[{"scopus_import":"1","acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","status":"public","citation":{"short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>, vol. 35, 100459, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>.","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>.","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” <i>Current Opinion in Systems Biology</i>, vol. 35. Elsevier, 2023.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. 2023;35. doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>","apa":"Minchington, T., Rus, S., &#38; Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>"},"file":[{"access_level":"open_access","success":1,"checksum":"8a75c4e29fd9b62e3c50663c2265b173","relation":"main_file","content_type":"application/pdf","file_name":"2023_CurrOpSystBioloy_Minchington.pdf","file_id":"14896","date_created":"2024-01-29T11:06:45Z","creator":"dernst","file_size":598842,"date_updated":"2024-01-29T11:06:45Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"corr_author":"1","month":"09","related_material":{"record":[{"id":"19763","relation":"dissertation_contains","status":"public"}]},"day":"01","doi":"10.1016/j.coisb.2023.100459","department":[{"_id":"AnKi"}],"publication_status":"published","file_date_updated":"2024-01-29T11:06:45Z","date_updated":"2026-06-24T22:30:33Z","type":"journal_article","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"publication_identifier":{"eissn":["2452-3100"]},"publication":"Current Opinion in Systems Biology","date_created":"2023-06-18T22:00:46Z","oa":1,"has_accepted_license":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Control of tissue dimensions in the developing neural tube and somites","article_number":"100459","year":"2023","publisher":"Elsevier","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"ddc":["570"],"article_processing_charge":"Yes (via OA deal)","date_published":"2023-09-01T00:00:00Z","volume":35,"intvolume":"        35","author":[{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington","first_name":"Thomas"},{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie","last_name":"Rus","first_name":"Stefanie","orcid":"0000-0001-8703-1093"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"_id":"13136"},{"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the origin and structure of haplotype blocks","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"has_accepted_license":"1","oa":1,"abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"date_created":"2023-01-12T12:09:17Z","publication":"Molecular Ecology","file_date_updated":"2023-08-16T08:15:41Z","date_updated":"2026-06-24T22:30:42Z","type":"journal_article","corr_author":"1","month":"03","related_material":{"record":[{"id":"20694","relation":"dissertation_contains","status":"public"}]},"day":"01","doi":"10.1111/mec.16793","department":[{"_id":"NiBa"}],"publication_status":"published","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","citation":{"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.","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>","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>.","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>.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","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."},"file":[{"creator":"dernst","file_size":7144607,"date_updated":"2023-08-16T08:15:41Z","file_name":"2023_MolecularEcology_Shipilina.pdf","file_id":"14062","date_created":"2023-08-16T08:15:41Z","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"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).","scopus_import":"1","external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"_id":"12159","issue":"6","author":[{"full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","orcid":"0000-0002-1145-9226","first_name":"Daria"},{"full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","orcid":"0000-0002-4530-8469","first_name":"Arka"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"isi":1,"intvolume":"        32","volume":32,"pmid":1,"date_published":"2023-03-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","page":"1441-1457","publisher":"Wiley","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"ddc":["570"],"year":"2023"},{"date_published":"2023-01-01T00:00:00Z","page":"1-7","article_processing_charge":"No","publisher":"Optica Publishing Group","year":"2023","issue":"1","_id":"14759","external_id":{"arxiv":["2208.11591"],"isi":["000906607900001"]},"author":[{"last_name":"Wald","full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","orcid":"0000-0002-5869-1604","first_name":"Sebastian"},{"last_name":"Diorico","full_name":"Diorico, Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4947-8924","first_name":"Fritz R"},{"first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","last_name":"Hosten"}],"isi":1,"intvolume":"        62","volume":62,"department":[{"_id":"OnHo"}],"publication_status":"published","doi":"10.1364/ao.474118","day":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20798"}]},"month":"01","corr_author":"1","oa_version":"Preprint","quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"citation":{"chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>.","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>.","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7.","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” <i>Applied Optics</i>, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. 