[{"volume":32,"publication":"Molecular Ecology","date_published":"2023-03-01T00:00:00Z","intvolume":"        32","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"publisher":"Wiley","doi":"10.1111/mec.16793","quality_controlled":"1","has_accepted_license":"1","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"ddc":["570"],"oa_version":"Published Version","article_type":"original","year":"2023","scopus_import":"1","file_date_updated":"2023-08-16T08:15:41Z","license":"https://creativecommons.org/licenses/by/4.0/","_id":"12159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","day":"01","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).","corr_author":"1","isi":1,"title":"On the origin and structure of haplotype blocks","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"oa":1,"citation":{"apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>.","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.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>."},"date_updated":"2026-08-02T22:30:45Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","type":"journal_article","month":"03","file":[{"creator":"dernst","file_id":"14062","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","success":1,"file_size":7144607,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2023_MolecularEcology_Shipilina.pdf","date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z"}],"page":"1441-1457","publication_status":"published","related_material":{"record":[{"status":"public","id":"20694","relation":"dissertation_contains"}]},"pmid":1,"author":[{"last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","full_name":"Shipilina, Daria"},{"first_name":"Arka","orcid":"0000-0002-4530-8469","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"date_created":"2023-01-12T12:09:17Z"},{"ec_funded":1,"date_published":"2023-11-10T00:00:00Z","publisher":"Institute of Science and Technology Austria","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. "}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"has_accepted_license":"1","doi":"10.15479/at:ista:14510","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2023","oa_version":"Published Version","ddc":["570"],"day":"10","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"14510","file_date_updated":"2024-11-23T23:30:38Z","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-08-02T22:30:56Z","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>"},"OA_place":"publisher","title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","corr_author":"1","month":"11","type":"dissertation","file":[{"file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_created":"2023-11-20T09:18:51Z","date_updated":"2024-11-23T23:30:38Z","access_level":"closed","relation":"source_file","embargo_to":"open_access","creator":"ngnyliuk","file_size":20824903,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14567","checksum":"3d5e680bfc61f98e308c434f45cc9bd6"},{"date_updated":"2024-11-23T23:30:38Z","embargo":"2024-11-23","date_created":"2023-11-20T09:23:11Z","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","relation":"main_file","access_level":"open_access","creator":"ngnyliuk","content_type":"application/pdf","file_size":24871844,"file_id":"14568","checksum":"bfc96d47fc4e7e857dd71656097214a4"}],"page":"180","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"date_created":"2023-11-10T09:10:06Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"author":[{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"14591","status":"public"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"8139","relation":"part_of_dissertation"}]}},{"_id":"14591","date_published":"2023-10-10T00:00:00Z","publication":"bioRxiv","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","corr_author":"1","language":[{"iso":"eng"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","OA_place":"repository","article_processing_charge":"No","citation":{"ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. .","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","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, <a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","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.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>","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. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>"},"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."}],"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"date_updated":"2026-08-02T22:30:55Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.09.561523"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1101/2023.10.09.561523","status":"public","month":"10","type":"preprint","related_material":{"record":[{"relation":"later_version","status":"public","id":"15330"},{"relation":"dissertation_contains","status":"public","id":"14510"}]},"oa_version":"Preprint","publication_status":"draft","author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nagel, Marie-Kristin","first_name":"Marie-Kristin","last_name":"Nagel"},{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Isono, Erika","last_name":"Isono","first_name":"Erika"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"year":"2023","date_created":"2023-11-22T10:17:49Z"},{"date_published":"2023-01-09T00:00:00Z","ec_funded":1,"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","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-026-8"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"doi":"10.15479/at:ista:12470","has_accepted_license":"1","year":"2023","ddc":["610"],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"09","supervisor":[{"full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-07-27T22:30:54Z","_id":"12470","citation":{"mla":"Michalska, Julia M. <i>A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>.","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.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>","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. