[{"department":[{"_id":"MaSe"}],"doi":"10.1103/physreva.107.062404","file":[{"content_type":"application/pdf","checksum":"0d71423888eeccaa60d8f41197f26306","success":1,"creator":"dernst","access_level":"open_access","date_created":"2023-06-13T07:28:36Z","relation":"main_file","date_updated":"2023-06-13T07:28:36Z","file_size":2524611,"file_name":"2023_PhysRevA_Sack.pdf","file_id":"13131"}],"type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2023-06-07T06:57:32Z","oa_version":"Published Version","day":"02","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"corr_author":"1","month":"06","intvolume":"       107","citation":{"mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., &#38; Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>.","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404."},"scopus_import":"1","publisher":"American Physical Society","status":"public","file_date_updated":"2023-06-13T07:28:36Z","article_number":"062404","arxiv":1,"issue":"6","ddc":["530"],"date_published":"2023-06-02T00:00:00Z","date_updated":"2026-10-31T23:30:57Z","ec_funded":1,"publication_status":"published","abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. ","lang":"eng"}],"publication":"Physical Review A","quality_controlled":"1","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","last_name":"Sack","full_name":"Sack, Stefan","first_name":"Stefan"},{"orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A","last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A"},{"last_name":"Kueng","full_name":"Kueng, Richard","first_name":"Richard"},{"first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","related_material":{"record":[{"id":"17208","status":"public","relation":"dissertation_contains"},{"id":"14622","status":"public","relation":"dissertation_contains"}]},"year":"2023","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"_id":"13125","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"article_processing_charge":"No","oa":1,"fulldoi":"https://doi.org/10.1103/physreva.107.062404","volume":107,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}]},{"acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"},{"grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity"}],"oa":1,"article_processing_charge":"Yes","volume":40,"fulldoi":"https://doi.org/10.1093/molbev/msad245","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"publication":"Molecular Biology and Evolution","quality_controlled":"1","author":[{"last_name":"Lasne","full_name":"Lasne, Clementine","first_name":"Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"},{"first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","related_material":{"record":[{"relation":"research_data","status":"public","id":"14614"},{"id":"19386","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage"}]},"year":"2023","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"14613","isi":1,"external_id":{"pmid":["37988296"],"isi":["001122489000003"]},"date_published":"2023-12-01T00:00:00Z","date_updated":"2026-10-31T23:30:58Z","pmid":1,"publication_status":"published","publisher":"Oxford University Press","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"status":"public","file_date_updated":"2024-01-02T11:39:38Z","article_number":"msad245","issue":"12","ddc":["570"],"corr_author":"1","month":"12","intvolume":"        40","citation":{"ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>."},"scopus_import":"1","oa_version":"Published Version","day":"01","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"doi":"10.1093/molbev/msad245","department":[{"_id":"BeVi"}],"file":[{"success":1,"creator":"dernst","content_type":"application/pdf","checksum":"47c1c72fb499f26ea52d216b242208c8","file_id":"14727","file_size":8623505,"date_updated":"2024-01-02T11:39:38Z","relation":"main_file","file_name":"2023_MolecularBioEvo_Lasne.pdf","date_created":"2024-01-02T11:39:38Z","access_level":"open_access"}],"has_accepted_license":"1","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2023-11-27T16:14:37Z"},{"abstract":[{"lang":"eng","text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator."}],"publication":"Nature Physics","quality_controlled":"1","author":[{"last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559"},{"orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","last_name":"Senior","full_name":"Senior, Jorden L"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime","first_name":"Jaime"},{"last_name":"Puglia","full_name":"Puglia, Denise","first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0003-1144-2763"},{"orcid":"0009-0005-0878-3032","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Andrew P","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17881"}]},"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"_id":"14032","external_id":{"isi":["001054563800006"]},"date_published":"2023-11-01T00:00:00Z","date_updated":"2026-10-31T23:31:00Z","ec_funded":1,"publication_status":"published","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"article_processing_charge":"Yes (in subscription