https://doi.org/10.15479/at:ista:14226","language":[{"iso":"eng"}],"day":"24","date_published":"2023-08-24T00:00:00Z","page":"43","date_updated":"2026-04-07T14:02:30Z","file_date_updated":"2024-02-26T23:30:03Z","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."}],"title":"Generalizing medial axes with homology switches","doi":"10.15479/at:ista:14226","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","status":"public","_id":"14226"},{"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1111/mec.16793","file":[{"date_updated":"2023-08-16T08:15:41Z","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_size":7144607,"creator":"dernst","success":1,"date_created":"2023-08-16T08:15:41Z","relation":"main_file","file_id":"14062","access_level":"open_access","content_type":"application/pdf","file_name":"2023_MolecularEcology_Shipilina.pdf"}],"day":"01","date_published":"2023-03-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/","page":"1441-1457","date_updated":"2026-09-30T22:30:43Z","title":"On the origin and structure of haplotype blocks","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2023-08-16T08:15:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","doi":"10.1111/mec.16793","status":"public","_id":"12159","type":"journal_article","project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","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"}],"author":[{"last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","last_name":"Pal"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"article_type":"original","publication_status":"published","ddc":["570"],"oa":1,"year":"2023","article_processing_charge":"Yes (via OA deal)","month":"03","oa_version":"Published Version","issue":"6","intvolume":" 32","citation":{"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","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.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","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.","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","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."},"corr_author":"1","has_accepted_license":"1","related_material":{"record":[{"id":"20694","relation":"dissertation_contains","status":"public"}]},"date_created":"2023-01-12T12:09:17Z","department":[{"_id":"NiBa"}],"scopus_import":"1","publication":"Molecular Ecology","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).","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"volume":32,"quality_controlled":"1"},{"date_created":"2023-11-10T09:10:06Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"citation":{"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.","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.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi: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.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"id":"9887","relation":"part_of_dissertation","status":"public"},{"id":"8139","relation":"part_of_dissertation","status":"public"}]},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"ec_funded":1,"OA_place":"publisher","supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh"}],"publication_status":"published","month":"11","oa_version":"Published Version","oa":1,"year":"2023","article_processing_charge":"No","degree_awarded":"PhD","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","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. "}],"file_date_updated":"2024-11-23T23:30:38Z","date_updated":"2026-09-30T22:30:56Z","page":"180","_id":"14510","status":"public","type":"dissertation","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14510","day":"10","date_published":"2023-11-10T00:00:00Z","language":[{"iso":"eng"}],"file":[{"date_updated":"2024-11-23T23:30:38Z","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_size":20824903,"creator":"ngnyliuk","date_created":"2023-11-20T09:18:51Z","relation":"source_file","file_id":"14567","embargo_to":"open_access","access_level":"closed","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","content_type":"application/pdf","embargo":"2024-11-23","access_level":"open_access","file_id":"14568","date_created":"2023-11-20T09:23:11Z","relation":"main_file","creator":"ngnyliuk","file_size":24871844,"checksum":"bfc96d47fc4e7e857dd71656097214a4","date_updated":"2024-11-23T23:30:38Z"}],"fulldoi":"https://doi.org/10.15479/at:ista:14510","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"day":"10","date_published":"2023-10-10T00:00:00Z","publication_status":"draft","fulldoi":"https://doi.org/10.1101/2023.10.09.561523","language":[{"iso":"eng"}],"author":[{"first_name":"Nataliia","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"last_name":"Nagel","full_name":"Nagel, Marie-Kristin","first_name":"Marie-Kristin"},{"last_name":"Monzer","first_name":"Aline","full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","last_name":"Hlavata"},{"full_name":"Isono, Erika","first_name":"Erika","last_name":"Isono"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"main_file_link":[{"url":"https://doi.org/10.1101/2023.10.09.561523","open_access":"1"}],"oa_version":"Preprint","month":"10","article_processing_charge":"No","oa":1,"year":"2023","abstract":[{"lang":"eng","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."}],"publication":"bioRxiv","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"date_created":"2023-11-22T10:17:49Z","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","related_material":{"record":[{"status":"public","relation":"later_version","id":"15330"},{"id":"14510","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-09-30T22:30:56Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","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.","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","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.","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","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.)."