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>.","apa":"Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>"},"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-07-06T12:50:45Z","corr_author":"1","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","OA_place":"publisher","alternative_title":["ISTA Thesis"],"file":[{"creator":"cchlebak","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_id":"12471","content_type":"application/pdf","file_size":41771714,"relation":"main_file","access_level":"open_access","date_created":"2023-01-31T15:11:42Z","date_updated":"2023-07-27T22:30:54Z","embargo":"2023-07-09","file_name":"20230109_PhD_thesis_JM_final.pdf"},{"file_name":"20230109_PhD_thesis_JM_final.docx","date_created":"2023-01-31T15:11:51Z","date_updated":"2023-07-10T22:30:04Z","access_level":"closed","relation":"source_file","embargo_to":"open_access","creator":"cchlebak","file_size":66983464,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_id":"12472"}],"page":"201","type":"dissertation","month":"01","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_created":"2023-01-31T15:10:53Z","related_material":{"record":[{"id":"11943","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11950","status":"public"}]},"publication_status":"published","author":[{"last_name":"Michalska","orcid":"0000-0003-3862-1235","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M"}]},{"year":"2023","article_type":"original","oa_version":"Published Version","ddc":["570"],"publication_identifier":{"issn":["2056-3744"]},"has_accepted_license":"1","quality_controlled":"1","doi":"10.1093/evlett/qrac004","publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","intvolume":"         7","date_published":"2023-02-01T00:00:00Z","publication":"Evolution Letters","ec_funded":1,"volume":7,"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"date_created":"2023-02-06T13:59:12Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"pmid":1,"author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea","full_name":"Mrnjavac, Andrea"},{"full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","orcid":"0000-0002-6246-1465","first_name":"Kseniia"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18531"}]},"publication_status":"published","file":[{"content_type":"application/pdf","file_size":2592189,"success":1,"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_id":"14068","creator":"dernst","date_updated":"2023-08-16T11:43:33Z","date_created":"2023-08-16T11:43:33Z","file_name":"2023_EvLetters_Mrnjavac.pdf","relation":"main_file","access_level":"open_access"}],"month":"02","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_updated":"2026-08-02T22:31:09Z","oa":1,"citation":{"ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","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.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (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.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>"},"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"}],"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","corr_author":"1","isi":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","day":"01","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12521","file_date_updated":"2023-08-16T11:43:33Z","scopus_import":"1"},{"_id":"14622","file_date_updated":"2024-11-30T23:30:03Z","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","day":"30","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_place":"publisher","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","corr_author":"1","date_updated":"2026-07-29T13:17:04Z","project":[{"name":"IMB PhD Nomination Fellowship - Stefan Sack","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"oa":1,"citation":{"apa":"Sack, S. (2023). <i>Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","mla":"Sack, Stefan. <i>Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023."},"degree_awarded":"PhD","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"month":"11","type":"dissertation","page":"142","file":[{"creator":"ssack","file_size":11947523,"content_type":"application/pdf","checksum":"068fd3570506ec42b2faa390de784bc4","file_id":"14635","file_name":"PhD_Thesis.pdf","date_updated":"2024-11-30T23:30:03Z","embargo":"2024-11-30","date_created":"2023-11-30T15:53:10Z","access_level":"open_access","relation":"main_file"},{"file_id":"14636","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_size":18422964,"content_type":"application/zip","creator":"ssack","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_name":"PhD Thesis (1).zip","date_created":"2023-11-30T15:54:11Z","date_updated":"2024-11-30T23:30:03Z"}],"alternative_title":["ISTA Thesis"],"author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan","orcid":"0000-0001-5400-8508"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"13125"},{"status":"public","id":"11471","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9760","status":"public"}]},"date_created":"2023-11-28T10:58:13Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"ec_funded":1,"doi_confirm":"1","date_published":"2023-11-30T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","doi":"10.15479/at:ista:14622","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","ddc":["530"],"year":"2023"},{"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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). ","day":"02","article_number":"062404","file_date_updated":"2023-06-13T07:28:36Z","scopus_import":"1","_id":"13125","oa":1,"citation":{"short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","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.” <i>Physical Review A</i>, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>.","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., &#38; Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>.","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>"},"project":[{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"date_updated":"2026-08-02T22:31:11Z","isi":1,"corr_author":"1","arxiv":1,"title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2023-06-13T07:28:36Z","date_created":"2023-06-13T07:28:36Z","file_name":"2023_PhysRevA_Sack.pdf","checksum":"0d71423888eeccaa60d8f41197f26306","success":1,"file_id":"13131","content_type":"application/pdf","file_size":2524611,"creator":"dernst"}],"type":"journal_article","month":"06","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","department":[{"_id":"MaSe"}],"date_created":"2023-06-07T06:57:32Z","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"related_material":{"record":[{"status":"public","id":"17208","relation":"dissertation_contains"},{"id":"14622","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan"},{"id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","first_name":"Raimel