journal)","oa":1,"fulldoi":"https://doi.org/10.1038/s41567-023-02161-w","volume":19,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","day":"01","page":"1630-1635","title":"Superconductivity from a melted insulator in Josephson junction arrays","acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"doi":"10.1038/s41567-023-02161-w","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"file":[{"checksum":"1fc86d71bfbf836e221c1e925343adc5","content_type":"application/pdf","creator":"dernst","success":1,"file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","file_size":1977706,"date_updated":"2024-01-29T11:25:38Z","relation":"main_file","file_id":"14899","date_created":"2024-01-29T11:25:38Z","access_level":"open_access"}],"type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2023-08-11T07:41:17Z","publisher":"Springer Nature","keyword":["General Physics and Astronomy"],"status":"public","file_date_updated":"2024-01-29T11:25:38Z","ddc":["530"],"corr_author":"1","month":"11","intvolume":"        19","citation":{"mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635."},"scopus_import":"1"},{"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"article_processing_charge":"Yes (via OA deal)","oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1093/evlett/qrac004","volume":7,"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18531"}]},"abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}],"publication":"Evolution Letters","quality_controlled":"1","isi":1,"_id":"12521","external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-02-01T00:00:00Z","date_updated":"2026-10-31T23:31:02Z","ec_funded":1,"pmid":1,"publication_status":"published","publisher":"Oxford University Press","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"issue":"1","ddc":["570"],"status":"public","article_number":"qrac004","file_date_updated":"2023-08-16T11:43:33Z","corr_author":"1","month":"02","citation":{"apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023)."},"scopus_import":"1","intvolume":"         7","oa_version":"Published Version","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","publication_identifier":{"issn":["2056-3744"]},"day":"01","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","doi":"10.1093/evlett/qrac004","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file":[{"creator":"dernst","success":1,"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","content_type":"application/pdf","file_id":"14068","file_name":"2023_EvLetters_Mrnjavac.pdf","relation":"main_file","file_size":2592189,"date_updated":"2023-08-16T11:43:33Z","date_created":"2023-08-16T11:43:33Z","access_level":"open_access"}],"date_created":"2023-02-06T13:59:12Z","has_accepted_license":"1","type":"journal_article","language":[{"iso":"eng"}]},{"related_material":{"record":[{"status":"public","id":"23072","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"17465"}]},"author":[{"last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"id":"94ec913c-dc85-11ea-9058-e5051ab2428b","last_name":"Kögler","full_name":"Kögler, Kevin","first_name":"Kevin"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"quality_controlled":"1","publication":"Proceedings of the 40th International Conference on Machine Learning","abstract":[{"lang":"eng","text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions."}],"external_id":{"arxiv":["2212.13468"]},"_id":"14459","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","date_updated":"2026-10-31T23:31:03Z","date_published":"2023-07-30T00:00:00Z","publication_status":"published","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.13468"}],"oa":1,"article_processing_charge":"No","conference":{"start_date":"2023-07-23","end_date":"2023-07-29","location":"Honolulu, Hawaii, HI, United States","name":"ICML: International Conference on Machine Learning"},"volume":202,"oa_version":"Preprint","publication_identifier":{"eissn":["2640-3498"]},"acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","page":"31151-31209","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","day":"30","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"date_created":"2023-10-29T23:01:17Z","alternative_title":["PMLR"],"language":[{"iso":"eng"}],"type":"conference","publisher":"ML Research Press","arxiv":1,"status":"public","month":"07","corr_author":"1","scopus_import":"1","citation":{"apa":"Shevchenko, A., Kögler, K., Hassani, H., &#38; Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:31151–209. ML Research Press, 2023.","ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:31151-31209.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 31151–209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209."},"intvolume":"       202"},{"oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":14,"fulldoi":"https://doi.org/10.1038/s41467-023-38761-6","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"date_published":"2023-05-24T00:00:00Z","ec_funded":1,"date_updated":"2026-10-31T23:31:07Z","pmid":1,"publication_status":"published","author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander V.","full_name":"Poshakinskiy, Alexander V.","last_name":"Poshakinskiy"},{"last_name":"Sett","full_name":"Sett, Riya","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7641-8348"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin"},{"first_name":"Alexander N.","last_name":"Poddubny","full_name":"Poddubny, Alexander N."