[{"date_created":"2023-11-10T09:10:06Z","file_date_updated":"2024-11-23T23:30:38Z","status":"public","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"14591","status":"public"},{"id":"9887","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8139","relation":"part_of_dissertation"}]},"ddc":["570"],"day":"10","alternative_title":["ISTA Thesis"],"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"has_accepted_license":"1","author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"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. "}],"oa_version":"Published Version","date_updated":"2026-07-01T22:31:02Z","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14510","publisher":"Institute of Science and Technology Austria","date_published":"2023-11-10T00:00:00Z","file":[{"creator":"ngnyliuk","relation":"source_file","date_created":"2023-11-20T09:18:51Z","file_size":20824903,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-11-23T23:30:38Z","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","embargo_to":"open_access","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","access_level":"closed","file_id":"14567"},{"date_created":"2023-11-20T09:23:11Z","creator":"ngnyliuk","relation":"main_file","file_id":"14568","checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo":"2024-11-23","access_level":"open_access","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_updated":"2024-11-23T23:30:38Z","content_type":"application/pdf","file_size":24871844}],"oa":1,"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"page":"180","year":"2023","month":"11","_id":"14510","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","degree_awarded":"PhD","corr_author":"1","type":"dissertation","publication_status":"published","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin"}],"citation":{"ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510."}},{"OA_place":"repository","author":[{"last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin","last_name":"Nagel"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"last_name":"Hlavata","full_name":"Hlavata, Annamaria","first_name":"Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Erika","last_name":"Isono","full_name":"Isono, Erika"},{"full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","publication_status":"draft","date_updated":"2026-07-01T22:31:01Z","citation":{"short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523"},"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"corr_author":"1","type":"preprint","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","month":"10","day":"10","_id":"14591","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"ec_funded":1,"year":"2023","related_material":{"record":[{"id":"15330","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14510"}]},"publication":"bioRxiv","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2023-11-22T10:17:49Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.09.561523"}],"status":"public","oa":1,"date_published":"2023-10-10T00:00:00Z","doi":"10.1101/2023.10.09.561523","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"date_published":"2023-04-13T00:00:00Z","language":[{"iso":"eng"}],"publisher":"European Geosciences Union","doi":"10.5194/egusphere-egu23-6157","status":"public","file_date_updated":"2024-01-24T11:19:54Z","oa":1,"date_created":"2024-01-22T12:08:12Z","file":[{"access_level":"open_access","checksum":"8cb88c1bc80ccee328478a62064d98f7","file_name":"2023_EGU_Polesello.pdf","file_id":"14883","file_size":296769,"date_updated":"2024-01-24T11:19:54Z","content_type":"application/pdf","date_created":"2024-01-24T11:19:54Z","success":1,"creator":"dernst","relation":"main_file"}],"article_processing_charge":"No","conference":{"location":"Vienna, Austria & Virtual","start_date":"2023-04-23","name":"EGU General Assembly","end_date":"2023-04-28"},"publication":"EGU General Assembly 2023","year":"2023","day":"13","month":"04","ddc":["550"],"title":"Intensification mechanisms of tropical cyclones","department":[{"_id":"CaMu"},{"_id":"GradSch"}],"_id":"14863","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Polesello, Andrea","last_name":"Polesello","first_name":"Andrea","id":"74c777f4-32da-11ee-b498-874db0835561"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J","last_name":"Muller"},{"last_name":"Pasquero","full_name":"Pasquero, Claudia","first_name":"Claudia"},{"first_name":"Agostino N.","last_name":"Meroni","full_name":"Meroni, Agostino N."}],"corr_author":"1","type":"conference_abstract","citation":{"ieee":"A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023.","apa":"Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157","ama":"Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6157","mla":"Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6157.","ista":"Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157.","chicago":"Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157.","short":"A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023."},"date_updated":"2026-07-02T06:42:45Z","article_number":"EGU23-6157","oa_version":"Published Version","publication_status":"published"},{"publication":"EGU General Assembly 2023","related_material":{"record":[{"relation":"later_version","id":"22123","status":"public"}]},"year":"2023","conference":{"start_date":"2023-04-23","location":"Vienna, Austria & Virtual","end_date":"2023-04-28","name":"EGU General Assembly"},"article_processing_charge":"No","extern":"1","date_published":"2023-09-14T00:00:00Z","doi":"10.5194/egusphere-egu23-5510","language":[{"iso":"eng"}],"publisher":"European Geosciences Union","date_created":"2026-06-22T12:19:10Z","status":"public","type":"conference_abstract","publication_status":"published","oa_version":"None","article_number":"EGU23-5510","citation":{"short":"J.M. Muñoz Hermosilla, E. De Andrés, K. Shahateet, J. Otero, F.J. Navarro, in:, EGU General Assembly 2023, European Geosciences Union, 2023.","chicago":"Muñoz Hermosilla, José M, Eva De Andrés, Kaian Shahateet, Jaime Otero, and Francisco J. Navarro. “A 3D Glacier Dynamics-Line Plume Model to Estimate the Frontal Ablation of Hansbreen, Svalbard.