2023;62(1):1-7. doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>","apa":"Wald, S., Diorico, F. R., &#38; Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>"},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.11591"}],"acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","article_type":"original","oa":1,"keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"publication":"Applied Optics","date_created":"2024-01-08T13:19:14Z","publication_identifier":{"eissn":["2155-3165"],"issn":["1559-128X"]},"abstract":[{"text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.","lang":"eng"}],"type":"journal_article","date_updated":"2026-06-24T22:30:43Z"},{"ddc":["530"],"publisher":"Springer Nature","project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"year":"2023","date_published":"2023-11-01T00:00:00Z","page":"1630-1635","article_processing_charge":"Yes (in subscription journal)","intvolume":"        19","volume":19,"_id":"14032","external_id":{"isi":["001054563800006"]},"isi":1,"author":[{"first_name":"Soham","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay"},{"orcid":"0000-0002-0672-9295","first_name":"Jorden L","last_name":"Senior","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"first_name":"Jaime","last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime"},{"last_name":"Puglia","full_name":"Puglia, Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0003-1144-2763","first_name":"Denise"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","orcid":"0000-0003-2607-2363"}],"citation":{"chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>"},"file":[{"file_id":"14899","date_created":"2024-01-29T11:25:38Z","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","date_updated":"2024-01-29T11:25:38Z","creator":"dernst","file_size":1977706,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"1fc86d71bfbf836e221c1e925343adc5","relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","scopus_import":"1","acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","day":"01","ec_funded":1,"doi":"10.1038/s41567-023-02161-w","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"corr_author":"1","month":"11","related_material":{"record":[{"status":"public","id":"17881","relation":"dissertation_contains"}]},"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication":"Nature Physics","date_created":"2023-08-11T07:41:17Z","abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"date_updated":"2026-06-24T22:30:55Z","type":"journal_article","file_date_updated":"2024-01-29T11:25:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Superconductivity from a melted insulator in Josephson junction arrays","article_type":"original","has_accepted_license":"1","oa":1,"keyword":["General Physics and Astronomy"]},{"intvolume":"       202","volume":202,"external_id":{"arxiv":["2212.13468"]},"_id":"14459","alternative_title":["PMLR"],"author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko","first_name":"Aleksandr"},{"last_name":"Kögler","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","full_name":"Kögler, Kevin","first_name":"Kevin"},{"last_name":"Hassani","full_name":"Hassani, Hamed","first_name":"Hamed"},{"first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"publisher":"ML Research Press","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"year":"2023","date_published":"2023-07-30T00:00:00Z","article_processing_charge":"No","page":"31151-31209","abstract":[{"text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.","lang":"eng"}],"publication_identifier":{"eissn":["2640-3498"]},"publication":"Proceedings of the 40th International Conference on Machine Learning","date_created":"2023-10-29T23:01:17Z","date_updated":"2026-06-24T22:30:54Z","type":"conference","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29","name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.13468"}],"status":"public","citation":{"ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:31151-31209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., &#38; Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 31151–209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:31151–209. ML Research Press, 2023."},"scopus_import":"1","acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","corr_author":"1","month":"07","related_material":{"record":[{"relation":"dissertation_contains","id":"17465","status":"public"}]},"day":"30","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"publication_status":"published","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint"},{"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publication_status":"published","ec_funded":1,"doi":"10.15479/at:ista:14510","day":"10","related_material":{"record":[{"status":"public","id":"14591","relation":"part_of_dissertation"},{"status":"public","id":"9887","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8139"}]},"corr_author":"1","month":"11","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","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>.","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>.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","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>","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>","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023."