},{"first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","related_material":{"record":[{"id":"13124","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"19533"}]},"abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"publication":"Nature Communications","quality_controlled":"1","isi":1,"_id":"13117","external_id":{"isi":["001001099700002"],"arxiv":["2205.03293"],"pmid":["37225689"]},"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","month":"05","citation":{"mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” <i>Nature Communications</i>, vol. 14, 2998, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38761-6\">10.1038/s41467-023-38761-6</a>.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38761-6\">https://doi.org/10.1038/s41467-023-38761-6</a>","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38761-6\">10.1038/s41467-023-38761-6</a>","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38761-6\">https://doi.org/10.1038/s41467-023-38761-6</a>.","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998."},"scopus_import":"1","intvolume":"        14","publisher":"Springer Nature","ddc":["530"],"status":"public","arxiv":1,"article_number":"2998","file_date_updated":"2023-06-06T07:31:20Z","doi":"10.1038/s41467-023-38761-6","department":[{"_id":"JoFi"}],"file":[{"file_id":"13123","file_size":1654389,"relation":"main_file","date_updated":"2023-06-06T07:31:20Z","file_name":"2023_NaturePhysics_Redchenko.pdf","date_created":"2023-06-06T07:31:20Z","access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"a857df40f0882859c48a1ff1e2001ec2"}],"date_created":"2023-06-04T22:01:02Z","type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","publication_identifier":{"eissn":["2041-1723"]},"day":"24","title":"Tunable directional photon scattering from a pair of superconducting qubits"},{"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"day":"01","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","page":"606-614","oa_version":"Published Version","date_created":"2023-01-23T14:14:19Z","type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"doi":"10.1038/s41593-023-01280-0","file":[{"checksum":"a33d91e398e548f34003170e10988368","content_type":"application/pdf","success":1,"creator":"dernst","relation":"main_file","date_updated":"2023-10-04T11:40:51Z","file_size":6144866,"file_name":"2023_NatureNeuroscience_Gupta.pdf","file_id":"14395","date_created":"2023-10-04T11:40:51Z","access_level":"open_access"}],"ddc":["570"],"status":"public","file_date_updated":"2023-10-04T11:40:51Z","publisher":"Springer Nature","citation":{"chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>, vol. 26, Springer Nature, 2023, pp. 606–14, doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” <i>Nature Neuroscience</i>, vol. 26. Springer Nature, pp. 606–614, 2023."},"scopus_import":"1","intvolume":"        26","corr_author":"1","month":"04","_id":"12349","isi":1,"external_id":{"pmid":["36959418"],"isi":["000955258300002"]},"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-7400-6665","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","first_name":"Divyansh","full_name":"Gupta, Divyansh","last_name":"Gupta"},{"first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton L","full_name":"Sumser, Anton L","last_name":"Sumser","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","full_name":"Symonova, Olga","last_name":"Symonova"},{"full_name":"Svaton, Jan","last_name":"Svaton","first_name":"Jan","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","orcid":"0000-0002-6198-2939"},{"first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","related_material":{"record":[{"id":"12370","status":"public","relation":"research_data"},{"status":"public","id":"18574","relation":"dissertation_contains"}]},"abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.","lang":"eng"}],"publication":"Nature Neuroscience","quality_controlled":"1","pmid":1,"publication_status":"published","date_published":"2023-04-01T00:00:00Z","date_updated":"2026-10-31T23:31:07Z","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and 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Version","day":"26","title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields","corr_author":"1","month":"01","citation":{"chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>.","apa":"Gupta, D., Sumser, A. L., &#38; Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","mla":"Gupta, Divyansh, et al. <i>Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023)."},"publisher":"Institute of Science and Technology Austria","status":"public","file_date_updated":"2023-01-26T10:51:34Z","ddc":["571"],"date_published":"2023-01-26T00:00:00Z","date_updated":"2026-10-31T23:31:08Z","ec_funded":1,"abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. 