A","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A"},{"last_name":"Kueng","first_name":"Richard","full_name":"Kueng, Richard"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"date_published":"2023-06-02T00:00:00Z","publication":"Physical Review A","volume":107,"ec_funded":1,"intvolume":"       107","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. "}],"publisher":"American Physical Society","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"quality_controlled":"1","doi":"10.1103/physreva.107.062404","has_accepted_license":"1","year":"2023","ddc":["530"],"oa_version":"Published Version","article_type":"original"},{"citation":{"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.","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.","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>.","ieee":"B. Basilico <i>et al.</i>, “Microglia control glutamatergic synapses in the adult mouse hippocampus,” <i>Glia</i>, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","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. <i>Glia</i>. Wiley. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>","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.” <i>Glia</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>.","ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. 2022;70(1):173-195. doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>"},"oa":1,"date_updated":"2024-10-09T21:04:02Z","corr_author":"1","isi":1,"title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","day":"01","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.","file_date_updated":"2022-03-04T08:55:27Z","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"10818","department":[{"_id":"GaNo"}],"external_id":{"isi":["000708025800001"],"pmid":["34661306"]},"date_created":"2022-03-04T08:53:37Z","publication_status":"published","pmid":1,"author":[{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico"},{"full_name":"Ferrucci, Laura","last_name":"Ferrucci","first_name":"Laura"},{"first_name":"Patrizia","last_name":"Ratano","full_name":"Ratano, Patrizia"},{"full_name":"Golia, Maria T.","last_name":"Golia","first_name":"Maria T."},{"full_name":"Grimaldi, Alfonso","last_name":"Grimaldi","first_name":"Alfonso"},{"first_name":"Maria","last_name":"Rosito","full_name":"Rosito, Maria"},{"last_name":"Ferretti","first_name":"Valentina","full_name":"Ferretti, Valentina"},{"last_name":"Reverte","first_name":"Ingrid","full_name":"Reverte, Ingrid"},{"full_name":"Sanchini, Caterina","last_name":"Sanchini","first_name":"Caterina"},{"full_name":"Marrone, Maria C.","first_name":"Maria C.","last_name":"Marrone"},{"full_name":"Giubettini, Maria","first_name":"Maria","last_name":"Giubettini"},{"full_name":"De Turris, Valeria","first_name":"Valeria","last_name":"De Turris"},{"full_name":"Salerno, Debora","first_name":"Debora","last_name":"Salerno"},{"last_name":"Garofalo","first_name":"Stefano","full_name":"Garofalo, Stefano"},{"full_name":"St‐Pierre, Marie‐Kim","first_name":"Marie‐Kim","last_name":"St‐Pierre"},{"last_name":"Carrier","first_name":"Micael","full_name":"Carrier, Micael"},{"full_name":"Renzi, Massimiliano","last_name":"Renzi","first_name":"Massimiliano"},{"full_name":"Pagani, Francesca","last_name":"Pagani","first_name":"Francesca"},{"first_name":"Brijesh","last_name":"Modi","full_name":"Modi, Brijesh"},{"last_name":"Raspa","first_name":"Marcello","full_name":"Raspa, Marcello"},{"first_name":"Ferdinando","last_name":"Scavizzi","full_name":"Scavizzi, Ferdinando"},{"last_name":"Gross","first_name":"Cornelius T.","full_name":"Gross, Cornelius T."},{"first_name":"Silvia","last_name":"Marinelli","full_name":"Marinelli, Silvia"},{"first_name":"Marie‐Ève","last_name":"Tremblay","full_name":"Tremblay, Marie‐Ève"},{"last_name":"Caprioli","first_name":"Daniele","full_name":"Caprioli, Daniele"},{"first_name":"Laura","last_name":"Maggi","full_name":"Maggi, Laura"},{"full_name":"Limatola, Cristina","first_name":"Cristina","last_name":"Limatola"},{"full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio","first_name":"Silvia"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"}],"month":"01","type":"journal_article","page":"173-195","file":[{"creator":"dernst","checksum":"f10a897290e66c0a062e04ba91db6c17","success":1,"file_id":"10819","content_type":"application/pdf","file_size":5340294,"relation":"main_file","access_level":"open_access","date_updated":"2022-03-04T08:55:27Z","date_created":"2022-03-04T08:55:27Z","file_name":"2021_Glia_Basilico.pdf"}],"keyword":["Cellular and Molecular Neuroscience","Neurology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"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."}],"publisher":"Wiley","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":70,"date_published":"2022-01-01T00:00:00Z","publication":"Glia","intvolume":"        70","year":"2022","oa_version":"Published Version","ddc":["570"],"article_type":"original","publication_identifier":{"eissn":["1098-1136"],"issn":["0894-1491"]},"doi":"10.1002/glia.24101","quality_controlled":"1","has_accepted_license":"1"},{"year":"2022","oa_version":"None","publication_identifier":{"eissn":["1875-3493"],"eisbn":["9783030679026"],"issn":["1875-3507"],"isbn":["9783030679019"]},"quality_controlled":"1","doi":"10.1007/978-3-030-67902-6_51","conference":{"location":"London, United Kingdom","start_date":"2019-09-02","end_date":"2019-09-06","name":"IUTAM Symposium"},"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."