},"file":[{"date_created":"2023-11-20T09:18:51Z","file_id":"14567","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_updated":"2024-11-23T23:30:38Z","creator":"ngnyliuk","file_size":20824903,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","relation":"source_file"},{"file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_created":"2023-11-20T09:23:11Z","file_id":"14568","file_size":24871844,"creator":"ngnyliuk","embargo":"2024-11-23","date_updated":"2024-11-23T23:30:38Z","access_level":"open_access","relation":"main_file","checksum":"bfc96d47fc4e7e857dd71656097214a4","content_type":"application/pdf"}],"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","OA_place":"publisher","has_accepted_license":"1","oa":1,"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-11-10T09:10:06Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"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. "}],"type":"dissertation","date_updated":"2026-06-24T22:30:59Z","file_date_updated":"2024-11-23T23:30:38Z","date_published":"2023-11-10T00:00:00Z","page":"180","article_processing_charge":"No","ddc":["570"],"project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","year":"2023","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"_id":"14510","author":[{"full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","first_name":"Nataliia"}]},{"isi":1,"author":[{"first_name":"Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","last_name":"Basilico"},{"last_name":"Ferrucci","full_name":"Ferrucci, Laura","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."},{"first_name":"Alfonso","full_name":"Grimaldi, Alfonso","last_name":"Grimaldi"},{"last_name":"Rosito","full_name":"Rosito, Maria","first_name":"Maria"},{"first_name":"Valentina","last_name":"Ferretti","full_name":"Ferretti, Valentina"},{"full_name":"Reverte, Ingrid","last_name":"Reverte","first_name":"Ingrid"},{"last_name":"Sanchini","full_name":"Sanchini, Caterina","first_name":"Caterina"},{"first_name":"Maria C.","last_name":"Marrone","full_name":"Marrone, Maria C."},{"full_name":"Giubettini, Maria","last_name":"Giubettini","first_name":"Maria"},{"first_name":"Valeria","last_name":"De Turris","full_name":"De Turris, Valeria"},{"first_name":"Debora","last_name":"Salerno","full_name":"Salerno, Debora"},{"last_name":"Garofalo","full_name":"Garofalo, Stefano","first_name":"Stefano"},{"first_name":"Marie‐Kim","last_name":"St‐Pierre","full_name":"St‐Pierre, Marie‐Kim"},{"full_name":"Carrier, Micael","last_name":"Carrier","first_name":"Micael"},{"full_name":"Renzi, Massimiliano","last_name":"Renzi","first_name":"Massimiliano"},{"first_name":"Francesca","full_name":"Pagani, Francesca","last_name":"Pagani"},{"full_name":"Modi, Brijesh","last_name":"Modi","first_name":"Brijesh"},{"first_name":"Marcello","full_name":"Raspa, Marcello","last_name":"Raspa"},{"full_name":"Scavizzi, Ferdinando","last_name":"Scavizzi","first_name":"Ferdinando"},{"last_name":"Gross","full_name":"Gross, Cornelius T.","first_name":"Cornelius T."},{"first_name":"Silvia","last_name":"Marinelli","full_name":"Marinelli, Silvia"},{"first_name":"Marie‐Ève","last_name":"Tremblay","full_name":"Tremblay, Marie‐Ève"},{"full_name":"Caprioli, Daniele","last_name":"Caprioli","first_name":"Daniele"},{"first_name":"Laura","full_name":"Maggi, Laura","last_name":"Maggi"},{"full_name":"Limatola, Cristina","last_name":"Limatola","first_name":"Cristina"},{"full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio","first_name":"Silvia"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"}],"_id":"10818","issue":"1","external_id":{"isi":["000708025800001"],"pmid":["34661306"]},"volume":70,"intvolume":"        70","article_processing_charge":"No","page":"173-195","pmid":1,"date_published":"2022-01-01T00:00:00Z","year":"2022","publisher":"Wiley","ddc":["570"],"keyword":["Cellular and Molecular Neuroscience","Neurology"],"has_accepted_license":"1","oa":1,"article_type":"original","title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2022-03-04T08:55:27Z","date_updated":"2024-10-09T21:04:02Z","type":"journal_article","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."}],"publication_identifier":{"eissn":["1098-1136"],"issn":["0894-1491"]},"date_created":"2022-03-04T08:53:37Z","publication":"Glia","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","month":"01","corr_author":"1","day":"01","doi":"10.1002/glia.24101","publication_status":"published","department":[{"_id":"GaNo"}],"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.","scopus_import":"1","status":"public","citation":{"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>","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>","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.","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.","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>.","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>.","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."},"file":[{"success":1,"access_level":"open_access","relation":"main_file","checksum":"f10a897290e66c0a062e04ba91db6c17","content_type":"application/pdf","file_name":"2021_Glia_Basilico.pdf","date_created":"2022-03-04T08:55:27Z","file_id":"10819","file_size":5340294,"creator":"dernst","date_updated":"2022-03-04T08:55:27Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"}},{"month":"01","publication_status":"published","department":[{"_id":"BjHo"}],"day":"01","doi":"10.1007/978-3-030-67902-6_51","oa_version":"None","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","citation":{"ista":"Liu J, Marensi E, Wu X. 2022. Effects of streaky structures on the instability of supersonic boundary layers. IUTAM Laminar-Turbulent Transition. IUTAM Symposium, IUTAM, vol. 38, 587–598.","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>.","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>.","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","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>","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>","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."