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-5510.","ista":"Muñoz Hermosilla JM, De Andrés E, Shahateet K, Otero J, Navarro FJ. 2023. A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. EGU General Assembly 2023. EGU General Assembly, EGU23-5510.","mla":"Muñoz Hermosilla, José M., et al. “A 3D Glacier Dynamics-Line Plume Model to Estimate the Frontal Ablation of Hansbreen, Svalbard.” EGU General Assembly 2023, EGU23-5510, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-5510.","ieee":"J. M. Muñoz Hermosilla, E. De Andrés, K. Shahateet, J. Otero, and F. J. Navarro, “A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023.","apa":"Muñoz Hermosilla, J. M., De Andrés, E., Shahateet, K., Otero, J., & Navarro, F. J. (2023). A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-5510","ama":"Muñoz Hermosilla JM, De Andrés E, Shahateet K, Otero J, Navarro FJ. A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-5510"},"date_updated":"2026-07-02T07:13:16Z","author":[{"last_name":"Muñoz Hermosilla","full_name":"Muñoz Hermosilla, José M","first_name":"José M","id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","orcid":"0000-0002-1990-8508"},{"first_name":"Eva","last_name":"De Andrés","full_name":"De Andrés, Eva"},{"full_name":"Shahateet, Kaian","last_name":"Shahateet","first_name":"Kaian"},{"first_name":"Jaime","full_name":"Otero, Jaime","last_name":"Otero"},{"last_name":"Navarro","full_name":"Navarro, Francisco J.","first_name":"Francisco J."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","OA_type":"gold","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"22125","ddc":["550"],"month":"09","day":"14","title":"A 3D glacier dynamics-line plume model to estimate the frontal ablation of Hansbreen, Svalbard"},{"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."}],"date_updated":"2024-10-09T21:04:02Z","intvolume":" 70","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"orcid":"0000-0003-1843-3173","first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","last_name":"Basilico"},{"first_name":"Laura","full_name":"Ferrucci, Laura","last_name":"Ferrucci"},{"first_name":"Patrizia","last_name":"Ratano","full_name":"Ratano, Patrizia"},{"last_name":"Golia","full_name":"Golia, Maria T.","first_name":"Maria T."},{"last_name":"Grimaldi","full_name":"Grimaldi, Alfonso","first_name":"Alfonso"},{"first_name":"Maria","last_name":"Rosito","full_name":"Rosito, Maria"},{"first_name":"Valentina","full_name":"Ferretti, Valentina","last_name":"Ferretti"},{"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"},{"last_name":"De Turris","full_name":"De Turris, Valeria","first_name":"Valeria"},{"full_name":"Salerno, Debora","last_name":"Salerno","first_name":"Debora"},{"first_name":"Stefano","full_name":"Garofalo, Stefano","last_name":"Garofalo"},{"last_name":"St‐Pierre","full_name":"St‐Pierre, Marie‐Kim","first_name":"Marie‐Kim"},{"last_name":"Carrier","full_name":"Carrier, Micael","first_name":"Micael"},{"first_name":"Massimiliano","full_name":"Renzi, Massimiliano","last_name":"Renzi"},{"full_name":"Pagani, Francesca","last_name":"Pagani","first_name":"Francesca"},{"first_name":"Brijesh","last_name":"Modi","full_name":"Modi, 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."},{"last_name":"Marinelli","full_name":"Marinelli, Silvia","first_name":"Silvia"},{"last_name":"Tremblay","full_name":"Tremblay, Marie‐Ève","first_name":"Marie‐Ève"},{"first_name":"Daniele","last_name":"Caprioli","full_name":"Caprioli, Daniele"},{"full_name":"Maggi, Laura","last_name":"Maggi","first_name":"Laura"},{"full_name":"Limatola, Cristina","last_name":"Limatola","first_name":"Cristina"},{"first_name":"Silvia","last_name":"Di Angelantonio","full_name":"Di Angelantonio, Silvia"},{"first_name":"Davide","last_name":"Ragozzino","full_name":"Ragozzino, Davide"}],"department":[{"_id":"GaNo"}],"has_accepted_license":"1","isi":1,"day":"01","ddc":["570"],"title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","publication":"Glia","publication_identifier":{"eissn":["1098-1136"],"issn":["0894-1491"]},"article_processing_charge":"No","acknowledgement":"The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003) to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University, Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza University, Rome and by the Italian Institute of Technology, Rome. The authors thank Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani for help with animal husbandry and transgenic colonies management. They also wish to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism. PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley, CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza within the CRUI-CARE Agreement.","file_date_updated":"2022-03-04T08:55:27Z","status":"public","date_created":"2022-03-04T08:53:37Z","volume":70,"corr_author":"1","type":"journal_article","citation":{"short":"B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito, V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris, D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi, M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L. Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:10.1002/glia.24101.","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia. Wiley, 2022. https://doi.org/10.1002/glia.24101.","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.","ieee":"B. Basilico et al., “Microglia control glutamatergic synapses in the adult mouse hippocampus,” Glia, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 2022;70(1):173-195. doi:10.1002/glia.24101","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. Wiley. https://doi.org/10.1002/glia.24101"},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10818","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)"},"scopus_import":"1","month":"01","pmid":1,"year":"2022","quality_controlled":"1","page":"173-195","external_id":{"isi":["000708025800001"],"pmid":["34661306"]},"keyword":["Cellular and Molecular Neuroscience","Neurology"],"article_type":"original","issue":"1","date_published":"2022-01-01T00:00:00Z","publisher":"Wiley","language":[{"iso":"eng"}],"doi":"10.1002/glia.24101","oa":1,"file":[{"date_created":"2022-03-04T08:55:27Z","relation":"main_file","creator":"dernst","success":1,"file_id":"10819","access_level":"open_access","checksum":"f10a897290e66c0a062e04ba91db6c17","file_name":"2021_Glia_Basilico.pdf","date_updated":"2022-03-04T08:55:27Z","content_type":"application/pdf","file_size":5340294}]},{"author":[{"full_name":"Liu, Jianxin","last_name":"Liu","first_name":"Jianxin"},{"full_name":"Marensi, Elena","last_name":"Marensi","orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena"},{"first_name":"Xuesong","full_name":"Wu, Xuesong","last_name":"Wu"}],"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."