},"OA_place":"repository","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"type":"preprint","_id":"14591","status":"public","ec_funded":1,"doi":"10.1101/2023.10.09.561523","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"corr_author":"1","citation":{"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.","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.","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.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470"},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11943"},{"id":"11950","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_created":"2023-01-31T15:10:53Z","supervisor":[{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-026-8"]},"ec_funded":1,"OA_place":"publisher","publication_status":"published","author":[{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska"}],"ddc":["610"],"article_processing_charge":"No","degree_awarded":"PhD","oa":1,"year":"2023","month":"01","oa_version":"Published Version","page":"201","date_updated":"2026-07-06T12:50:45Z","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","file_date_updated":"2023-07-27T22:30:54Z","abstract":[{"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.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:12470","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24"}],"type":"dissertation","status":"public","_id":"12470","file":[{"checksum":"1a2306e5f59f52df598e7ecfadf921ac","date_updated":"2023-07-27T22:30:54Z","file_size":41771714,"creator":"cchlebak","relation":"main_file","date_created":"2023-01-31T15:11:42Z","file_id":"12471","access_level":"open_access","file_name":"20230109_PhD_thesis_JM_final.pdf","content_type":"application/pdf","embargo":"2023-07-09"},{"file_id":"12472","embargo_to":"open_access","access_level":"closed","file_name":"20230109_PhD_thesis_JM_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-07-10T22:30:04Z","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_size":66983464,"creator":"cchlebak","date_created":"2023-01-31T15:11:51Z","relation":"source_file"}],"fulldoi":"https://doi.org/10.15479/at:ista:12470","language":[{"iso":"eng"}],"day":"09","date_published":"2023-01-09T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"date_updated":"2026-09-30T22:31:12Z","pmid":1,"file_date_updated":"2023-06-06T07:31:20Z","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."}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","doi":"10.1038/s41467-023-38761-6","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_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"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"_id":"13117","status":"public","file":[{"file_id":"13123","access_level":"open_access","file_name":"2023_NaturePhysics_Redchenko.pdf","content_type":"application/pdf","checksum":"a857df40f0882859c48a1ff1e2001ec2","date_updated":"2023-06-06T07:31:20Z","file_size":1654389,"creator":"dernst","success":1,"relation":"main_file","date_created":"2023-06-06T07:31:20Z"}],"fulldoi":"https://doi.org/10.1038/s41467-023-38761-6","isi":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["37225689"],"isi":["001001099700002"],"arxiv":["2205.03293"]},"date_published":"2023-05-24T00:00:00Z","day":"24","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"13124"},{"status":"public","relation":"dissertation_contains","id":"19533"}]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"has_accepted_license":"1","corr_author":"1","citation":{"short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","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","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.","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.","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","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."},"publication":"Nature Communications","scopus_import":"1","department":[{"_id":"JoFi"}],"date_created":"2023-06-04T22:01:02Z","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.","article_number":"2998","quality_controlled":"1","arxiv":1,"publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"volume":14,"publication_status":"published","article_type":"original","author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"last_name":"Poshakinskiy","first_name":"Alexander V.","full_name":"Poshakinskiy, Alexander V."},{"first_name":"Riya","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett"},{"last_name":"Zemlicka","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Poddubny","first_name":"Alexander N.","full_name":"Poddubny, Alexander N."},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"ddc":["530"],"article_processing_charge":"No","year":"2023","oa":1,"intvolume":" 14","oa_version":"Published Version","month":"05"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13125"},{"id":"11471","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9760"}]},"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","corr_author":"1","citation":{"ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","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.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","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.","short":"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."},"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"date_created":"2023-11-28T10:58:13Z","supervisor":[{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"publication_status":"published","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack"}],"ddc":["530"],"degree_awarded":"PhD","article_processing_charge":"No","year":"2023","oa":1,"oa_version":"Published Version","month":"11","page":"142","date_updated":"2026-09-14T08:36:32Z","file_date_updated":"2024-11-30T23:30:03Z","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"}],"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","doi":"10.15479/at:ista:14622","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IBM PhD Nomination Fellowship - Stefan