},"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).","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Effects of streaky structures on the instability of supersonic boundary layers","OA_type":"closed access","conference":{"location":"London, United Kingdom","end_date":"2019-09-06","name":"IUTAM Symposium","start_date":"2019-09-02"},"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."}],"publication":"IUTAM Laminar-Turbulent Transition","date_created":"2022-03-04T09:14:34Z","publication_identifier":{"eisbn":["9783030679026"],"isbn":["9783030679019"],"eissn":["1875-3493"],"issn":["1875-3507"]},"type":"conference","date_updated":"2025-05-20T06:08:26Z","date_published":"2022-01-01T00:00:00Z","article_processing_charge":"No","page":"587-598","publisher":"Springer Nature","year":"2022","alternative_title":["IUTAM"],"_id":"10820","external_id":{"isi":["000709087600051"]},"isi":1,"author":[{"full_name":"Liu, Jianxin","last_name":"Liu","first_name":"Jianxin"},{"full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","orcid":"0000-0001-7173-4923","first_name":"Elena"},{"first_name":"Xuesong","last_name":"Wu","full_name":"Wu, Xuesong"}],"intvolume":"        38","volume":38},{"author":[{"orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Hans J.","full_name":"Herrmann, Hans J.","last_name":"Herrmann"},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"first_name":"Dietmar","last_name":"Plenz","full_name":"Plenz, Dietmar"},{"first_name":"Silvia","full_name":"Scarpetta, Silvia","last_name":"Scarpetta"},{"first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"},{"first_name":"Oren","full_name":"Shriki, Oren","last_name":"Shriki"}],"_id":"10821","article_processing_charge":"No","page":"25","date_published":"2022-03-04T00:00:00Z","year":"2022","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"publisher":"Cold Spring Harbor Laboratory","oa":1,"OA_place":"repository","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","date_updated":"2025-04-15T06:55:02Z","abstract":[{"text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.","lang":"eng"}],"publication":"bioRxiv","date_created":"2022-03-04T22:20:59Z","oa_version":"Preprint","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"14402","relation":"later_version","status":"public"}]},"month":"03","corr_author":"1","department":[{"_id":"GaTk"}],"publication_status":"draft","ec_funded":1,"day":"04","doi":"10.1101/2022.03.03.482657","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.03.482657","open_access":"1"}],"status":"public","citation":{"ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (n.d.). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (n.d.).","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>."}},{"article_processing_charge":"No","page":"777-793.e20","pmid":1,"date_published":"2022-02-22T00:00:00Z","year":"2022","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"publisher":"Cell Press","ddc":["570"],"author":[{"first_name":"Ayaka","last_name":"Yanagida","full_name":"Yanagida, Ayaka"},{"first_name":"Elena","last_name":"Corujo-Simon","full_name":"Corujo-Simon, Elena"},{"first_name":"Christopher K.","full_name":"Revell, Christopher K.","last_name":"Revell"},{"full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","last_name":"Sahu","first_name":"Preeti"},{"full_name":"Stirparo, Giuliano G.","last_name":"Stirparo","first_name":"Giuliano G."},{"full_name":"Aspalter, Irene M.","last_name":"Aspalter","first_name":"Irene M."},{"last_name":"Winkel","full_name":"Winkel, Alex K.","first_name":"Alex K."},{"first_name":"Ruby","full_name":"Peters, Ruby","last_name":"Peters"},{"full_name":"De Belly, Henry","last_name":"De Belly","first_name":"Henry"},{"full_name":"Cassani, Davide A.D.","last_name":"Cassani","first_name":"Davide A.D."},{"last_name":"Achouri","full_name":"Achouri, Sarra","first_name":"Sarra"},{"first_name":"Raphael","full_name":"Blumenfeld, Raphael","last_name":"Blumenfeld"},{"first_name":"Kristian","last_name":"Franze","full_name":"Franze, Kristian"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."}],"isi":1,"_id":"10825","issue":"5","external_id":{"isi":["000796293700007"],"pmid":["35196500"]},"volume":185,"intvolume":"       185","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"02","department":[{"_id":"EdHa"}],"publication_status":"published","ec_funded":1,"day":"22","doi":"10.1016/j.cell.2022.01.022","scopus_import":"1","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.","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_updated":"2022-03-07T07:55:23Z","creator":"dernst","file_size":8478995,"date_created":"2022-03-07T07:55:23Z","file_id":"10831","file_name":"2022_Cell_Yanagida.pdf","content_type":"application/pdf","checksum":"ae305060e8031297771b89dae9e36a29","relation":"main_file","access_level":"open_access","success":1}],"citation":{"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.","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>.","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>.","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.","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."