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P.M.  was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). 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During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. 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Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1916–1926, 2023.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>."},"scopus_import":"1","oa_version":"Published Version","day":"01","title":"Chiral and nematic phases of flexible active filaments","page":"1916-1926","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-023-02218-w","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"file":[{"creator":"dernst","success":1,"content_type":"application/pdf","checksum":"bc7673ca07d37309013a86166577b2f7","access_level":"open_access","date_created":"2024-01-30T14:28:30Z","file_id":"14916","file_name":"2023_NaturePhysics_Dunajova.pdf","relation":"main_file","date_updated":"2024-01-30T14:28:30Z","file_size":22471673}],"has_accepted_license":"1","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2023-07-27T14:44:45Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments"}],"article_processing_charge":"Yes (in subscription journal)","oa":1,"volume":19,"fulldoi":"https://doi.org/10.1038/s41567-023-02218-w","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"quality_controlled":"1","publication":"Nature Physics","author":[{"first_name":"Zuzana","full_name":"Dunajova, Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu"},{"first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"last_name":"Brandis","full_name":"Brandis, Dörte","first_name":"Dörte","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd"},{"first_name":"Philipp","last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Wong, Richard W.","last_name":"Wong","first_name":"Richard W."},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","related_material":{"record":[{"id":"13116","status":"public","relation":"research_data"},{"relation":"research_data","id":"21439","status":"public"},{"status":"public","id":"21423","relation":"dissertation_contains"}]},"year":"2023","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"_id":"13314","external_id":{"pmid":["38075437"],"isi":["001178645300041"]},"date_published":"2023-12-01T00:00:00Z","date_updated":"2026-10-31T23:31:09Z","ec_funded":1,"pmid":1,"publication_status":"published"},{"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":35,"fulldoi":"https://doi.org/10.1016/j.coisb.2023.100459","article_processing_charge":"Yes (via OA deal)","oa":1,"project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011"}],"publication_status":"published","date_updated":"2026-10-31T23:31:12Z","date_published":"2023-09-01T00:00:00Z","_id":"13136","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"article_type":"original","author":[{"first_name":"Thomas","last_name":"Minchington","full_name":"Minchington, Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"first_name":"Stefanie","last_name":"Rus","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","publication":"Current Opinion in Systems Biology","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"scopus_import":"1","citation":{"ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","apa":"Minchington, T., Rus, S., &#38; Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. 2023;35. doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” <i>Current Opinion in Systems Biology</i>, vol. 35. Elsevier, 2023.","mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>, vol. 35, 100459, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>."},"intvolume":"        35","month":"09","corr_author":"1","ddc":["570"],"article_number":"100459","file_date_updated":"2024-01-29T11:06:45Z","status":"public","publisher":"Elsevier","date_created":"2023-06-18T22:00:46Z","language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","file":[{"checksum":"8a75c4e29fd9b62e3c50663c2265b173","content_type":"application/pdf","success":1,"creator":"dernst","date_created":"2024-01-29T11:06:45Z","access_level":"open_access","file_size":598842,"relation":"main_file","date_updated":"2024-01-29T11:06:45Z","file_name":"2023_CurrOpSystBioloy_Minchington.pdf","file_id":"14896"}],"department":[{"_id":"AnKi"}],"doi":"10.1016/j.coisb.2023.100459","publication_identifier":{"eissn":["2452-3100"]},"acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","title":"Control of tissue dimensions in the developing neural tube and somites","day":"01","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","date_created":"2023-01-12T12:09:17Z","file":[{"date_created":"2023-08-16T08:15:41Z","access_level":"open_access","file_id":"14062","file_name":"2023_MolecularEcology_Shipilina.pdf","relation":"main_file","file_size":7144607,"date_updated":"2023-08-16T08:15:41Z","creator":"dernst","success":1,"content_type":"application/pdf","checksum":"b10e0f8fa3dc4d72aaf77a557200978a"}],"department":[{"_id":"NiBa"}],"doi":"10.1111/mec.16793","page":"1441-1457","title":"On the origin and structure of haplotype blocks","day":"01","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","oa_version":"Published Version","intvolume":"        32","scopus_import":"1","citation":{"ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023."