}],"date_updated":"2025-05-20T06:08:26Z","intvolume":" 38","oa_version":"None","day":"01","alternative_title":["IUTAM"],"title":"Effects of streaky structures on the instability of supersonic boundary layers","department":[{"_id":"BjHo"}],"OA_type":"closed access","isi":1,"publication_identifier":{"issn":["1875-3507"],"eisbn":["9783030679026"],"eissn":["1875-3493"],"isbn":["9783030679019"]},"conference":{"start_date":"2019-09-02","location":"London, United Kingdom","name":"IUTAM Symposium","end_date":"2019-09-06"},"publication":"IUTAM Laminar-Turbulent Transition","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).","status":"public","date_created":"2022-03-04T09:14:34Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":38,"citation":{"ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in IUTAM Laminar-Turbulent Transition, London, United Kingdom, 2022, vol. 38, pp. 587–598.","apa":"Liu, J., Marensi, E., & Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In IUTAM Laminar-Turbulent Transition (Vol. 38, pp. 587–598). London, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-67902-6_51","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. Vol 38. Springer Nature; 2022:587-598. doi:10.1007/978-3-030-67902-6_51","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In IUTAM Laminar-Turbulent Transition, 38:587–98. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67902-6_51.","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” IUTAM Laminar-Turbulent Transition, vol. 38, Springer Nature, 2022, pp. 587–98, doi:10.1007/978-3-030-67902-6_51.","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."},"publication_status":"published","scopus_import":"1","month":"01","_id":"10820","page":"587-598","external_id":{"isi":["000709087600051"]},"year":"2022","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2022-01-01T00:00:00Z","doi":"10.1007/978-3-030-67902-6_51","publisher":"Springer Nature"},{"day":"04","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"department":[{"_id":"GaTk"}],"author":[{"last_name":"Lombardi","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","orcid":"0000-0003-2623-5249"},{"first_name":"Hans J.","last_name":"Herrmann","full_name":"Herrmann, Hans J."},{"last_name":"Parrino","full_name":"Parrino, Liborio","first_name":"Liborio"},{"last_name":"Plenz","full_name":"Plenz, Dietmar","first_name":"Dietmar"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano"},{"full_name":"de Arcangelis, Lucilla","last_name":"de Arcangelis","first_name":"Lucilla"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"}],"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"}],"date_updated":"2025-04-15T06:55:02Z","oa_version":"Preprint","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.","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.03.482657"}],"date_created":"2022-03-04T22:20:59Z","article_processing_charge":"No","ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"14402","status":"public"}]},"publication":"bioRxiv","month":"03","_id":"10821","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","type":"preprint","corr_author":"1","citation":{"mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2022.03.03.482657.","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, 10.1101/2022.03.03.482657.","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2022.03.03.482657.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (n.d.).","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. doi:10.1101/2022.03.03.482657","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. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.03.03.482657","ieee":"F. Lombardi et al., “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory."},"publication_status":"draft","date_published":"2022-03-04T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1101/2022.03.03.482657","publisher":"Cold Spring Harbor Laboratory","oa":1,"page":"25","year":"2022"},{"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.","date_created":"2022-03-06T23:01:52Z","status":"public","file_date_updated":"2022-03-07T07:55:23Z","article_processing_charge":"No","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"ec_funded":1,"publication":"Cell","ddc":["570"],"day":"22","title":"Cell surface fluctuations regulate early embryonic lineage sorting","department":[{"_id":"EdHa"}],"project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020"}],"has_accepted_license":"1","isi":1,"author":[{"first_name":"Ayaka","full_name":"Yanagida, Ayaka","last_name":"Yanagida"},{"full_name":"Corujo-Simon, Elena","last_name":"Corujo-Simon","first_name":"Elena"},{"full_name":"Revell, Christopher K.","last_name":"Revell","first_name":"Christopher K."},{"id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti","last_name":"Sahu","full_name":"Sahu, Preeti"},{"full_name":"Stirparo, Giuliano G.","last_name":"Stirparo","first_name":"Giuliano G."},{"last_name":"Aspalter","full_name":"Aspalter, Irene M.","first_name":"Irene M."},{"first_name":"Alex K.","full_name":"Winkel, Alex K.","last_name":"Winkel"},{"full_name":"Peters, Ruby","last_name":"Peters","first_name":"Ruby"},{"first_name":"Henry","last_name":"De Belly","full_name":"De Belly, Henry"},{"first_name":"Davide A.D.","last_name":"Cassani","full_name":"Cassani, Davide A.D."