Sack"},{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"_id":"14622","status":"public","file":[{"date_created":"2023-11-30T15:53:10Z","relation":"main_file","creator":"ssack","file_size":11947523,"date_updated":"2024-11-30T23:30:03Z","checksum":"068fd3570506ec42b2faa390de784bc4","content_type":"application/pdf","file_name":"PhD_Thesis.pdf","embargo":"2024-11-30","access_level":"open_access","file_id":"14635"},{"content_type":"application/zip","file_name":"PhD Thesis (1).zip","file_id":"14636","embargo_to":"open_access","access_level":"closed","creator":"ssack","relation":"source_file","date_created":"2023-11-30T15:54:11Z","date_updated":"2024-11-30T23:30:03Z","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_size":18422964}],"fulldoi":"https://doi.org/10.15479/at:ista:14622","language":[{"iso":"eng"}],"day":"30","date_published":"2023-11-30T00:00:00Z","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"doi_confirm":"1"},{"publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/physreva.107.062404","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"type":"journal_article","status":"public","_id":"13125","date_updated":"2026-09-30T22:31:16Z","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","file_date_updated":"2023-06-13T07:28:36Z","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"external_id":{"arxiv":["2209.01159"],"isi":["001016927100012"]},"fulldoi":"https://doi.org/10.1103/physreva.107.062404","file":[{"file_size":2524611,"checksum":"0d71423888eeccaa60d8f41197f26306","date_updated":"2023-06-13T07:28:36Z","date_created":"2023-06-13T07:28:36Z","relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_id":"13131","content_type":"application/pdf","file_name":"2023_PhysRevA_Sack.pdf"}],"isi":1,"language":[{"iso":"eng"}],"date_published":"2023-06-02T00:00:00Z","day":"02","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","article_number":"062404","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"volume":107,"ec_funded":1,"quality_controlled":"1","arxiv":1,"corr_author":"1","citation":{"short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404.","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404.","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404"},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17208"},{"relation":"dissertation_contains","status":"public","id":"14622"}]},"has_accepted_license":"1","scopus_import":"1","department":[{"_id":"MaSe"}],"date_created":"2023-06-07T06:57:32Z","publication":"Physical Review A","article_processing_charge":"No","year":"2023","oa":1,"month":"06","intvolume":" 107","issue":"6","oa_version":"Published Version","publication_status":"published","article_type":"original","author":[{"last_name":"Sack","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"},{"id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869","first_name":"Raimel A","last_name":"Medina Ramos"},{"first_name":"Richard","full_name":"Kueng, Richard","last_name":"Kueng"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"ddc":["530"]},{"month":"11","oa_version":"Published Version","intvolume":" 19","article_processing_charge":"Yes (in subscription journal)","year":"2023","oa":1,"ddc":["530"],"publication_status":"published","article_type":"original","author":[{"last_name":"Mukhopadhyay","first_name":"Soham","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L","last_name":"Senior"},{"last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","first_name":"Jaime"},{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","orcid":"0000-0003-1144-2763","first_name":"Denise","last_name":"Puglia"},{"orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M"},{"first_name":"Andrew P","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"volume":19,"ec_funded":1,"quality_controlled":"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.).","scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"date_created":"2023-08-11T07:41:17Z","publication":"Nature Physics","corr_author":"1","citation":{"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.","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","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023.","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.","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.","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","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."},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17881"}]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"keyword":["General Physics and Astronomy"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2023-11-01T00:00:00Z","day":"01","external_id":{"isi":["001054563800006"]},"isi":1,"fulldoi":"https://doi.org/10.1038/s41567-023-02161-w","file":[{"file_size":1977706,"date_updated":"2024-01-29T11:25:38Z","checksum":"1fc86d71bfbf836e221c1e925343adc5","date_created":"2024-01-29T11:25:38Z","relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_id":"14899","content_type":"application/pdf","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"status":"public","_id":"14032","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41567-023-02161-w","title":"Superconductivity from a melted insulator in Josephson junction arrays","file_date_updated":"2024-01-29T11:25:38Z","abstract":[{"lang":"eng","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."}],"page":"1630-1635","date_updated":"2026-09-30T22:31:19Z"},{"publication":"Current Opinion in Systems Biology","department":[{"_id":"AnKi"}],"scopus_import":"1","date_created":"2023-06-18T22:00:46Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19763"}]},"has_accepted_license":"1","corr_author":"1","citation":{"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.","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","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","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.","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","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.","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."