}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"IUTAM Laminar-Turbulent Transition","date_published":"2022-01-01T00:00:00Z","volume":38,"OA_type":"closed access","intvolume":"        38","department":[{"_id":"BjHo"}],"external_id":{"isi":["000709087600051"]},"date_created":"2022-03-04T09:14:34Z","publication_status":"published","author":[{"first_name":"Jianxin","last_name":"Liu","full_name":"Liu, Jianxin"},{"full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","orcid":"0000-0001-7173-4923","first_name":"Elena","last_name":"Marensi"},{"first_name":"Xuesong","last_name":"Wu","full_name":"Wu, Xuesong"}],"alternative_title":["IUTAM"],"page":"587-598","type":"conference","month":"01","status":"public","citation":{"apa":"Liu, J., Marensi, E., &#38; Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In <i>IUTAM Laminar-Turbulent Transition</i> (Vol. 38, pp. 587–598). London, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In <i>IUTAM Laminar-Turbulent Transition</i>, 38:587–98. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: <i>IUTAM Laminar-Turbulent Transition</i>. Vol 38. Springer Nature; 2022:587-598. doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","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.","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in <i>IUTAM Laminar-Turbulent Transition</i>, London, United Kingdom, 2022, vol. 38, pp. 587–598.","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” <i>IUTAM Laminar-Turbulent Transition</i>, vol. 38, Springer Nature, 2022, pp. 587–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>."},"date_updated":"2025-05-20T06:08:26Z","isi":1,"title":"Effects of streaky structures on the instability of supersonic boundary layers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","day":"01","scopus_import":"1","_id":"10820"},{"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"quality_controlled":"1","doi":"10.1016/j.cell.2022.01.022","has_accepted_license":"1","year":"2022","oa_version":"Published Version","ddc":["570"],"article_type":"original","publication":"Cell","date_published":"2022-02-22T00:00:00Z","ec_funded":1,"volume":185,"intvolume":"       185","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"}],"publisher":"Cell Press","language":[{"iso":"eng"}],"article_processing_charge":"No","page":"777-793.e20","file":[{"file_id":"10831","success":1,"checksum":"ae305060e8031297771b89dae9e36a29","file_size":8478995,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","file_name":"2022_Cell_Yanagida.pdf","date_updated":"2022-03-07T07:55:23Z","date_created":"2022-03-07T07:55:23Z"}],"type":"journal_article","month":"02","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"EdHa"}],"external_id":{"isi":["000796293700007"],"pmid":["35196500"]},"date_created":"2022-03-06T23:01:52Z","publication_status":"published","author":[{"full_name":"Yanagida, Ayaka","first_name":"Ayaka","last_name":"Yanagida"},{"full_name":"Corujo-Simon, Elena","first_name":"Elena","last_name":"Corujo-Simon"},{"full_name":"Revell, Christopher K.","first_name":"Christopher K.","last_name":"Revell"},{"full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti","last_name":"Sahu"},{"full_name":"Stirparo, Giuliano G.","first_name":"Giuliano G.","last_name":"Stirparo"},{"first_name":"Irene M.","last_name":"Aspalter","full_name":"Aspalter, Irene M."},{"full_name":"Winkel, Alex K.","first_name":"Alex K.","last_name":"Winkel"},{"last_name":"Peters","first_name":"Ruby","full_name":"Peters, Ruby"},{"last_name":"De Belly","first_name":"Henry","full_name":"De Belly, Henry"},{"last_name":"Cassani","first_name":"Davide A.D.","full_name":"Cassani, Davide A.D."},{"last_name":"Achouri","first_name":"Sarra","full_name":"Achouri, Sarra"},{"full_name":"Blumenfeld, Raphael","first_name":"Raphael","last_name":"Blumenfeld"},{"full_name":"Franze, Kristian","first_name":"Kristian","last_name":"Franze"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"full_name":"Chalut, Kevin J.","first_name":"Kevin J.","last_name":"Chalut"}],"pmid":1,"issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","day":"22","file_date_updated":"2022-03-07T07:55:23Z","scopus_import":"1","_id":"10825","oa":1,"citation":{"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.","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.","ieee":"A. Yanagida <i>et al.</i>, “Cell surface fluctuations regulate early embryonic lineage sorting,” <i>Cell</i>, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>.","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. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. 2022;185(5):777-793.e20. doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>","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.” <i>Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>."},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"date_updated":"2025-07-10T11:50:00Z","isi":1,"title":"Cell surface fluctuations regulate early embryonic lineage sorting"},{"year":"2022","article_type":"original","ddc":["570"],"oa_version":"Published Version","publication_identifier":{"eissn":["2050-084X"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"quality_controlled":"1","doi":"10.7554/eLife.68040","publisher":"eLife Sciences Publications","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"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"        11","date_published":"2022-02-24T00:00:00Z","publication":"eLife","volume":11,"external_id":{"pmid":["35201977"],"isi":["000763432300001"]},"date_created":"2022-03-06T23:01:52Z","department":[{"_id":"MaDe"}],"pmid":1,"author":[{"last_name":"Valperga","first_name":"Giulio","orcid":"0000-0001-6726-3890","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E","full_name":"Valperga, Giulio"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono","full_name":"De Bono, Mario"}],"publication_status":"published","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4095591,"checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","file_id":"10830","success":1,"date_updated":"2022-03-07T07:39:25Z","date_created":"2022-03-07T07:39:25Z","file_name":"2022_eLife_Valperga.pdf","relation":"main_file","access_level":"open_access"}],"month":"02","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"date_updated":"2026-04-02T12:45:39Z","citation":{"mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>.","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","short":"G. Valperga, M. de Bono, ELife 11 (2022).","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.