},{"first_name":"Sarra","full_name":"Achouri, Sarra","last_name":"Achouri"},{"last_name":"Blumenfeld","full_name":"Blumenfeld, Raphael","first_name":"Raphael"},{"last_name":"Franze","full_name":"Franze, Kristian","first_name":"Kristian"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"first_name":"Ewa K.","full_name":"Paluch, Ewa K.","last_name":"Paluch"},{"first_name":"Jennifer","full_name":"Nichols, Jennifer","last_name":"Nichols"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","date_updated":"2025-07-10T11:50:00Z","intvolume":" 185","date_published":"2022-02-22T00:00:00Z","doi":"10.1016/j.cell.2022.01.022","publisher":"Cell Press","language":[{"iso":"eng"}],"issue":"5","file":[{"relation":"main_file","creator":"dernst","success":1,"date_created":"2022-03-07T07:55:23Z","date_updated":"2022-03-07T07:55:23Z","content_type":"application/pdf","file_size":8478995,"file_id":"10831","checksum":"ae305060e8031297771b89dae9e36a29","access_level":"open_access","file_name":"2022_Cell_Yanagida.pdf"}],"oa":1,"article_type":"original","page":"777-793.e20","external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"quality_controlled":"1","year":"2022","pmid":1,"month":"02","scopus_import":"1","_id":"10825","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":185,"publication_status":"published","citation":{"ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 2022;185(5):777-793.e20. doi:10.1016/j.cell.2022.01.022","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. Cell. Cell Press. https://doi.org/10.1016/j.cell.2022.01.022","ieee":"A. Yanagida et al., “Cell surface fluctuations regulate early embryonic lineage sorting,” Cell, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:10.1016/j.cell.2022.01.022.","ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell. Cell Press, 2022. https://doi.org/10.1016/j.cell.2022.01.022.","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."}},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"10826","scopus_import":"1","month":"02","pmid":1,"citation":{"apa":"Valperga, G., & de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68040","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 2022;11. doi:10.7554/eLife.68040","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” eLife, vol. 11. eLife Sciences Publications, 2022.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.68040.","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife, vol. 11, e68040, eLife Sciences Publications, 2022, doi:10.7554/eLife.68040.","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","short":"G. Valperga, M. de Bono, ELife 11 (2022)."},"publication_status":"published","type":"journal_article","corr_author":"1","volume":11,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","oa":1,"file":[{"access_level":"open_access","checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","file_name":"2022_eLife_Valperga.pdf","file_id":"10830","file_size":4095591,"date_updated":"2022-03-07T07:39:25Z","content_type":"application/pdf","date_created":"2022-03-07T07:39:25Z","success":1,"creator":"dernst","relation":"main_file"}],"language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","date_published":"2022-02-24T00:00:00Z","doi":"10.7554/eLife.68040","year":"2022","quality_controlled":"1","external_id":{"pmid":["35201977"],"isi":["000763432300001"]},"has_accepted_license":"1","isi":1,"project":[{"grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function"}],"department":[{"_id":"MaDe"}],"title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","day":"24","ddc":["570"],"intvolume":" 11","date_updated":"2026-04-02T12:45:39Z","oa_version":"Published Version","article_number":"e68040","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."}],"author":[{"full_name":"Valperga, Giulio","last_name":"Valperga","orcid":"0000-0001-6726-3890","first_name":"Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E"},{"last_name":"De Bono","full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443"}],"article_processing_charge":"No","file_date_updated":"2022-03-07T07:39:25Z","status":"public","date_created":"2022-03-06T23:01:52Z","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).","publication":"eLife","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"publication_identifier":{"eissn":["2050-084X"]}},{"oa":1,"issue":"7","doi":"10.1063/5.0079844","language":[{"iso":"eng"}],"publisher":"AIP Publishing","date_published":"2022-02-16T00:00:00Z","article_type":"original","external_id":{"arxiv":["2111.12968"],"pmid":["35183078"],"isi":["000796704500014"]},"year":"2022","quality_controlled":"1","arxiv":1,"scopus_import":"1","month":"02","pmid":1,"_id":"10827","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” The Journal of Chemical Physics, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:10.1063/5.0079844.","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” The Journal of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0079844.","apa":"Lee, J. G., Pickard, C. J., & Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0079844","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 2022;156(7). doi:10.1063/5.0079844","ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” The Journal of chemical physics, vol. 156, no. 7. AIP Publishing, 2022."},"publication_status":"published","type":"journal_article","volume":156,"corr_author":"1","status":"public","date_created":"2022-03-06T23:01:53Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.12968"}],"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).","article_processing_charge":"No","publication_identifier":{"eissn":["1089-7690"]},"publication":"The Journal of chemical physics","title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","day":"16","isi":1,"department":[{"_id":"BiCh"}],"author":[{"last_name":"Lee","full_name":"Lee, Jacob G.","first_name":"Jacob G."},{"first_name":"Chris J.","last_name":"Pickard","full_name":"Pickard, Chris J."},{"full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}],"intvolume":" 156","date_updated":"2026-04-02T12:37:16Z","article_number":"074106","oa_version":"Preprint","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."}]},{"year":"2022","quality_controlled":"1","external_id":{"arxiv":["2111.05663"],"isi":["000800559503126"]},"page":"3824-3834","oa":1,"publisher":"IEEE","date_published":"2022-01-13T00:00:00Z","doi":"10.1109/BigData52589.2021.9671483","language":[{"iso":"eng"}],"citation":{"ieee":"T. Heiss et al., “The impact of changes in resolution on the persistent homology of images,” in 2021 IEEE International Conference on Big Data, Orlando, FL, United States; Virtuell, 2022, pp. 3824–3834.","ama":"Heiss T, Tymochko S, Story B, et al. The impact of changes in resolution on the persistent homology of images. In: 2021 IEEE International Conference on Big Data. IEEE; 2022:3824-3834. doi:10.1109/BigData52589.2021.9671483","apa":"Heiss, T., Tymochko, S., Story, B., Garin, A., Bui, H., Bleile, B., & Robins, V. (2022). The impact of changes in resolution on the persistent homology of images. In 2021 IEEE International Conference on Big Data (pp. 3824–3834). Orlando, FL, United States; Virtuell: IEEE. https://doi.org/10.1109/BigData52589.2021.9671483","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.” 