},"quality_controlled":"1","publication_identifier":{"eissn":["2452-3100"]},"volume":35,"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.","article_number":"100459","ddc":["570"],"article_type":"original","publication_status":"published","author":[{"last_name":"Minchington","full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"last_name":"Rus","first_name":"Stefanie","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"intvolume":" 35","oa_version":"Published Version","month":"09","article_processing_charge":"Yes (via OA deal)","oa":1,"year":"2023","file_date_updated":"2024-01-29T11:06:45Z","abstract":[{"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.","lang":"eng"}],"title":"Control of tissue dimensions in the developing neural tube and somites","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2026-09-30T22:31:18Z","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"type":"journal_article","status":"public","_id":"13136","doi":"10.1016/j.coisb.2023.100459","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-09-01T00:00:00Z","day":"01","fulldoi":"https://doi.org/10.1016/j.coisb.2023.100459","file":[{"file_name":"2023_CurrOpSystBioloy_Minchington.pdf","content_type":"application/pdf","file_id":"14896","access_level":"open_access","success":1,"creator":"dernst","relation":"main_file","date_created":"2024-01-29T11:06:45Z","date_updated":"2024-01-29T11:06:45Z","checksum":"8a75c4e29fd9b62e3c50663c2265b173","file_size":598842}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"status":"public","_id":"14613","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","grant_number":"ESP39 49461"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Oxford University Press","doi":"10.1093/molbev/msad245","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","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."}],"file_date_updated":"2024-01-02T11:39:38Z","pmid":1,"date_updated":"2026-09-30T22:31:19Z","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2023-12-01T00:00:00Z","day":"01","external_id":{"pmid":["37988296"],"isi":["001122489000003"]},"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1093/molbev/msad245","file":[{"file_size":8623505,"date_updated":"2024-01-02T11:39:38Z","checksum":"47c1c72fb499f26ea52d216b242208c8","relation":"main_file","date_created":"2024-01-02T11:39:38Z","success":1,"creator":"dernst","access_level":"open_access","file_id":"14727","file_name":"2023_MolecularBioEvo_Lasne.pdf","content_type":"application/pdf"}],"volume":40,"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"quality_controlled":"1","article_number":"msad245","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_created":"2023-11-27T16:14:37Z","department":[{"_id":"BeVi"}],"scopus_import":"1","publication":"Molecular Biology and Evolution","citation":{"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.","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.","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","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","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.","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."},"corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","related_material":{"link":[{"description":"News on ISTA webpage","url":"https://ista.ac.at/en/news/on-the-hunt/","relation":"press_release"}],"record":[{"id":"14614","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"19386"}]},"month":"12","issue":"12","intvolume":" 40","oa_version":"Published Version","oa":1,"year":"2023","article_processing_charge":"Yes","ddc":["570"],"author":[{"last_name":"Lasne","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","first_name":"Clementine"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f","first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"article_type":"original","publication_status":"published"},{"day":"01","date_published":"2023-02-01T00:00:00Z","external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"fulldoi":"https://doi.org/10.1093/evlett/qrac004","isi":1,"file":[{"file_id":"14068","access_level":"open_access","content_type":"application/pdf","file_name":"2023_EvLetters_Mrnjavac.pdf","date_updated":"2023-08-16T11:43:33Z","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_size":2592189,"creator":"dernst","success":1,"date_created":"2023-08-16T11:43:33Z","relation":"main_file"}],"language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","file_date_updated":"2023-08-16T11:43:33Z","abstract":[{"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.","lang":"eng"}],"pmid":1,"date_updated":"2026-09-30T22:31:21Z","project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"type":"journal_article","status":"public","_id":"12521","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1093/evlett/qrac004","ddc":["570"],"article_type":"original","publication_status":"published","author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"month":"02","oa_version":"Published Version","issue":"1","intvolume":" 7","article_processing_charge":"Yes (via OA deal)","oa":1,"year":"2023","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"scopus_import":"1","date_created":"2023-02-06T13:59:12Z","publication":"Evolution Letters","corr_author":"1","citation":{"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.","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.","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).","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","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.","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."},"related_material":{"record":[{"id":"18531","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","volume":7,"publication_identifier":{"issn":["2056-3744"]},"ec_funded":1,"quality_controlled":"1","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).","article_number":"qrac004"},{"fulldoi":"https://doi.org/10.5281/zenodo.10308791","author":[{"last_name":"Lemoult","full_name":"Lemoult, Grégoire","first_name":"Grégoire"}],"day":"08","date_published":"2023-12-08T00:00:00Z","article_processing_charge":"No","year":"2023","oa":1,"month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.10308791"}],"oa_version":"None","citation":{"mla":"Lemoult, Grégoire. Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence. Zenodo, 2023, doi:10.5281/zenodo.10308791.","ama":"Lemoult G. Directed percolation and puff jamming near the transition to pipe turbulence. 2023. doi:10.5281/zenodo.10308791","ista":"Lemoult G. 2023. Directed percolation and puff jamming near the transition to pipe turbulence, Zenodo, 10.5281/zenodo.10308791.","chicago":"Lemoult, Grégoire. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” Zenodo, 2023. https://doi.org/10.5281/zenodo.10308791.","ieee":"G. Lemoult, “Directed percolation and puff jamming near the transition to pipe turbulence.” Zenodo, 2023.","apa":"Lemoult, G. (2023). Directed percolation and puff jamming near the transition to pipe turbulence. Zenodo. https://doi.org/10.5281/zenodo.10308791","short":"G. Lemoult, (2023)."},"related_material":{"record":[{"id":"17128","status":"public","relation":"used_in_publication"}]},"date_updated":"2026-10-01T07:50:31Z","department":[{"_id":"BjHo"}],"title":"Directed percolation and puff jamming near the transition to pipe turbulence","date_created":"2026-10-01T07:47:57Z","abstract":[{"lang":"eng","text":"The onset of turbulence in pipe flow has defied detailed understanding ever since Reynolds' first observations revealed the spatially-heterogeneous nature of the transition. While recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed percolation non-equilibrium phase transition, whether these findings are generic and apply also to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behavior virtually impossible. Here, we circumvent these limitations by experimentally characterizing all pairwise interactions between localized patches of turbulence (\"puffs\"), and using these interactions as input to renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. We show that the universality class of the transition is directed percolation, from which emerges a jammed phase of puffs above the critical point. The stronger interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed percolation scaling applies beyond simple closed shear flows, and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases."}],"publisher":"Zenodo","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.5281/zenodo.10308791","type":"research_data_reference","status":"public","_id":"23012","OA_type":"green","OA_place":"repository"},{"page":"173-195","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2024-10-09T21:04:02Z","pmid":1,"file_date_updated":"2022-03-04T08:55:27Z","abstract":[{"lang":"eng","text":"Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses."}],"title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","doi":"10.1002/glia.24101","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","_id":"10818","status":"public","file":[{"content_type":"application/pdf","file_name":"2021_Glia_Basilico.pdf","file_id":"10819","access_level":"open_access","creator":"dernst","success":1,"relation":"main_file","date_created":"2022-03-04T08:55:27Z","checksum":"f10a897290e66c0a062e04ba91db6c17","date_updated":"2022-03-04T08:55:27Z","file_size":5340294}],"fulldoi":"https://doi.org/10.1002/glia.24101","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000708025800001"],"pmid":["34661306"]},"day":"01","date_published":"2022-01-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"keyword":["Cellular and Molecular Neuroscience","Neurology"],"has_accepted_license":"1","corr_author":"1","citation":{"ista":"Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 70(1), 173–195.","ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 2022;70(1):173-195. doi:10.1002/glia.24101","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:10.1002/glia.24101.","short":"B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito, V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris, D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi, M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L. Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. Wiley. https://doi.org/10.1002/glia.24101","ieee":"B. Basilico et al., “Microglia control glutamatergic synapses in the adult mouse hippocampus,” Glia, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia. Wiley, 2022. https://doi.org/10.1002/glia.24101."},"publication":"Glia","department":[{"_id":"GaNo"}],"scopus_import":"1","date_created":"2022-03-04T08:53:37Z","acknowledgement":"The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003) to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University, Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza University, Rome and by the Italian Institute of Technology, Rome. The authors thank Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani for help with animal husbandry and transgenic colonies management. They also wish to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism. PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley, CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza within the CRUI-CARE Agreement.","quality_controlled":"1","publication_identifier":{"eissn":["1098-1136"],"issn":["0894-1491"]},"volume":70,"publication_status":"published","article_type":"original","author":[{"last_name":"Basilico","first_name":"Bernadette","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"first_name":"Laura","full_name":"Ferrucci, Laura","last_name":"Ferrucci"},{"last_name":"Ratano","first_name":"Patrizia","full_name":"Ratano, Patrizia"},{"last_name":"Golia","full_name":"Golia, Maria T.","first_name":"Maria T."},{"last_name":"Grimaldi","full_name":"Grimaldi, Alfonso","first_name":"Alfonso"},{"first_name":"Maria","full_name":"Rosito, Maria","last_name":"Rosito"},{"first_name":"Valentina","full_name":"Ferretti, Valentina","last_name":"Ferretti"},{"first_name":"Ingrid","full_name":"Reverte, Ingrid","last_name":"Reverte"},{"full_name":"Sanchini, Caterina","first_name":"Caterina","last_name":"Sanchini"},{"last_name":"Marrone","first_name":"Maria C.","full_name":"Marrone, Maria C."