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>","apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>"},"oa":1,"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"}],"title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","isi":1,"corr_author":"1","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).","day":"24","article_number":"e68040","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"10826","file_date_updated":"2022-03-07T07:39:25Z","scopus_import":"1"},{"_id":"10827","scopus_import":"1","acknowledgement":"J.G.L. and B.C. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).","day":"16","article_number":"074106","issue":"7","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","corr_author":"1","isi":1,"arxiv":1,"date_updated":"2026-04-02T12:37:16Z","citation":{"mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>.","ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” <i>The Journal of chemical physics</i>, vol. 156, no. 7. AIP Publishing, 2022.","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>.","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of chemical physics</i>. 2022;156(7). doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>","apa":"Lee, J. G., Pickard, C. J., &#38; Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>"},"oa":1,"status":"public","type":"journal_article","month":"02","pmid":1,"author":[{"full_name":"Lee, Jacob G.","first_name":"Jacob G.","last_name":"Lee"},{"first_name":"Chris J.","last_name":"Pickard","full_name":"Pickard, Chris J."},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"publication_status":"published","date_created":"2022-03-06T23:01:53Z","external_id":{"pmid":["35183078"],"isi":["000796704500014"],"arxiv":["2111.12968"]},"department":[{"_id":"BiCh"}],"intvolume":"       156","publication":"The Journal of chemical physics","date_published":"2022-02-16T00:00:00Z","volume":156,"language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"AIP Publishing","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.12968"}],"abstract":[{"lang":"eng","text":"Titanium dioxide has been extensively studied in the rutile or anatase phase, while its high-pressure phases are less well-understood, despite that many are thought to have interesting optical, mechanical, and electrochemical properties. First-principles methods, such as density functional theory (DFT), are often used to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus, impractical for long time scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stabilities of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO2, we design an empirical model as a baseline and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called Δ-learning potential contains long-range electrostatic interactions and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range 0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition processes by compressing anatase at different temperatures. At 300 K, we predominantly observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic two-step mechanism with a highly ordered and collective atomic motion. At 2000 K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases, and our method is generally applicable to other functional materials with multiple polymorphs."}],"quality_controlled":"1","doi":"10.1063/5.0079844","publication_identifier":{"eissn":["1089-7690"]},"article_type":"original","oa_version":"Preprint","year":"2022"},{"publication_status":"published","related_material":{"record":[{"id":"18667","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","first_name":"Teresa","last_name":"Heiss"},{"first_name":"Sarah","last_name":"Tymochko","full_name":"Tymochko, Sarah"},{"full_name":"Story, Brittany","first_name":"Brittany","last_name":"Story"},{"full_name":"Garin, Adélie","last_name":"Garin","first_name":"Adélie"},{"full_name":"Bui, Hoa","last_name":"Bui","first_name":"Hoa"},{"first_name":"Bea","last_name":"Bleile","full_name":"Bleile, Bea"},{"last_name":"Robins","first_name":"Vanessa","full_name":"Robins, Vanessa"}],"department":[{"_id":"HeEd"}],"date_created":"2022-03-06T23:01:53Z","external_id":{"arxiv":["2111.05663"],"isi":["000800559503126"]},"status":"public","type":"conference","month":"01","page":"3824-3834","arxiv":1,"isi":1,"title":"The impact of changes in resolution on the persistent homology of images","oa":1,"citation":{"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.","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.","ieee":"T. Heiss <i>et al.</i>, “The impact of changes in resolution on the persistent homology of images,” in <i>2021 IEEE International Conference on Big Data</i>, Orlando, FL, United States; Virtuell, 2022, pp. 3824–3834.","mla":"Heiss, Teresa, et al. “The Impact of Changes in Resolution on the Persistent Homology of Images.” <i>2021 IEEE International Conference on Big Data</i>, IEEE, 2022, pp. 3824–34, doi:<a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">10.1109/BigData52589.2021.9671483</a>.","apa":"Heiss, T., Tymochko, S., Story, B., Garin, A., Bui, H., Bleile, B., &#38; Robins, V. (2022). The impact of changes in resolution on the persistent homology of images. In <i>2021 IEEE International Conference on Big Data</i> (pp. 3824–3834). Orlando, FL, United States; Virtuell: IEEE. <a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">https://doi.org/10.1109/BigData52589.2021.9671483</a>","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 <i>2021 IEEE International Conference on Big Data</i>, 3824–34. IEEE, 2022. <a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">https://doi.org/10.1109/BigData52589.2021.9671483</a>.","ama":"Heiss T, Tymochko S, Story B, et al. The impact of changes in resolution on the persistent homology of images. In: <i>2021 IEEE International Conference on Big Data</i>. IEEE; 2022:3824-3834. doi:<a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">10.1109/BigData52589.2021.9671483</a>"},"date_updated":"2026-04-07T12:54:09Z","scopus_import":"1","_id":"10828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"13","oa_version":"Preprint","year":"2022","conference":{"name":"Big Data: International Conference on Big Data","end_date":"2021-12-18","location":"Orlando, FL, United