},"has_accepted_license":"1","oa":1,"article_type":"original","title":"Cell surface fluctuations regulate early embryonic lineage sorting","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-03-07T07:55:23Z","type":"journal_article","date_updated":"2025-07-10T11:50:00Z","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"}],"publication":"Cell","date_created":"2022-03-06T23:01:52Z","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]}},{"intvolume":"        11","volume":11,"_id":"10826","external_id":{"isi":["000763432300001"],"pmid":["35201977"]},"author":[{"orcid":"0000-0001-6726-3890","first_name":"Giulio","last_name":"Valperga","full_name":"Valperga, Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E"},{"full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","orcid":"0000-0001-8347-0443","first_name":"Mario"}],"isi":1,"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"}],"publisher":"eLife Sciences Publications","ddc":["570"],"year":"2022","article_number":"e68040","pmid":1,"date_published":"2022-02-24T00:00:00Z","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"publication":"eLife","date_created":"2022-03-06T23:01:52Z","publication_identifier":{"eissn":["2050-084X"]},"file_date_updated":"2022-03-07T07:39:25Z","type":"journal_article","date_updated":"2026-04-02T12:45:39Z","article_type":"original","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"has_accepted_license":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","relation":"main_file","date_created":"2022-03-07T07:39:25Z","file_id":"10830","file_name":"2022_eLife_Valperga.pdf","date_updated":"2022-03-07T07:39:25Z","creator":"dernst","file_size":4095591}],"citation":{"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.","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>","short":"G. Valperga, M. de Bono, ELife 11 (2022).","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>.","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>.","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040."},"scopus_import":"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).","month":"02","corr_author":"1","publication_status":"published","department":[{"_id":"MaDe"}],"day":"24","doi":"10.7554/eLife.68040","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1"},{"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).","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.12968"}],"citation":{"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>","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>","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.","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.","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>.","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","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>."},"arxiv":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"quality_controlled":"1","month":"02","corr_author":"1","department":[{"_id":"BiCh"}],"publication_status":"published","day":"16","doi":"10.1063/5.0079844","type":"journal_article","date_updated":"2026-04-02T12:37:16Z","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."}],"date_created":"2022-03-06T23:01:53Z","publication":"The Journal of chemical physics","publication_identifier":{"eissn":["1089-7690"]},"oa":1,"article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","year":"2022","article_number":"074106","publisher":"AIP Publishing","article_processing_charge":"No","pmid":1,"date_published":"2022-02-16T00:00:00Z","volume":156,"intvolume":"       156","author":[{"full_name":"Lee, Jacob G.","last_name":"Lee","first_name":"Jacob G."},{"first_name":"Chris J.","full_name":"Pickard, Chris J.","last_name":"Pickard"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"isi":1,"_id":"10827","issue":"7","external_id":{"arxiv":["2111.12968"],"isi":["000796704500014"],"pmid":["35183078"]}},{"publisher":"IEEE","year":"2022","date_published":"2022-01-13T00:00:00Z","article_processing_charge":"No","page":"3824-3834","_id":"10828","external_id":{"isi":["000800559503126"],"arxiv":["2111.05663"]},"isi":1,"author":[{"first_name":"Teresa","orcid":"0000-0002-1780-2689","last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","full_name":"Heiss, Teresa"},{"last_name":"Tymochko","full_name":"Tymochko, Sarah","first_name":"Sarah"},{"full_name":"Story, Brittany","last_name":"Story","first_name":"Brittany"},{"first_name":"Adélie","last_name":"Garin","full_name":"Garin, Adélie"},{"first_name":"Hoa","full_name":"Bui, Hoa","last_name":"Bui"},{"full_name":"Bleile, Bea","last_name":"Bleile","first_name":"Bea"},{"first_name":"Vanessa","last_name":"Robins","full_name":"Robins, Vanessa"}],"main_file_link":[{"url":"https://arxiv.org/abs/2111.05663","open_access":"1"}],"status":"public","citation":{"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>","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>","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.","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.","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.","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>.","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>."