},{"first_name":"Maria","full_name":"Giubettini, Maria","last_name":"Giubettini"},{"first_name":"Valeria","full_name":"De Turris, Valeria","last_name":"De Turris"},{"first_name":"Debora","full_name":"Salerno, Debora","last_name":"Salerno"},{"first_name":"Stefano","full_name":"Garofalo, Stefano","last_name":"Garofalo"},{"first_name":"Marie‐Kim","full_name":"St‐Pierre, Marie‐Kim","last_name":"St‐Pierre"},{"first_name":"Micael","full_name":"Carrier, Micael","last_name":"Carrier"},{"last_name":"Renzi","first_name":"Massimiliano","full_name":"Renzi, Massimiliano"},{"first_name":"Francesca","full_name":"Pagani, Francesca","last_name":"Pagani"},{"last_name":"Modi","full_name":"Modi, Brijesh","first_name":"Brijesh"},{"first_name":"Marcello","full_name":"Raspa, Marcello","last_name":"Raspa"},{"last_name":"Scavizzi","first_name":"Ferdinando","full_name":"Scavizzi, Ferdinando"},{"last_name":"Gross","first_name":"Cornelius T.","full_name":"Gross, Cornelius T."},{"last_name":"Marinelli","full_name":"Marinelli, Silvia","first_name":"Silvia"},{"last_name":"Tremblay","full_name":"Tremblay, Marie‐Ève","first_name":"Marie‐Ève"},{"full_name":"Caprioli, Daniele","first_name":"Daniele","last_name":"Caprioli"},{"last_name":"Maggi","full_name":"Maggi, Laura","first_name":"Laura"},{"last_name":"Limatola","first_name":"Cristina","full_name":"Limatola, Cristina"},{"last_name":"Di Angelantonio","first_name":"Silvia","full_name":"Di Angelantonio, Silvia"},{"first_name":"Davide","full_name":"Ragozzino, Davide","last_name":"Ragozzino"}],"ddc":["570"],"article_processing_charge":"No","year":"2022","oa":1,"oa_version":"Published Version","issue":"1","intvolume":" 70","month":"01"},{"type":"conference","status":"public","_id":"10820","doi":"10.1007/978-3-030-67902-6_51","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"London, United Kingdom","start_date":"2019-09-02","name":"IUTAM Symposium","end_date":"2019-09-06"},"abstract":[{"lang":"eng","text":"Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating."}],"title":"Effects of streaky structures on the instability of supersonic boundary layers","date_updated":"2025-05-20T06:08:26Z","page":"587-598","day":"01","date_published":"2022-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/978-3-030-67902-6_51","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000709087600051"]},"OA_type":"closed access","quality_controlled":"1","volume":38,"publication_identifier":{"eisbn":["9783030679026"],"isbn":["9783030679019"],"eissn":["1875-3493"],"issn":["1875-3507"]},"acknowledgement":"The work is supported by the National Key Research and Development Program of China (No. 2016YFA0401200), the National Natural Science Foundation of China (Grant Nos. 91952202 and 11402167).","publication":"IUTAM Laminar-Turbulent Transition","scopus_import":"1","department":[{"_id":"BjHo"}],"date_created":"2022-03-04T09:14:34Z","alternative_title":["IUTAM"],"citation":{"ista":"Liu J, Marensi E, Wu X. 2022. Effects of streaky structures on the instability of supersonic boundary layers. IUTAM Laminar-Turbulent Transition. IUTAM Symposium, IUTAM, vol. 38, 587–598.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. Vol 38. Springer Nature; 2022:587-598. doi:10.1007/978-3-030-67902-6_51","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” IUTAM Laminar-Turbulent Transition, vol. 38, Springer Nature, 2022, pp. 587–98, doi:10.1007/978-3-030-67902-6_51.","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in IUTAM Laminar-Turbulent Transition, London, United Kingdom, 2022, vol. 38, pp. 587–598.","apa":"Liu, J., Marensi, E., & Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In IUTAM Laminar-Turbulent Transition (Vol. 38, pp. 587–598). London, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-67902-6_51","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In IUTAM Laminar-Turbulent Transition, 38:587–98. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67902-6_51."},"oa_version":"None","intvolume":" 38","month":"01","article_processing_charge":"No","year":"2022","publication_status":"published","author":[{"full_name":"Liu, Jianxin","first_name":"Jianxin","last_name":"Liu"},{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","orcid":"0000-0001-7173-4923","full_name":"Marensi, Elena","last_name":"Marensi"},{"last_name":"Wu","full_name":"Wu, Xuesong","first_name":"Xuesong"}]},{"publication_status":"published","article_type":"original","author":[{"last_name":"Yanagida","full_name":"Yanagida, Ayaka","first_name":"Ayaka"},{"full_name":"Corujo-Simon, Elena","first_name":"Elena","last_name":"Corujo-Simon"},{"first_name":"Christopher K.","full_name":"Revell, Christopher K.","last_name":"Revell"},{"full_name":"Sahu, Preeti","first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","last_name":"Sahu"},{"last_name":"Stirparo","first_name":"Giuliano G.","full_name":"Stirparo, Giuliano G."},{"first_name":"Irene M.","full_name":"Aspalter, Irene M.","last_name":"Aspalter"},{"last_name":"Winkel","full_name":"Winkel, Alex K.","first_name":"Alex K."},{"first_name":"Ruby","full_name":"Peters, Ruby","last_name":"Peters"},{"full_name":"De Belly, Henry","first_name":"Henry","last_name":"De Belly"},{"full_name":"Cassani, Davide A.D.","first_name":"Davide A.D.","last_name":"Cassani"},{"last_name":"Achouri","first_name":"Sarra","full_name":"Achouri, Sarra"},{"last_name":"Blumenfeld","full_name":"Blumenfeld, Raphael","first_name":"Raphael"},{"full_name":"Franze, Kristian","first_name":"Kristian","last_name":"Franze"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Paluch","full_name":"Paluch, Ewa K.","first_name":"Ewa K."},{"last_name":"Nichols","first_name":"Jennifer","full_name":"Nichols, Jennifer"},{"first_name":"Kevin J.","full_name":"Chalut, Kevin J.","last_name":"Chalut"}],"ddc":["570"],"article_processing_charge":"No","oa":1,"year":"2022","issue":"5","oa_version":"Published Version","intvolume":" 185","month":"02","has_accepted_license":"1","citation":{"mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:10.1016/j.cell.2022.01.022.","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 2022;185(5):777-793.e20. doi:10.1016/j.cell.2022.01.022","ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell. Cell Press, 2022. https://doi.org/10.1016/j.cell.2022.01.022.","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. Cell. Cell Press. https://doi.org/10.1016/j.cell.2022.01.022","ieee":"A. Yanagida et al., “Cell surface fluctuations regulate early embryonic lineage sorting,” Cell, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20."