},"month":"03","corr_author":"1","file_date_updated":"2023-08-16T08:15:41Z","status":"public","ddc":["570"],"issue":"6","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"publisher":"Wiley","publication_status":"published","pmid":1,"date_updated":"2026-10-31T23:31:13Z","date_published":"2023-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"_id":"12159","isi":1,"publication":"Molecular Ecology","quality_controlled":"1","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20694"}]},"author":[{"first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","volume":32,"fulldoi":"https://doi.org/10.1111/mec.16793","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}]},{"date_created":"2023-07-12T07:32:46Z","language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","file":[{"content_type":"application/pdf","checksum":"6012b7e4a2f680ee6c1f84001e2b945f","creator":"dernst","success":1,"file_name":"2023_MolecularPlant_Chen.pdf","relation":"main_file","date_updated":"2024-01-29T10:37:05Z","file_size":1000871,"file_id":"14894","date_created":"2024-01-29T10:37:05Z","access_level":"open_access"}],"department":[{"_id":"JiFr"}],"doi":"10.1016/j.molp.2023.06.007","publication_identifier":{"issn":["1752-9867"],"eissn":["1674-2052"]},"acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","page":"1117-1119","day":"01","oa_version":"Published Version","scopus_import":"1","citation":{"mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” <i>Molecular Plant</i>, vol. 16, no. 7, Elsevier, 2023, pp. 1117–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">10.1016/j.molp.2023.06.007</a>.","short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” <i>Molecular Plant</i>, vol. 16, no. 7. Elsevier, pp. 1117–1119, 2023.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” <i>Molecular Plant</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">https://doi.org/10.1016/j.molp.2023.06.007</a>.","ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. <i>Molecular Plant</i>. 2023;16(7):1117-1119. doi:<a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">10.1016/j.molp.2023.06.007</a>","apa":"Chen, H., Li, L., Zou, M., Qi, L., &#38; Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">https://doi.org/10.1016/j.molp.2023.06.007</a>","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119."},"intvolume":"        16","month":"07","corr_author":"1","ddc":["580"],"issue":"7","file_date_updated":"2024-01-29T10:37:05Z","status":"public","publisher":"Elsevier","publication_status":"published","pmid":1,"ec_funded":1,"date_updated":"2026-10-31T23:31:15Z","date_published":"2023-07-01T00:00:00Z","das_tickbox":"1","external_id":{"isi":["001044410900001"],"pmid":["37393433"]},"isi":1,"_id":"13212","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","related_material":{"record":[{"status":"public","id":"19478","relation":"dissertation_contains"}]},"author":[{"last_name":"Chen","full_name":"Chen, Huihuang","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia","last_name":"Zou"},{"id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","last_name":"Qi","full_name":"Qi, Linlin","first_name":"Linlin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"article_type":"letter_note","publication":"Molecular Plant","quality_controlled":"1","abstract":[{"text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.1016/j.molp.2023.06.007","volume":16,"article_processing_charge":"Yes (via OA deal)","oa":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}]},{"month":"01","corr_author":"1","scopus_import":"1","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.","ieee":"B. Basilico <i>et al.</i>, “Microglia control glutamatergic synapses in the adult mouse hippocampus,” <i>Glia</i>, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>.","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.","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. Wiley. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>.","ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. 2022;70(1):173-195. doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>"},"intvolume":"        70","keyword":["Cellular and Molecular Neuroscience","Neurology"],"publisher":"Wiley","ddc":["570"],"issue":"1","file_date_updated":"2022-03-04T08:55:27Z","status":"public","file":[{"access_level":"open_access","date_created":"2022-03-04T08:55:27Z","file_id":"10819","relation":"main_file","file_size":5340294,"date_updated":"2022-03-04T08:55:27Z","file_name":"2021_Glia_Basilico.pdf","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"f10a897290e66c0a062e04ba91db6c17"}],"doi":"10.1002/glia.24101","license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"GaNo"}],"date_created":"2022-03-04T08:53:37Z","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","oa_version":"Published