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 3824–34, doi:10.1109/BigData52589.2021.9671483.","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.","chicago":"Heiss, Teresa, Sarah Tymochko, Brittany Story, Adélie Garin, Hoa Bui, Bea Bleile, and Vanessa Robins. “The Impact of Changes in Resolution on the Persistent Homology of Images.” In 2021 IEEE International Conference on Big Data, 3824–34. IEEE, 2022. https://doi.org/10.1109/BigData52589.2021.9671483."},"publication_status":"published","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10828","arxiv":1,"month":"01","scopus_import":"1","publication":"2021 IEEE International Conference on Big Data","related_material":{"record":[{"id":"18667","relation":"dissertation_contains","status":"public"}]},"conference":{"name":"Big Data: International Conference on Big Data","end_date":"2021-12-18","location":"Orlando, FL, United States; Virtuell","start_date":"2021-12-15"},"publication_identifier":{"isbn":["9781665439022"]},"article_processing_charge":"No","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.05663"}],"date_created":"2022-03-06T23:01:53Z","date_updated":"2026-04-07T12:54:09Z","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."}],"author":[{"first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","last_name":"Heiss","full_name":"Heiss, Teresa"},{"full_name":"Tymochko, Sarah","last_name":"Tymochko","first_name":"Sarah"},{"full_name":"Story, Brittany","last_name":"Story","first_name":"Brittany"},{"first_name":"Adélie","full_name":"Garin, Adélie","last_name":"Garin"},{"full_name":"Bui, Hoa","last_name":"Bui","first_name":"Hoa"},{"last_name":"Bleile","full_name":"Bleile, Bea","first_name":"Bea"},{"first_name":"Vanessa","full_name":"Robins, Vanessa","last_name":"Robins"}],"isi":1,"department":[{"_id":"HeEd"}],"title":"The impact of changes in resolution on the persistent homology of images","day":"13"},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"10833"}]},"publication":"ACS Sensors","publication_identifier":{"eissn":["2379-3694"]},"article_processing_charge":"No","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)","status":"public","file_date_updated":"2022-03-07T08:15:01Z","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"}],"date_updated":"2026-04-02T12:33:46Z","intvolume":" 7","oa_version":"Published Version","author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"first_name":"Ciril","last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril"},{"first_name":"Stefan","full_name":"Fossati, Stefan","last_name":"Fossati"},{"first_name":"Patrik","last_name":"Aspermair","full_name":"Aspermair, Patrik"},{"last_name":"Dostalek","full_name":"Dostalek, Jakub","first_name":"Jakub"},{"orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","full_name":"Lee, Seungho","last_name":"Lee"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bintinger","full_name":"Bintinger, Johannes","first_name":"Johannes"},{"first_name":"Wolfgang","full_name":"Knoll, Wolfgang","last_name":"Knoll"}],"department":[{"_id":"MaIb"}],"isi":1,"has_accepted_license":"1","day":"08","ddc":["540"],"title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","year":"2022","quality_controlled":"1","page":"504-512","external_id":{"isi":["000765113000016"],"pmid":["35134289"]},"article_type":"original","issue":"2","doi":"10.1021/acssensors.1c02313","language":[{"iso":"eng"}],"publisher":"American Chemical Society","date_published":"2022-02-08T00:00:00Z","oa":1,"file":[{"content_type":"application/pdf","date_updated":"2022-03-07T08:15:01Z","file_size":2969415,"file_id":"10832","file_name":"2022_ACSSensors_Hasler.pdf","access_level":"open_access","checksum":"d704af7262cd484da9bb84b7d84e2b09","relation":"main_file","creator":"dernst","success":1,"date_created":"2022-03-07T08:15:01Z"}],"type":"journal_article","volume":7,"citation":{"ieee":"R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” ACS Sensors, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. American Chemical Society. https://doi.org/10.1021/acssensors.1c02313","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. 2022;7(2):504-512. doi:10.1021/acssensors.1c02313","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.","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” ACS Sensors. American Chemical Society, 2022. https://doi.org/10.1021/acssensors.1c02313.","mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” ACS Sensors, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:10.1021/acssensors.1c02313.","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."},"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"10829","scopus_import":"1","month":"02","pmid":1},{"year":"2022","related_material":{"record":[{"status":"public","id":"10829","relation":"used_in_publication"}]},"status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}],"date_created":"2022-03-07T08:19:11Z","doi":"10.5281/ZENODO.5500360","publisher":"Zenodo","date_published":"2022-02-08T00:00:00Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"first_name":"Ciril","last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril"},{"first_name":"Stefan","last_name":"Fossati","full_name":"Fossati, Stefan"},{"first_name":"Patrik","full_name":"Aspermair, Patrik","last_name":"Aspermair"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","full_name":"Lee, Seungho"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"first_name":"Wolfgang","last_name":"Knoll","full_name":"Knoll, Wolfgang"}],"date_updated":"2026-04-02T12:33:44Z","citation":{"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:10.5281/ZENODO.5500360","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. https://doi.org/10.5281/ZENODO.5500360","ieee":"R. Hasler et al., “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, 10.5281/ZENODO.5500360.","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. https://doi.org/10.5281/ZENODO.5500360.","mla":"Hasler, Roger, et al. Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device. Zenodo, 2022, doi:10.5281/ZENODO.5500360.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022)."},"oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Detailed information about the data set see \"dataset description.txt\" file.","lang":"eng"}],"title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","day":"08","month":"02","ddc":["540"],"_id":"10833","department":[{"_id":"MaIb"}]},{"publication_status":"published","citation":{"ieee":"D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, 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. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071","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. Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac071","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.","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.” Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac071.","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.","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."},"type":"journal_article","volume":34,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10841","pmid":1,"scopus_import":"1","month":"06","quality_controlled":"1","year":"2022","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"page":"2150-2173","article_type":"original","oa":1,"publisher":"Oxford University Press","language":[{"iso":"eng"}],"date_published":"2022-06-01T00:00:00Z","doi":"10.1093/plcell/koac071","issue":"6","oa_version":"Preprint","date_updated":"2025-05-14T11:06:15Z","intvolume":" 34","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"}],"author":[{"first_name":"DA","full_name":"Dahhan, DA","last_name":"Dahhan"},{"first_name":"GD","last_name":"Reynolds","full_name":"Reynolds, GD"},{"first_name":"JJ","full_name":"Cárdenas, JJ","last_name":"Cárdenas"},{"full_name":"Eeckhout, D","last_name":"Eeckhout","first_name":"D"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"first_name":"K","full_name":"Yperman, K","last_name":"Yperman"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"N","last_name":"Vang","full_name":"Vang, N"},{"first_name":"X","last_name":"Yan","full_name":"Yan, X"},{"last_name":"Hwang","full_name":"Hwang, I","first_name":"I"},{"first_name":"A","last_name":"Heese","full_name":"Heese, A"},{"full_name":"De Jaeger, G","last_name":"De Jaeger","first_name":"G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Van Damme","full_name":"Van Damme, D","first_name":"D"},{"last_name":"Pan","full_name":"Pan, J","first_name":"J"},{"first_name":"SY","full_name":"Bednarek, SY","last_name":"Bednarek"}],"isi":1,"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","day":"01","publication":"Plant Cell","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"date_created":"2022-03-08T13:47:51Z","status":"public","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)."},{"external_id":{"isi":["000766422000002"]},"page":"933-948","year":"2022","quality_controlled":"1","issue":"4","date_published":"2022-07-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1007/s12095-022-00557-8","article_type":"original","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” Cryptography and Communications, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:10.1007/s12095-022-00557-8.","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” Cryptography and Communications. Springer Nature, 2022. https://doi.org/10.1007/s12095-022-00557-8.","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","apa":"Köse, S., & Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. Springer Nature. https://doi.org/10.1007/s12095-022-00557-8","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 2022;14(4):933-948. doi:10.1007/s12095-022-00557-8","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” Cryptography and Communications, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022."},"publication_status":"published","volume":14,"type":"journal_article","month":"07","scopus_import":"1","_id":"10842","publication_identifier":{"eissn":["1936-2455"],"issn":["1936-2447"]},"publication":"Cryptography and Communications","status":"public","date_created":"2022-03-10T12:16:19Z","acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","article_processing_charge":"No","author":[{"full_name":"Köse, Seyda","last_name":"Köse","first_name":"Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"},{"full_name":"Özbudak, Ferruh","last_name":"Özbudak","first_name":"Ferruh"}],"date_updated":"2023-09-05T15:35:55Z","intvolume":" 14","oa_version":"None","abstract":[{"lang":"eng","text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory."}],"title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","day":"01","isi":1,"department":[{"_id":"GradSch"}]},{"quality_controlled":"1","year":"2022","external_id":{"arxiv":["2111.13570"]},"article_type":"original","file":[{"file_id":"10848","access_level":"open_access","checksum":"62f64b3421a969656ebf52467fa7b6e8","file_name":"2022_PhysicalReviewResearch_Maslov.pdf","date_updated":"2022-03-14T08:38:49Z","content_type":"application/pdf","file_size":1258324,"date_created":"2022-03-14T08:38:49Z","creator":"dernst","relation":"main_file","success":1}],"oa":1,"date_published":"2022-03-01T00:00:00Z","publisher":"American Physical Society","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevResearch.4.013160","publication_status":"published","citation":{"ieee":"M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the vicinity of the Fermi energy,” Physical Review Research, vol. 4. American Physical Society, 2022.","ama":"Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 2022;4. doi:10.1103/PhysRevResearch.4.013160","apa":"Maslov, M., Lemeshko, M., & Volosniev, A. (2022). Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.4.013160","mla":"Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” Physical Review Research, vol. 4, 013160, American Physical Society, 2022, doi:10.1103/PhysRevResearch.4.013160.","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” Physical Review Research. American Physical Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.013160.","ista":"Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 4, 013160.","short":"M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022)."