},"publication":"Cell","department":[{"_id":"EdHa"}],"scopus_import":"1","date_created":"2022-03-06T23:01:52Z","acknowledgement":"We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","quality_controlled":"1","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"ec_funded":1,"volume":185,"file":[{"date_updated":"2022-03-07T07:55:23Z","checksum":"ae305060e8031297771b89dae9e36a29","file_size":8478995,"creator":"dernst","success":1,"date_created":"2022-03-07T07:55:23Z","relation":"main_file","file_id":"10831","access_level":"open_access","content_type":"application/pdf","file_name":"2022_Cell_Yanagida.pdf"}],"fulldoi":"https://doi.org/10.1016/j.cell.2022.01.022","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000796293700007"],"pmid":["35196500"]},"day":"22","date_published":"2022-02-22T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"777-793.e20","date_updated":"2025-07-10T11:50:00Z","pmid":1,"file_date_updated":"2022-03-07T07:55:23Z","abstract":[{"text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.","lang":"eng"}],"title":"Cell surface fluctuations regulate early embryonic lineage sorting","doi":"10.1016/j.cell.2022.01.022","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"status":"public","_id":"10825"},{"oa":1,"year":"2022","article_processing_charge":"No","month":"02","oa_version":"Published Version","intvolume":" 11","author":[{"full_name":"Valperga, Giulio","orcid":"0000-0001-6726-3890","first_name":"Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E","last_name":"Valperga"},{"last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario"}],"publication_status":"published","article_type":"original","ddc":["570"],"article_number":"e68040","acknowledgement":"We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB).","volume":11,"publication_identifier":{"eissn":["2050-084X"]},"quality_controlled":"1","citation":{"mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife, vol. 11, e68040, eLife Sciences Publications, 2022, doi:10.7554/eLife.68040.","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 2022;11. doi:10.7554/eLife.68040","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.68040.","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” eLife, vol. 11. eLife Sciences Publications, 2022.","apa":"Valperga, G., & de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68040","short":"G. Valperga, M. de Bono, ELife 11 (2022)."},"corr_author":"1","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"date_created":"2022-03-06T23:01:52Z","department":[{"_id":"MaDe"}],"scopus_import":"1","publication":"eLife","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"external_id":{"pmid":["35201977"],"isi":["000763432300001"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"10830","file_name":"2022_eLife_Valperga.pdf","content_type":"application/pdf","file_size":4095591,"date_updated":"2022-03-07T07:39:25Z","checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","relation":"main_file","date_created":"2022-03-07T07:39:25Z","success":1,"creator":"dernst"}],"fulldoi":"https://doi.org/10.7554/eLife.68040","isi":1,"date_published":"2022-02-24T00:00:00Z","day":"24","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.68040","_id":"10826","status":"public","project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"}],"type":"journal_article","pmid":1,"date_updated":"2026-04-02T12:45:39Z","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","abstract":[{"text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.","lang":"eng"}],"file_date_updated":"2022-03-07T07:39:25Z"},{"date_published":"2022-01-13T00:00:00Z","day":"13","external_id":{"isi":["000800559503126"],"arxiv":["2111.05663"]},"fulldoi":"https://doi.org/10.1109/BigData52589.2021.9671483","isi":1,"language":[{"iso":"eng"}],"type":"conference","_id":"10828","status":"public","publisher":"IEEE","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1109/BigData52589.2021.9671483","title":"The impact of changes in resolution on the persistent homology of images","conference":{"start_date":"2021-12-15","location":"Orlando, FL, United States; Virtuell","name":"Big Data: International Conference on Big Data","end_date":"2021-12-18"},"abstract":[{"lang":"eng","text":"Digital images enable quantitative analysis of material properties at micro and macro length scales, but choosing an appropriate resolution when acquiring the image is challenging. A high resolution means longer image acquisition and larger data requirements for a given sample, but if the resolution is too low, significant information may be lost. This paper studies the impact of changes in resolution on persistent homology, a tool from topological data analysis that provides a signature of structure in an image across all length scales. Given prior information about a function, the geometry of an object, or its density distribution at a given resolution, we provide methods to select the coarsest resolution yielding results within an acceptable tolerance. We present numerical case studies for an illustrative synthetic example and samples from porous materials where the theoretical bounds are unknown."}],"date_updated":"2026-04-07T12:54:09Z","page":"3824-3834","month":"01","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.05663"}],"article_processing_charge":"No","oa":1,"year":"2022","publication_status":"published","author":[{"orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss"},{"first_name":"Sarah","full_name":"Tymochko, Sarah","last_name":"Tymochko"},{"last_name":"Story","first_name":"Brittany","full_name":"Story, Brittany"},{"last_name":"Garin","full_name":"Garin, Adélie","first_name":"Adélie"},{"full_name":"Bui, Hoa","first_name":"Hoa","last_name":"Bui"},{"last_name":"Bleile","first_name":"Bea","full_name":"Bleile, Bea"},{"full_name":"Robins, Vanessa","first_name":"Vanessa","last_name":"Robins"}],"publication_identifier":{"isbn":["9781665439022"]},"arxiv":1,"quality_controlled":"1","department":[{"_id":"HeEd"}],"scopus_import":"1","date_created":"2022-03-06T23:01:53Z","publication":"2021 IEEE International Conference on Big Data","citation":{"ista":"Heiss T, Tymochko S, Story B, Garin A, Bui H, Bleile B, Robins V. 2022. The impact of changes in resolution on the persistent homology of images. 