Version","publication_identifier":{"issn":["0894-1491"],"eissn":["1098-1136"]},"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.","page":"173-195","title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","day":"01","article_processing_charge":"No","oa":1,"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"volume":70,"fulldoi":"https://doi.org/10.1002/glia.24101","date_updated":"2024-10-09T21:04:02Z","date_published":"2022-01-01T00:00:00Z","publication_status":"published","pmid":1,"article_type":"original","author":[{"orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","full_name":"Basilico, Bernadette","last_name":"Basilico"},{"full_name":"Ferrucci, Laura","last_name":"Ferrucci","first_name":"Laura"},{"first_name":"Patrizia","full_name":"Ratano, Patrizia","last_name":"Ratano"},{"first_name":"Maria T.","full_name":"Golia, Maria T.","last_name":"Golia"},{"first_name":"Alfonso","last_name":"Grimaldi","full_name":"Grimaldi, Alfonso"},{"full_name":"Rosito, Maria","last_name":"Rosito","first_name":"Maria"},{"last_name":"Ferretti","full_name":"Ferretti, Valentina","first_name":"Valentina"},{"full_name":"Reverte, Ingrid","last_name":"Reverte","first_name":"Ingrid"},{"last_name":"Sanchini","full_name":"Sanchini, Caterina","first_name":"Caterina"},{"last_name":"Marrone","full_name":"Marrone, Maria C.","first_name":"Maria C."},{"full_name":"Giubettini, Maria","last_name":"Giubettini","first_name":"Maria"},{"first_name":"Valeria","last_name":"De Turris","full_name":"De Turris, Valeria"},{"first_name":"Debora","full_name":"Salerno, Debora","last_name":"Salerno"},{"full_name":"Garofalo, Stefano","last_name":"Garofalo","first_name":"Stefano"},{"full_name":"St‐Pierre, Marie‐Kim","last_name":"St‐Pierre","first_name":"Marie‐Kim"},{"first_name":"Micael","full_name":"Carrier, Micael","last_name":"Carrier"},{"first_name":"Massimiliano","full_name":"Renzi, Massimiliano","last_name":"Renzi"},{"first_name":"Francesca","last_name":"Pagani","full_name":"Pagani, Francesca"},{"first_name":"Brijesh","last_name":"Modi","full_name":"Modi, Brijesh"},{"first_name":"Marcello","full_name":"Raspa, Marcello","last_name":"Raspa"},{"last_name":"Scavizzi","full_name":"Scavizzi, Ferdinando","first_name":"Ferdinando"},{"first_name":"Cornelius T.","full_name":"Gross, Cornelius T.","last_name":"Gross"},{"last_name":"Marinelli","full_name":"Marinelli, Silvia","first_name":"Silvia"},{"full_name":"Tremblay, Marie‐Ève","last_name":"Tremblay","first_name":"Marie‐Ève"},{"first_name":"Daniele","last_name":"Caprioli","full_name":"Caprioli, Daniele"},{"full_name":"Maggi, Laura","last_name":"Maggi","first_name":"Laura"},{"first_name":"Cristina","last_name":"Limatola","full_name":"Limatola, Cristina"},{"last_name":"Di Angelantonio","full_name":"Di Angelantonio, Silvia","first_name":"Silvia"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"}],"publication":"Glia","quality_controlled":"1","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."}],"external_id":{"pmid":["34661306"],"isi":["000708025800001"]},"isi":1,"_id":"10818","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2022"},{"month":"01","scopus_import":"1","citation":{"ista":"Liu J, Marensi E, Wu X. 2022. Effects of streaky structures on the instability of supersonic boundary layers. IUTAM Laminar-Turbulent Transition. IUTAM Symposium, IUTAM, vol. 38, 587–598.","apa":"Liu, J., Marensi, E., &#38; Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In <i>IUTAM Laminar-Turbulent Transition</i> (Vol. 38, pp. 587–598). London, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In <i>IUTAM Laminar-Turbulent Transition</i>, 38:587–98. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: <i>IUTAM Laminar-Turbulent Transition</i>. Vol 38. Springer Nature; 2022:587-598. doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in <i>IUTAM Laminar-Turbulent Transition</i>, London, United Kingdom, 2022, vol. 38, pp. 587–598.","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” <i>IUTAM Laminar-Turbulent Transition</i>, vol. 38, Springer Nature, 2022, pp. 587–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>."},"intvolume":"        38","publisher":"Springer Nature","status":"public","doi":"10.1007/978-3-030-67902-6_51","department":[{"_id":"BjHo"}],"date_created":"2022-03-04T09:14:34Z","alternative_title":["IUTAM"],"language":[{"iso":"eng"}],"type":"conference","oa_version":"None","publication_identifier":{"eisbn":["9783030679026"],"eissn":["1875-3493"],"issn":["1875-3507"],"isbn":["9783030679019"]},"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).","title":"Effects of streaky structures on the instability of supersonic boundary layers","page":"587-598","day":"01","article_processing_charge":"No","conference":{"start_date":"2019-09-02","end_date":"2019-09-06","location":"London, United Kingdom","name":"IUTAM Symposium"},"volume":38,"fulldoi":"https://doi.org/10.1007/978-3-030-67902-6_51","OA_type":"closed access","date_updated":"2025-05-20T06:08:26Z","date_published":"2022-01-01T00:00:00Z","publication_status":"published","author":[{"first_name":"Jianxin","last_name":"Liu","full_name":"Liu, Jianxin"},{"full_name":"Marensi, Elena","last_name":"Marensi","first_name":"Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","orcid":"0000-0001-7173-4923"},{"first_name":"Xuesong","last_name":"Wu","full_name":"Wu, Xuesong"}],"quality_controlled":"1","publication":"IUTAM Laminar-Turbulent Transition","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."