States; Virtuell","start_date":"2021-12-15"},"doi":"10.1109/BigData52589.2021.9671483","quality_controlled":"1","publication_identifier":{"isbn":["9781665439022"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.05663"}],"date_published":"2022-01-13T00:00:00Z","publication":"2021 IEEE International Conference on Big Data"},{"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","month":"02","file":[{"checksum":"d704af7262cd484da9bb84b7d84e2b09","success":1,"file_id":"10832","content_type":"application/pdf","file_size":2969415,"creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2022-03-07T08:15:01Z","date_updated":"2022-03-07T08:15:01Z","file_name":"2022_ACSSensors_Hasler.pdf"}],"page":"504-512","pmid":1,"author":[{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"last_name":"Reiner-Rozman","first_name":"Ciril","full_name":"Reiner-Rozman, Ciril"},{"full_name":"Fossati, Stefan","first_name":"Stefan","last_name":"Fossati"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"first_name":"Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"full_name":"Knoll, Wolfgang","last_name":"Knoll","first_name":"Wolfgang"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"10833","relation":"research_data"}]},"external_id":{"pmid":["35134289"],"isi":["000765113000016"]},"date_created":"2022-03-06T23:01:54Z","department":[{"_id":"MaIb"}],"_id":"10829","scopus_import":"1","file_date_updated":"2022-03-07T08:15:01Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"08","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)","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","issue":"2","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","isi":1,"date_updated":"2026-04-02T12:33:46Z","citation":{"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.” <i>ACS Sensors</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>.","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. <i>ACS Sensors</i>. 2022;7(2):504-512. doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>","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. <i>ACS Sensors</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>","mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>.","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” <i>ACS Sensors</i>, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","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.","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."},"oa":1,"has_accepted_license":"1","doi":"10.1021/acssensors.1c02313","quality_controlled":"1","publication_identifier":{"eissn":["2379-3694"]},"article_type":"original","oa_version":"Published Version","ddc":["540"],"year":"2022","intvolume":"         7","volume":7,"date_published":"2022-02-08T00:00:00Z","publication":"ACS Sensors","article_processing_charge":"No","language":[{"iso":"eng"}],"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"}]},{"title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"citation":{"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. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>","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. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>","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.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>.","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, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","mla":"Hasler, Roger, et al. <i>Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022."},"oa":1,"date_updated":"2026-04-02T12:33:44Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}],"publisher":"Zenodo","_id":"10833","date_published":"2022-02-08T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"08","oa_version":"Published Version","ddc":["540"],"related_material":{"record":[{"relation":"used_in_publication","id":"10829","status":"public"}]},"author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"last_name":"Reiner-Rozman","first_name":"Ciril","full_name":"Reiner-Rozman, Ciril"},{"last_name":"Fossati","first_name":"Stefan","full_name":"Fossati, Stefan"},{"full_name":"Aspermair, Patrik","first_name":"Patrik","last_name":"Aspermair"},{"first_name":"Jakub","last_name":"Dostalek","full_name":"Dostalek, Jakub"},{"full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"last_name":"Bintinger","first_name":"Johannes","full_name":"Bintinger, Johannes"},{"first_name":"Wolfgang","last_name":"Knoll","full_name":"Knoll, Wolfgang"}],"department":[{"_id":"MaIb"}],"year":"2022","date_created":"2022-03-07T08:19:11Z","doi":"10.5281/ZENODO.5500360","status":"public","month":"02","type":"research_data_reference"},{"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"doi":"10.1093/plcell/koac071","quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"year":"2022","article_type":"original","oa_version":"Preprint","intvolume":"        34","volume":34,"publication":"Plant Cell","date_published":"2022-06-01T00:00:00Z","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"journal_article","month":"06","page":"2150-2173","status":"public","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"date_created":"2022-03-08T13:47:51Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"pmid":1,"author":[{"full_name":"Dahhan, DA","last_name":"Dahhan","first_name":"DA"},{"full_name":"Reynolds, GD","last_name":"Reynolds","first_name":"GD"},{"last_name":"Cárdenas","first_name":"JJ","full_name":"Cárdenas, JJ"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"full_name":"Yperman, K","first_name":"K","last_name":"Yperman"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315"},{"full_name":"Vang, N","last_name":"Vang","first_name":"N"},{"last_name":"Yan","first_name":"X","full_name":"Yan, X"},{"first_name":"I","last_name":"Hwang","full_name":"Hwang, I"},{"full_name":"Heese, A","last_name":"Heese","first_name":"A"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Van Damme","first_name":"D","full_name":"Van Damme, D"},{"first_name":"J","last_name":"Pan","full_name":"Pan, J"},{"first_name":"SY","last_name":"Bednarek","full_name":"Bednarek, SY"}],"publication_status":"published","day":"01","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","_id":"10841","scopus_import":"1","date_updated":"2025-05-14T11:06:15Z","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"citation":{"short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>."