2021 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 3824–3834.","mla":"Heiss, Teresa, et al. “The Impact of Changes in Resolution on the Persistent Homology of Images.” 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 3824–34, doi:10.1109/BigData52589.2021.9671483.","ama":"Heiss T, Tymochko S, Story B, et al. The impact of changes in resolution on the persistent homology of images. In: 2021 IEEE International Conference on Big Data. IEEE; 2022:3824-3834. doi:10.1109/BigData52589.2021.9671483","short":"T. Heiss, S. Tymochko, B. Story, A. Garin, H. Bui, B. Bleile, V. Robins, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 3824–3834.","ieee":"T. Heiss et al., “The impact of changes in resolution on the persistent homology of images,” in 2021 IEEE International Conference on Big Data, Orlando, FL, United States; Virtuell, 2022, pp. 3824–3834.","apa":"Heiss, T., Tymochko, S., Story, B., Garin, A., Bui, H., Bleile, B., & Robins, V. (2022). The impact of changes in resolution on the persistent homology of images. In 2021 IEEE International Conference on Big Data (pp. 3824–3834). Orlando, FL, United States; Virtuell: IEEE. https://doi.org/10.1109/BigData52589.2021.9671483","chicago":"Heiss, Teresa, Sarah Tymochko, Brittany Story, Adélie Garin, Hoa Bui, Bea Bleile, and Vanessa Robins. “The Impact of Changes in Resolution on the Persistent Homology of Images.” In 2021 IEEE International Conference on Big Data, 3824–34. IEEE, 2022. https://doi.org/10.1109/BigData52589.2021.9671483."},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18667"}]}},{"quality_controlled":"1","volume":7,"publication_identifier":{"eissn":["2379-3694"]},"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research. The data that support the findings of this study are openly available in Zenodo (DOI: 10.5281/zenodo.5500360)","publication":"ACS Sensors","date_created":"2022-03-06T23:01:54Z","department":[{"_id":"MaIb"}],"scopus_import":"1","has_accepted_license":"1","related_material":{"record":[{"id":"10833","status":"public","relation":"research_data"}]},"citation":{"short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, ACS Sensors 7 (2022) 504–512.","ieee":"R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” ACS Sensors, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. American Chemical Society. https://doi.org/10.1021/acssensors.1c02313","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” ACS Sensors. American Chemical Society, 2022. https://doi.org/10.1021/acssensors.1c02313.","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. 7(2), 504–512.","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. 2022;7(2):504-512. doi:10.1021/acssensors.1c02313","mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” ACS Sensors, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:10.1021/acssensors.1c02313."},"oa_version":"Published Version","issue":"2","intvolume":" 7","month":"02","year":"2022","oa":1,"article_processing_charge":"No","ddc":["540"],"author":[{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"last_name":"Fossati","first_name":"Stefan","full_name":"Fossati, Stefan"},{"full_name":"Aspermair, Patrik","first_name":"Patrik","last_name":"Aspermair"},{"last_name":"Dostalek","first_name":"Jakub","full_name":"Dostalek, Jakub"},{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"},{"last_name":"Bintinger","full_name":"Bintinger, Johannes","first_name":"Johannes"},{"last_name":"Knoll","first_name":"Wolfgang","full_name":"Knoll, Wolfgang"}],"publication_status":"published","article_type":"original","_id":"10829","status":"public","type":"journal_article","doi":"10.1021/acssensors.1c02313","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"American Chemical Society","abstract":[{"text":"A novel multivariable system, combining a transistor with fiber optic-based surface plasmon resonance spectroscopy with the gate electrode simultaneously acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows for discrimination of mass and charge contributions for binding assays on the same sensor surface. Furthermore, we optimize the sensor geometry by investigating the influence of the fiber area to transistor channel area ratio and distance. We show that larger fiber optic tip diameters are favorable for electronic and optical signals and demonstrate the reversibility of plasmon resonance wavelength shifts after electric field application. As a proof of principle, a layer-by-layer assembly of polyelectrolytes is performed to benchmark the system against multivariable sensing platforms with planar surface plasmon resonance configurations. Furthermore, the biosensing performance is assessed using a thrombin binding assay with surface-immobilized aptamers as receptors, allowing for the detection of medically relevant thrombin concentrations.","lang":"eng"}],"file_date_updated":"2022-03-07T08:15:01Z","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","date_updated":"2026-04-02T12:33:46Z","page":"504-512","pmid":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"date_published":"2022-02-08T00:00:00Z","day":"08","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1021/acssensors.1c02313","file":[{"file_size":2969415,"checksum":"d704af7262cd484da9bb84b7d84e2b09","date_updated":"2022-03-07T08:15:01Z","relation":"main_file","date_created":"2022-03-07T08:15:01Z","success":1,"creator":"dernst","access_level":"open_access","file_id":"10832","file_name":"2022_ACSSensors_Hasler.pdf","content_type":"application/pdf"}],"isi":1,"external_id":{"isi":["000765113000016"],"pmid":["35134289"]}}]