}],"external_id":{"isi":["000709087600051"]},"_id":"10820","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022"},{"file_date_updated":"2022-03-07T07:55:23Z","status":"public","ddc":["570"],"issue":"5","publisher":"Cell Press","intvolume":"       185","scopus_import":"1","citation":{"ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. 2022;185(5):777-793.e20. doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>.","short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20.","ieee":"A. Yanagida <i>et al.</i>, “Cell surface fluctuations regulate early embryonic lineage sorting,” <i>Cell</i>, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>."},"month":"02","title":"Cell surface fluctuations regulate early embryonic lineage sorting","page":"777-793.e20","day":"22","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"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.","oa_version":"Published Version","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","date_created":"2022-03-06T23:01:52Z","file":[{"success":1,"creator":"dernst","content_type":"application/pdf","checksum":"ae305060e8031297771b89dae9e36a29","access_level":"open_access","date_created":"2022-03-07T07:55:23Z","file_id":"10831","file_size":8478995,"date_updated":"2022-03-07T07:55:23Z","relation":"main_file","file_name":"2022_Cell_Yanagida.pdf"}],"department":[{"_id":"EdHa"}],"doi":"10.1016/j.cell.2022.01.022","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"fulldoi":"https://doi.org/10.1016/j.cell.2022.01.022","volume":185,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"isi":1,"_id":"10825","quality_controlled":"1","publication":"Cell","abstract":[{"text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.","lang":"eng"}],"author":[{"full_name":"Yanagida, Ayaka","last_name":"Yanagida","first_name":"Ayaka"},{"first_name":"Elena","last_name":"Corujo-Simon","full_name":"Corujo-Simon, Elena"},{"full_name":"Revell, Christopher K.","last_name":"Revell","first_name":"Christopher K."},{"full_name":"Sahu, Preeti","last_name":"Sahu","first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"first_name":"Giuliano G.","last_name":"Stirparo","full_name":"Stirparo, Giuliano G."},{"first_name":"Irene M.","full_name":"Aspalter, Irene M.","last_name":"Aspalter"},{"first_name":"Alex K.","last_name":"Winkel","full_name":"Winkel, Alex K."},{"first_name":"Ruby","last_name":"Peters","full_name":"Peters, Ruby"},{"first_name":"Henry","last_name":"De Belly","full_name":"De Belly, Henry"},{"last_name":"Cassani","full_name":"Cassani, Davide A.D.","first_name":"Davide A.D."},{"full_name":"Achouri, Sarra","last_name":"Achouri","first_name":"Sarra"},{"first_name":"Raphael","full_name":"Blumenfeld, Raphael","last_name":"Blumenfeld"},{"first_name":"Kristian","full_name":"Franze, Kristian","last_name":"Franze"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."},{"first_name":"Jennifer","last_name":"Nichols","full_name":"Nichols, Jennifer"},{"first_name":"Kevin J.","full_name":"Chalut, Kevin J.","last_name":"Chalut"}],"article_type":"original","publication_status":"published","pmid":1,"ec_funded":1,"date_updated":"2025-07-10T11:50:00Z","date_published":"2022-02-22T00:00:00Z"},{"publisher":"eLife Sciences Publications","file_date_updated":"2022-03-07T07:39:25Z","article_number":"e68040","status":"public","ddc":["570"],"month":"02","corr_author":"1","intvolume":"        11","scopus_import":"1","citation":{"chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>","apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>.","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","short":"G. Valperga, M. de Bono, ELife 11 (2022)."},"oa_version":"Published Version","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","day":"24","publication_identifier":{"eissn":["2050-084X"]},"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).","file":[{"access_level":"open_access","date_created":"2022-03-07T07:39:25Z","file_size":4095591,"relation":"main_file","date_updated":"2022-03-07T07:39:25Z","file_name":"2022_eLife_Valperga.pdf","file_id":"10830","content_type":"application/pdf","checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","success":1,"creator":"dernst"}],"department":[{"_id":"MaDe"}],"doi":"10.7554/eLife.68040","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","date_created":"2022-03-06T23:01:52Z","project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"article_processing_charge":"No","oa":1,"fulldoi":"https://doi.org/10.7554/eLife.68040","volume":11,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"eLife","quality_controlled":"1","abstract":[{"text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.","lang":"eng"}],"article_type":"original","author":[{"last_name":"Valperga","full_name":"Valperga, Giulio","first_name":"Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E","orcid":"0000-0001-6726-3890"},{"first_name":"Mario","last_name":"De