},"oa":1,"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","isi":1},{"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory."}],"publisher":"Springer Nature","volume":14,"date_published":"2022-07-01T00:00:00Z","publication":"Cryptography and Communications","intvolume":"        14","oa_version":"None","article_type":"original","year":"2022","doi":"10.1007/s12095-022-00557-8","quality_controlled":"1","publication_identifier":{"issn":["1936-2447"],"eissn":["1936-2455"]},"isi":1,"title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","citation":{"short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” <i>Cryptography and Communications</i>, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.","mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>.","apa":"Köse, S., &#38; Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>.","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. 2022;14(4):933-948. doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>"},"date_updated":"2023-09-05T15:35:55Z","scopus_import":"1","_id":"10842","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","day":"01","acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","publication_status":"published","author":[{"first_name":"Seyda","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","full_name":"Köse, Seyda"},{"full_name":"Özbudak, Ferruh","last_name":"Özbudak","first_name":"Ferruh"}],"department":[{"_id":"GradSch"}],"date_created":"2022-03-10T12:16:19Z","external_id":{"isi":["000766422000002"]},"keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"status":"public","month":"07","type":"journal_article","page":"933-948"},{"has_accepted_license":"1","doi":"10.1103/PhysRevResearch.4.013160","quality_controlled":"1","publication_identifier":{"issn":["2643-1564"]},"article_type":"original","oa_version":"Published Version","ddc":["530"],"year":"2022","intvolume":"         4","ec_funded":1,"volume":4,"publication":"Physical Review Research","date_published":"2022-03-01T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"American Physical Society","abstract":[{"text":"We study an impurity with a resonance level whose position coincides with the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation of the scattering phase shift for fermions at the Fermi surface, introducing a new characteristic length scale into the problem. We investigate manifestations of this length scale in the self-energy of the impurity and in the density of the bath. Our calculations reveal a model-independent deformation of the density of the Fermi gas, which is determined by the width of the resonance. To provide a broader picture, we investigate time evolution of the density in quench dynamics, and study the behavior of the system at finite temperatures. Finally, we briefly discuss implications of our findings for the Fermi-polaron problem.","lang":"eng"}],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","month":"03","file":[{"creator":"dernst","file_size":1258324,"content_type":"application/pdf","success":1,"file_id":"10848","checksum":"62f64b3421a969656ebf52467fa7b6e8","file_name":"2022_PhysicalReviewResearch_Maslov.pdf","date_created":"2022-03-14T08:38:49Z","date_updated":"2022-03-14T08:38:49Z","access_level":"open_access","relation":"main_file"}],"author":[{"full_name":"Maslov, Mikhail","first_name":"Mikhail","orcid":"0000-0003-4074-2570","last_name":"Maslov","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19048"}]},"external_id":{"arxiv":["2111.13570"]},"date_created":"2022-03-13T23:01:46Z","department":[{"_id":"MiLe"}],"_id":"10845","file_date_updated":"2022-03-14T08:38:49Z","scopus_import":"1","day":"01","article_number":"013160","acknowledgement":"M.L. acknowledges support by the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council (ERC) starting Grant No. 801770 (ANGULON). A.G.V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Impurity with a resonance in the vicinity of the Fermi energy","arxiv":1,"corr_author":"1","date_updated":"2026-04-07T11:52:53Z","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"citation":{"ama":"Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. 2022;4. doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>.","apa":"Maslov, M., Lemeshko, M., &#38; Volosniev, A. (2022). Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>","mla":"Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>, vol. 4, 013160, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>.","ieee":"M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the vicinity of the Fermi energy,” <i>Physical Review Research</i>, vol. 4. American Physical Society, 2022.","ista":"Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 4, 013160.","short":"M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022)."},"oa":1},{"has_accepted_license":"1","quality_controlled":"1","doi":"10.1016/j.jfa.2022.109455","publication_identifier":{"issn":["0022-1236"]},"article_type":"original","oa_version":"Published Version","ddc":["510"],"year":"2022","intvolume":"       282","publication":"Journal of Functional Analysis","date_published":"2022-06-15T00:00:00Z","ec_funded":1,"volume":282,"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","publisher":"Elsevier","abstract":[{"text":"We study two interacting quantum particles forming a bound state in d-dimensional free\r\nspace, and constrain the particles in k directions to (0, ∞)k ×Rd−k, with Neumann boundary\r\nconditions. First, we prove that the ground state energy strictly decreases upon going from k\r\nto k+1. This shows that the particles stick to the corner where all boundary planes intersect.