},"scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"18667","status":"public"}]},"month":"01","publication_status":"published","department":[{"_id":"HeEd"}],"day":"13","doi":"10.1109/BigData52589.2021.9671483","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Digital images enable quantitative analysis of material properties at micro and macro length scales, but choosing an appropriate resolution when acquiring the image is challenging. A high resolution means longer image acquisition and larger data requirements for a given sample, but if the resolution is too low, significant information may be lost. This paper studies the impact of changes in resolution on persistent homology, a tool from topological data analysis that provides a signature of structure in an image across all length scales. Given prior information about a function, the geometry of an object, or its density distribution at a given resolution, we provide methods to select the coarsest resolution yielding results within an acceptable tolerance. We present numerical case studies for an illustrative synthetic example and samples from porous materials where the theoretical bounds are unknown."}],"date_created":"2022-03-06T23:01:53Z","publication":"2021 IEEE International Conference on Big Data","publication_identifier":{"isbn":["9781665439022"]},"type":"conference","date_updated":"2026-04-07T12:54:09Z","title":"The impact of changes in resolution on the persistent homology of images","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","conference":{"end_date":"2021-12-18","location":"Orlando, FL, United States; Virtuell","start_date":"2021-12-15","name":"Big Data: International Conference on Big Data"},"oa":1},{"volume":7,"intvolume":"         7","isi":1,"author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril","first_name":"Ciril"},{"first_name":"Stefan","last_name":"Fossati","full_name":"Fossati, Stefan"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"first_name":"Jakub","full_name":"Dostalek, Jakub","last_name":"Dostalek"},{"orcid":"0000-0002-6962-8598","first_name":"Seungho","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"first_name":"Wolfgang","last_name":"Knoll","full_name":"Knoll, Wolfgang"}],"_id":"10829","external_id":{"isi":["000765113000016"],"pmid":["35134289"]},"issue":"2","year":"2022","ddc":["540"],"publisher":"American Chemical Society","page":"504-512","article_processing_charge":"No","pmid":1,"date_published":"2022-02-08T00:00:00Z","date_updated":"2026-04-02T12:33:46Z","type":"journal_article","file_date_updated":"2022-03-07T08:15:01Z","publication_identifier":{"eissn":["2379-3694"]},"publication":"ACS Sensors","date_created":"2022-03-06T23:01:54Z","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"}],"oa":1,"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","article_type":"original","scopus_import":"1","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)","file":[{"relation":"main_file","checksum":"d704af7262cd484da9bb84b7d84e2b09","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":2969415,"creator":"dernst","date_updated":"2022-03-07T08:15:01Z","file_name":"2022_ACSSensors_Hasler.pdf","date_created":"2022-03-07T08:15:01Z","file_id":"10832"}],"citation":{"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.","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>.","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>.","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>","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>","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."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","day":"08","doi":"10.1021/acssensors.1c02313","publication_status":"published","department":[{"_id":"MaIb"}],"month":"02","related_material":{"record":[{"relation":"research_data","id":"10833","status":"public"}]}},{"month":"02","date_published":"2022-02-08T00:00:00Z","related_material":{"record":[{"status":"public","id":"10829","relation":"used_in_publication"}]},"day":"08","doi":"10.5281/ZENODO.5500360","department":[{"_id":"MaIb"}],"article_processing_charge":"No","oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}],"status":"public","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>","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 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, Zenodo, <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>.","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>."},"ddc":["540"],"year":"2022","_id":"10833","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","author":[{"first_name":"Roger","full_name":"Hasler, Roger","last_name":"Hasler"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"first_name":"Stefan","last_name":"Fossati","full_name":"Fossati, Stefan"},{"first_name":"Patrik","full_name":"Aspermair, Patrik","last_name":"Aspermair"},{"first_name":"Jakub","last_name":"Dostalek","full_name":"Dostalek, Jakub"},{"first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho","last_name":"Lee"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"first_name":"Johannes","last_name":"Bintinger","full_name":"Bintinger, Johannes"},{"last_name":"Knoll","full_name":"Knoll, Wolfgang","first_name":"Wolfgang"}],"oa":1,"abstract":[{"text":"Detailed information about the data set see \"dataset description.txt\" file.","lang":"eng"}],"date_created":"2022-03-07T08:19:11Z","date_updated":"2026-04-02T12:33:44Z","type":"research_data_reference"},{"_id":"10841","issue":"6","external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"author":[{"first_name":"DA","full_name":"Dahhan, DA","last_name":"Dahhan"},{"full_name":"Reynolds, GD","last_name":"Reynolds","first_name":"GD"},{"last_name":"Cárdenas","full_name":"Cárdenas, JJ","first_name":"JJ"},{"first_name":"D","last_name":"Eeckhout","full_name":"Eeckhout, D"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vang","full_name":"Vang, N","first_name":"N"},{"first_name":"X","full_name":"Yan, X","last_name":"Yan"},{"last_name":"Hwang","full_name":"Hwang, I","first_name":"I"},{"first_name":"A","full_name":"Heese, A","last_name":"Heese"},{"last_name":"De