},"type":"journal_article","corr_author":"1","volume":4,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"10845","arxiv":1,"month":"03","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"19048","status":"public"}]},"publication":"Physical Review Research","ec_funded":1,"publication_identifier":{"issn":["2643-1564"]},"article_processing_charge":"No","date_created":"2022-03-13T23:01:46Z","file_date_updated":"2022-03-14T08:38:49Z","status":"public","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.","oa_version":"Published Version","article_number":"013160","intvolume":" 4","date_updated":"2026-04-07T11:52:53Z","abstract":[{"lang":"eng","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."}],"author":[{"last_name":"Maslov","full_name":"Maslov, Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0003-4074-2570"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"has_accepted_license":"1","department":[{"_id":"MiLe"}],"project":[{"grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment"},{"call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"title":"Impurity with a resonance in the vicinity of the Fermi energy","ddc":["530"],"day":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” Autophagy, vol. 18, no. 5, Taylor & Francis, 2022, pp. 1208–10, doi:10.1080/15548627.2022.2039523.","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.","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.” Autophagy. Taylor & Francis, 2022. https://doi.org/10.1080/15548627.2022.2039523.","short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 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,” Autophagy, vol. 18, no. 5. Taylor & Francis, pp. 1208–1210, 2022.","apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., & Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. Taylor & Francis. https://doi.org/10.1080/15548627.2022.2039523","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. Autophagy. 2022;18(5):1208-1210. doi:10.1080/15548627.2022.2039523"},"publication_status":"published","type":"journal_article","volume":18,"month":"02","scopus_import":"1","pmid":1,"_id":"10846","external_id":{"isi":["000758859600001"],"pmid":["35188063"]},"page":"1208-1210","year":"2022","quality_controlled":"1","oa":1,"issue":"5","doi":"10.1080/15548627.2022.2039523","publisher":"Taylor & Francis","language":[{"iso":"eng"}],"date_published":"2022-02-19T00:00:00Z","article_type":"original","author":[{"orcid":"0000-0001-8945-6992","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","last_name":"Artan"},{"first_name":"Jooyeon","last_name":"Sohn","full_name":"Sohn, Jooyeon"},{"first_name":"Cheolju","last_name":"Lee","full_name":"Lee, Cheolju"},{"last_name":"Park","full_name":"Park, Seung Yeol","first_name":"Seung Yeol"},{"first_name":"Seung Jae V.","full_name":"Lee, Seung Jae V.","last_name":"Lee"}],"date_updated":"2026-06-18T10:40:40Z","intvolume":" 18","oa_version":"Published Version","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"}],"title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","day":"19","ddc":["570"],"isi":1,"department":[{"_id":"MaDe"}],"publication_identifier":{"eissn":["1554-8635"],"issn":["1554-8627"]},"publication":"Autophagy","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2022.2039523"}],"date_created":"2022-03-13T23:01:47Z","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).","article_processing_charge":"No"},{"related_material":{"record":[{"id":"14374","relation":"dissertation_contains","status":"public"}]},"publication":"Journal of Functional Analysis","publication_identifier":{"issn":["0022-1236"]},"ec_funded":1,"article_processing_charge":"Yes (via OA deal)","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.","status":"public","file_date_updated":"2022-08-02T10:37:55Z","date_created":"2022-03-16T08:41:53Z","abstract":[{"lang":"eng","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."}],"date_updated":"2026-04-07T13:27:39Z","intvolume":" 282","article_number":"109455","oa_version":"Published Version","author":[{"last_name":"Roos","full_name":"Roos, Barbara","first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"project":[{"call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"isi":1,"has_accepted_license":"1","day":"15","ddc":["510"],"title":"Two-particle bound states at interfaces and corners","year":"2022","quality_controlled":"1","external_id":{"arxiv":["2105.04874"],"isi":["000795160200009"]},"keyword":["Analysis"],"article_type":"original","issue":"12","language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2022.109455","date_published":"2022-06-15T00:00:00Z","publisher":"Elsevier","oa":1,"file":[{"file_name":"2022_JourFunctionalAnalysis_Roos.pdf","checksum":"63efcefaa1f2717244ef5407bd564426","access_level":"open_access","file_id":"11720","file_size":631391,"content_type":"application/pdf","date_updated":"2022-08-02T10:37:55Z","date_created":"2022-08-02T10:37:55Z","success":1,"relation":"main_file","creator":"dernst"}],"volume":282,"type":"journal_article","corr_author":"1","citation":{"ieee":"B. Roos and R. Seiringer, “Two-particle bound states at interfaces and corners,” Journal of Functional Analysis, vol. 282, no. 12. Elsevier, 2022.","apa":"Roos, B., & Seiringer, R. (2022). Two-particle bound states at interfaces and corners. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109455","ama":"Roos B, Seiringer R. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 2022;282(12). doi:10.1016/j.jfa.2022.109455","mla":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” Journal of Functional Analysis, vol. 282, no. 12, 109455, Elsevier, 2022, doi:10.1016/j.jfa.2022.109455.","chicago":"Roos, Barbara, and Robert Seiringer. “Two-Particle Bound States at Interfaces and Corners.” Journal of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109455.","ista":"Roos B, Seiringer R. 2022. Two-particle bound states at interfaces and corners. Journal of Functional Analysis. 282(12), 109455.","short":"B. Roos, R. Seiringer, Journal of Functional Analysis 282 (2022)."