\r\nSecond, we show that for all k the resulting Hamiltonian, after removing the free part of the\r\nkinetic energy, has only finitely many eigenvalues below the essential spectrum. This paper\r\ngeneralizes the work of Egger, Kerner and Pankrashkin (J. Spectr. Theory 10(4):1413–1444,\r\n2020) to dimensions d > 1.","lang":"eng"}],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Analysis"],"file":[{"date_updated":"2022-08-02T10:37:55Z","date_created":"2022-08-02T10:37:55Z","file_name":"2022_JourFunctionalAnalysis_Roos.pdf","relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":631391,"checksum":"63efcefaa1f2717244ef5407bd564426","success":1,"file_id":"11720"}],"month":"06","type":"journal_article","author":[{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","orcid":"0000-0002-9071-5880","last_name":"Roos","full_name":"Roos, Barbara"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14374"}]},"publication_status":"published","external_id":{"arxiv":["2105.04874"],"isi":["000795160200009"]},"date_created":"2022-03-16T08:41:53Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"_id":"10850","scopus_import":"1","file_date_updated":"2022-08-02T10:37:55Z","acknowledgement":"We thank Rupert Frank for contributing Appendix B. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 is gratefully acknowledged.","day":"15","article_number":"109455","issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Two-particle bound states at interfaces and corners","corr_author":"1","isi":1,"arxiv":1,"date_updated":"2026-04-07T13:27:39Z","oa":1,"citation":{"apa":"Roos, B., &#38; Seiringer, R. (2022). Two-particle bound states at interfaces and corners. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">https://doi.org/10.1016/j.jfa.2022.109455</a>","ama":"Roos B, Seiringer R. Two-particle bound states at interfaces and corners. <i>Journal of Functional Analysis</i>. 2022;282(12). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">10.1016/j.jfa.2022.109455</a>","chicago":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">https://doi.org/10.1016/j.jfa.2022.109455</a>.","short":"B. Roos, R. Seiringer, Journal of Functional Analysis 282 (2022).","ista":"Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 282(12), 109455.","ieee":"B. Roos and R. Seiringer, “Two-particle bound states at interfaces and corners,” <i>Journal of Functional Analysis</i>, vol. 282, no. 12. Elsevier, 2022.","mla":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” <i>Journal of Functional Analysis</i>, vol. 282, no. 12, 109455, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109455\">10.1016/j.jfa.2022.109455</a>."},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}]},{"scopus_import":"1","_id":"10851","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"10","day":"11","article_number":"107701","acknowledgement":"M. S. acknowledges useful discussions with A. Levchenko and P. A. Lee, and E. Berg. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. J. S. and A. G. acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.W. M. Hatefipour, W. M. Strickland and J. Shabani acknowledge funding from Office of Naval Research Award No. N00014-21-1-2450.","arxiv":1,"isi":1,"corr_author":"1","title":"Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"oa":1,"citation":{"ista":"Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn M, Higginbotham AP. 2022. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. Physical Review Letters. 128(10), 107701.","short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, Physical Review Letters 128 (2022).","mla":"Phan, Duc T., et al. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” <i>Physical Review Letters</i>, vol. 128, no. 10, 107701, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevlett.128.107701\">10.1103/physrevlett.128.107701</a>.","ieee":"D. T. Phan <i>et al.</i>, “Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit,” <i>Physical Review Letters</i>, vol. 128, no. 10. American Physical Society, 2022.","apa":"Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M., Shabani, J., … Higginbotham, A. P. (2022). Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.128.107701\">https://doi.org/10.1103/physrevlett.128.107701</a>","ama":"Phan DT, Senior JL, Ghazaryan A, et al. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. <i>Physical Review Letters</i>. 2022;128(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.128.107701\">10.1103/physrevlett.128.107701</a>","chicago":"Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland, J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevlett.128.107701\">https://doi.org/10.1103/physrevlett.128.107701</a>."},"date_updated":"2026-04-07T13:25:51Z","keyword":["General Physics and Astronomy"],"status":"public","type":"journal_article","month":"03","publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/characterizing-super-semi-sandwiches-for-quantum-computing/"}],"record":[{"relation":"earlier_version","id":"10029","status":"public"},{"id":"14547","status":"public","relation":"dissertation_contains"}]},"pmid":1,"author":[{"full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295","first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"full_name":"Hatefipour, M.","last_name":"Hatefipour","first_name":"M."},{"full_name":"Strickland, W. M.","first_name":"W. M.","last_name":"Strickland"},{"first_name":"J.","last_name":"Shabani","full_name":"Shabani, J."},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"}],"department":[{"_id":"MaSe"},{"_id":"AnHi"}],"external_id":{"pmid":[" 35333085"],"arxiv":["2107.03695"],"isi":["000771391100002"]},"date_created":"2022-03-17T11:37:47Z","volume":128,"ec_funded":1,"date_published":"2022-03-11T00:00:00Z","publication":"Physical Review Letters","intvolume":"       128","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"text":"Superconductor-semiconductor hybrid devices are at the heart of several proposed approaches to quantum information processing, but their basic properties remain to be understood. We embed a twodimensional Al-InAs hybrid system in a resonant microwave circuit, probing the breakdown of superconductivity due to an applied magnetic field. We find a fingerprint from the two-component nature of the hybrid system, and quantitatively compare with a theory that includes the contribution of intraband p±ip pairing in the InAs, as well as the emergence of Bogoliubov-Fermi surfaces due to magnetic field. Separately resolving the Al and InAs contributions allows us to determine the carrier density and mobility in the InAs.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.03695","open_access":"1"}],"publisher":"American Physical Society","doi":"10.1103/physrevlett.128.107701","quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa_version":"Preprint","article_type":"original","year":"2022"}]