Jaeger","full_name":"De Jaeger, G","first_name":"G"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"full_name":"Pan, J","last_name":"Pan","first_name":"J"},{"first_name":"SY","full_name":"Bednarek, SY","last_name":"Bednarek"}],"isi":1,"intvolume":"        34","volume":34,"pmid":1,"date_published":"2022-06-01T00:00:00Z","article_processing_charge":"No","page":"2150-2173","publisher":"Oxford University Press","project":[{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"year":"2022","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","oa":1,"abstract":[{"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.","lang":"eng"}],"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"publication":"Plant Cell","date_created":"2022-03-08T13:47:51Z","date_updated":"2025-05-14T11:06:15Z","type":"journal_article","month":"06","day":"01","doi":"10.1093/plcell/koac071","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publication_status":"published","acknowledged_ssus":[{"_id":"EM-Fac"}],"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"status":"public","citation":{"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>.","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.","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>.","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.","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>","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>"},"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).","scopus_import":"1"},{"volume":4,"intvolume":"         4","author":[{"full_name":"Maslov, Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","last_name":"Maslov","orcid":"0000-0003-4074-2570","first_name":"Mikhail"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"_id":"10845","external_id":{"arxiv":["2111.13570"]},"year":"2022","article_number":"013160","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"publisher":"American Physical Society","ddc":["530"],"article_processing_charge":"No","date_published":"2022-03-01T00:00:00Z","file_date_updated":"2022-03-14T08:38:49Z","type":"journal_article","date_updated":"2026-04-07T11:52:53Z","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"}],"date_created":"2022-03-13T23:01:46Z","publication":"Physical Review Research","publication_identifier":{"issn":["2643-1564"]},"oa":1,"has_accepted_license":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Impurity with a resonance in the vicinity of the Fermi energy","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.","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_created":"2022-03-14T08:38:49Z","file_id":"10848","file_name":"2022_PhysicalReviewResearch_Maslov.pdf","date_updated":"2022-03-14T08:38:49Z","file_size":1258324,"creator":"dernst","success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"62f64b3421a969656ebf52467fa7b6e8"}],"citation":{"ista":"Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 4, 013160.","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>.","short":"M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022).","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>.","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>","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>","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."},"arxiv":1,"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"19048","relation":"dissertation_contains","status":"public"}]},"corr_author":"1","month":"03","department":[{"_id":"MiLe"}],"publication_status":"published","day":"01","ec_funded":1,"doi":"10.1103/PhysRevResearch.4.013160"},{"ddc":["570"],"publisher":"Taylor & Francis","year":"2022","pmid":1,"date_published":"2022-02-19T00:00:00Z","page":"1208-1210","article_processing_charge":"No","intvolume":"        18","volume":18,"external_id":{"pmid":["35188063"],"isi":["000758859600001"]},"_id":"10846","issue":"5","isi":1,"author":[{"id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","last_name":"Artan","first_name":"Murat","orcid":"0000-0001-8945-6992"},{"last_name":"Sohn","full_name":"Sohn, Jooyeon","first_name":"Jooyeon"},{"last_name":"Lee","full_name":"Lee, Cheolju","first_name":"Cheolju"},{"first_name":"Seung Yeol","last_name":"Park","full_name":"Park, Seung Yeol"},{"full_name":"Lee, Seung Jae V.","last_name":"Lee","first_name":"Seung Jae V."}],"citation":{"chicago":"Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>.","mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>, vol. 18, no. 5, Taylor &#38; Francis, 2022, pp. 1208–10, doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>.","short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.","ista":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. 18(5), 1208–1210.","ieee":"M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications,” <i>Autophagy</i>, vol. 18, no. 5. Taylor &#38; Francis, pp. 1208–1210, 2022.","apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., &#38; Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>","ama":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. 