},"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10850","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"06","scopus_import":"1","arxiv":1},{"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.","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.03695"}],"date_created":"2022-03-17T11:37:47Z","article_processing_charge":"No","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication":"Physical Review Letters","related_material":{"link":[{"url":"https://ista.ac.at/en/news/characterizing-super-semi-sandwiches-for-quantum-computing/","description":"News on ISTA Website","relation":"press_release"}],"record":[{"status":"public","id":"10029","relation":"earlier_version"},{"id":"14547","relation":"dissertation_contains","status":"public"}]},"day":"11","title":"Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"department":[{"_id":"MaSe"},{"_id":"AnHi"}],"isi":1,"author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T"},{"last_name":"Senior","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","orcid":"0000-0002-0672-9295"},{"orcid":"0000-0001-9666-3543","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"first_name":"M.","full_name":"Hatefipour, M.","last_name":"Hatefipour"},{"last_name":"Strickland","full_name":"Strickland, W. M.","first_name":"W. M."},{"first_name":"J.","last_name":"Shabani","full_name":"Shabani, J."},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"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."}],"intvolume":" 128","date_updated":"2026-04-07T13:25:51Z","article_number":"107701","oa_version":"Preprint","issue":"10","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.128.107701","publisher":"American Physical Society","date_published":"2022-03-11T00:00:00Z","oa":1,"keyword":["General Physics and Astronomy"],"article_type":"original","external_id":{"pmid":[" 35333085"],"arxiv":["2107.03695"],"isi":["000771391100002"]},"year":"2022","quality_controlled":"1","scopus_import":"1","month":"03","pmid":1,"arxiv":1,"_id":"10851","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","volume":128,"corr_author":"1","citation":{"ieee":"D. T. Phan et al., “Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit,” Physical Review Letters, vol. 128, no. 10. American Physical Society, 2022.","apa":"Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M., Shabani, J., … Higginbotham, A. P. (2022). Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.128.107701","ama":"Phan DT, Senior JL, Ghazaryan A, et al. Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit. Physical Review Letters. 2022;128(10). doi:10.1103/physrevlett.128.107701","short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, Physical Review Letters 128 (2022).","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.” Physical Review Letters. American Physical Society, 2022. https://doi.org/10.1103/physrevlett.128.107701.","mla":"Phan, Duc T., et al. “Detecting Induced P±ip Pairing at the Al-InAs Interface with a Quantum Microwave Circuit.” Physical Review Letters, vol. 128, no. 10, 107701, American Physical Society, 2022, doi:10.1103/physrevlett.128.107701."},"publication_status":"published"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":105,"citation":{"short":"M. Davydova, M. Serbyn, H. Ishizuka, Physical Review B 105 (2022).","ista":"Davydova M, Serbyn M, Ishizuka H. 2022. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. 105, L121407.","mla":"Davydova, Margarita, et al. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” Physical Review B, vol. 105, L121407, American Physical Society, 2022, doi:10.1103/PhysRevB.105.L121407.","chicago":"Davydova, Margarita, Maksym Serbyn, and Hiroaki Ishizuka. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” Physical Review B. American Physical Society, 2022. https://doi.org/10.1103/PhysRevB.105.L121407.","ama":"Davydova M, Serbyn M, Ishizuka H. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. 2022;105. doi:10.1103/PhysRevB.105.L121407","apa":"Davydova, M., Serbyn, M., & Ishizuka, H. (2022). Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.105.L121407","ieee":"M. Davydova, M. Serbyn, and H. Ishizuka, “Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials,” Physical Review B, vol. 105. American Physical Society, 2022."},"publication_status":"published","scopus_import":"1","month":"03","arxiv":1,"_id":"10863","external_id":{"isi":["000800752500001"],"arxiv":["2101.08277"]},"year":"2022","quality_controlled":"1","date_published":"2022-03-17T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.105.L121407","publisher":"American Physical Society","oa":1,"article_type":"letter_note","author":[{"first_name":"Margarita","full_name":"Davydova, Margarita","last_name":"Davydova"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"first_name":"Hiroaki","full_name":"Ishizuka, Hiroaki","last_name":"Ishizuka"}],"abstract":[{"text":"Nonlinear optical responses are commonly used as a probe for studying the electronic properties of materials. For topological materials, studies thus far focused on photogalvanic electric currents, which are forbidden in centrosymmetric materials because they require broken inversion symmetry. In this Letter, we propose a class of symmetry-allowed responses for inversion-symmetric topological insulators with two doubly degenerate bands. We consider a specific example of such a response, the orbital current, and show that the sign of the response reflects the Z2 topological index, i.e., the orbital current changes sign at the transition between trivial and topological insulator phases. This is illustrated in two models of topological insulators: the Bernevig-Hughes-Zhang model and the 1T′ phase of transition metal dichalcogenides.","lang":"eng"}],"date_updated":"2023-08-03T06:09:56Z","intvolume":" 105","article_number":"L121407","oa_version":"Preprint","day":"17","title":"Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials","department":[{"_id":"MaSe"}],"isi":1,"publication_identifier":{"issn":["2469-9969"]},"publication":"Physical Review B","acknowledgement":"We are grateful to Takahiro Morimoto and Zhanybek Alpichshev for fruitful discussions. MD was supported by Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH) and by the John Seo Fellowship at MIT. HI was supported by JSPS KAKENHI Grant Numbers JP19K14649 and JP18H03676, and by UTokyo Global Activity Support Program for\r\nYoung Researchers.","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2101.08277"}],"date_created":"2022-03-18T10:20:46Z","article_processing_charge":"No"}]