2022;18(5):1208-1210. doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>"},"status":"public","main_file_link":[{"url":"https://doi.org/10.1080/15548627.2022.2039523","open_access":"1"}],"acknowledgement":"This work is funded by National Research Foundation of Korea (NRF) grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P, S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).","scopus_import":"1","doi":"10.1080/15548627.2022.2039523","day":"19","department":[{"_id":"MaDe"}],"publication_status":"published","month":"02","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"publication":"Autophagy","date_created":"2022-03-13T23:01:47Z","abstract":[{"text":"The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our data using cultured mammalian cells indicate that MON2 translocates from the Golgi to the endosome under starvation conditions, subsequently increasing autophagic flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to be an evolutionarily conserved process for the upregulation of autophagy, which contributes to organismal longevity.","lang":"eng"}],"date_updated":"2026-06-18T10:40:40Z","type":"journal_article","title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1},{"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"06","corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14374"}]},"doi":"10.1016/j.jfa.2022.109455","ec_funded":1,"day":"15","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","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.","scopus_import":"1","status":"public","file":[{"date_updated":"2022-08-02T10:37:55Z","creator":"dernst","file_size":631391,"date_created":"2022-08-02T10:37:55Z","file_id":"11720","file_name":"2022_JourFunctionalAnalysis_Roos.pdf","content_type":"application/pdf","checksum":"63efcefaa1f2717244ef5407bd564426","relation":"main_file","access_level":"open_access","success":1}],"citation":{"ista":"Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 282(12), 109455.","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>.","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).","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>","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."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Analysis"],"oa":1,"has_accepted_license":"1","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Two-particle bound states at interfaces and corners","file_date_updated":"2022-08-02T10:37:55Z","date_updated":"2026-04-07T13:27:39Z","type":"journal_article","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"}],"publication_identifier":{"issn":["0022-1236"]},"date_created":"2022-03-16T08:41:53Z","publication":"Journal of Functional Analysis","article_processing_charge":"Yes (via OA deal)","date_published":"2022-06-15T00:00:00Z","article_number":"109455","year":"2022","publisher":"Elsevier","project":[{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"ddc":["510"],"author":[{"orcid":"0000-0002-9071-5880","first_name":"Barbara","full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","last_name":"Roos"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"isi":1,"_id":"10850","external_id":{"arxiv":["2105.04874"],"isi":["000795160200009"]},"issue":"12","volume":282,"intvolume":"       282"},{"intvolume":"       128","volume":128,"external_id":{"arxiv":["2107.03695"],"isi":["000771391100002"],"pmid":[" 35333085"]},"_id":"10851","issue":"10","isi":1,"author":[{"last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T","first_name":"Duc T"},{"orcid":"0000-0002-0672-9295","first_name":"Jorden L","last_name":"Senior","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","first_name":"Areg","orcid":"0000-0001-9666-3543"},{"last_name":"Hatefipour","full_name":"Hatefipour, M.","first_name":"M."},{"full_name":"Strickland, W. M.","last_name":"Strickland","first_name":"W. M."},{"full_name":"Shabani, J.","last_name":"Shabani","first_name":"J."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","orcid":"0000-0003-2607-2363"}],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"American Physical Society","year":"2022","article_number":"107701","pmid":1,"date_published":"2022-03-11T00:00:00Z","article_processing_charge":"No","publication":"Physical Review Letters","date_created":"2022-03-17T11:37:47Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"abstract":[{"lang":"eng","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."}],"type":"journal_article","date_updated":"2026-04-07T13:25:51Z","title":"Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","oa":1,"keyword":["General Physics and Astronomy"],"citation":{"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>","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>","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.","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.","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>.","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>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.03695"}],"status":"public","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.","scopus_import":"1","publication_status":"published","department":[{"_id":"MaSe"},{"_id":"AnHi"}],"day":"11","doi":"10.1103/physrevlett.128.107701","ec_funded":1,"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/characterizing-super-semi-sandwiches-for-quantum-computing/","relation":"press_release"}],"record":[{"status":"public","id":"10029","relation":"earlier_version"},{"id":"14547","relation":"dissertation_contains","status":"public"}]},"month":"03","corr_author":"1","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"arxiv":1}]