Bono","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2022","external_id":{"pmid":["35201977"],"isi":["000763432300001"]},"_id":"10826","isi":1,"date_updated":"2026-04-02T12:45:39Z","date_published":"2022-02-24T00:00:00Z","publication_status":"published","pmid":1},{"publication_identifier":{"eissn":["2379-3694"]},"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research. The data that support the findings of this study are openly available in Zenodo (DOI: 10.5281/zenodo.5500360)","page":"504-512","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","day":"08","oa_version":"Published Version","date_created":"2022-03-06T23:01:54Z","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","file":[{"relation":"main_file","date_updated":"2022-03-07T08:15:01Z","file_size":2969415,"file_name":"2022_ACSSensors_Hasler.pdf","file_id":"10832","access_level":"open_access","date_created":"2022-03-07T08:15:01Z","checksum":"d704af7262cd484da9bb84b7d84e2b09","content_type":"application/pdf","success":1,"creator":"dernst"}],"department":[{"_id":"MaIb"}],"doi":"10.1021/acssensors.1c02313","ddc":["540"],"issue":"2","file_date_updated":"2022-03-07T08:15:01Z","status":"public","publisher":"American Chemical Society","scopus_import":"1","citation":{"mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>.","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” <i>ACS Sensors</i>, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","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.","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>.","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. 2022;7(2):504-512. doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>","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."},"intvolume":"         7","month":"02","external_id":{"isi":["000765113000016"],"pmid":["35134289"]},"_id":"10829","isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2022","related_material":{"record":[{"relation":"research_data","id":"10833","status":"public"}]},"author":[{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","last_name":"Fossati","first_name":"Stefan"},{"first_name":"Patrik","last_name":"Aspermair","full_name":"Aspermair, Patrik"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598"},{"first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes","last_name":"Bintinger","full_name":"Bintinger, Johannes"},{"full_name":"Knoll, Wolfgang","last_name":"Knoll","first_name":"Wolfgang"}],"article_type":"original","quality_controlled":"1","publication":"ACS Sensors","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"}],"publication_status":"published","pmid":1,"date_updated":"2026-04-02T12:33:46Z","date_published":"2022-02-08T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":7,"fulldoi":"https://doi.org/10.1021/acssensors.1c02313","oa":1,"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"10829","relation":"used_in_publication"}]},"author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","last_name":"Fossati","first_name":"Stefan"},{"first_name":"Patrik","last_name":"Aspermair","full_name":"Aspermair, Patrik"},{"first_name":"Jakub","full_name":"Dostalek, Jakub","last_name":"Dostalek"},{"full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"last_name":"Knoll","full_name":"Knoll, Wolfgang","first_name":"Wolfgang"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","year":"2022","day":"08","_id":"10833","department":[{"_id":"MaIb"}],"doi":"10.5281/ZENODO.5500360","date_updated":"2026-04-02T12:33:44Z","date_published":"2022-02-08T00:00:00Z","type":"research_data_reference","date_created":"2022-03-07T08:19:11Z","publisher":"Zenodo","status":"public","ddc":["540"],"article_processing_charge":"No","oa":1,"month":"02","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5500360","open_access":"1"}],"fulldoi":"https://doi.org/10.5281/ZENODO.5500360","citation":{"mla":"Hasler, Roger, et al. <i>Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>.","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>."}},{"oa_version":"Preprint","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","page":"2150-2173","day":"01","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"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).","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"doi":"10.1093/plcell/koac071","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2022-03-08T13:47:51Z","publisher":"Oxford University Press","status":"public","issue":"6","month":"06","intvolume":"        34","scopus_import":"1","citation":{"chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","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.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","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."},"publication":"Plant Cell","quality_controlled":"1","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"article_type":"original","author":[{"first_name":"DA","last_name":"Dahhan","full_name":"Dahhan, DA"},{"last_name":"Reynolds","full_name":"Reynolds, GD","first_name":"GD"},{"full_name":"Cárdenas, JJ","last_name":"Cárdenas","first_name":"JJ"},{"last_name":"Eeckhout","full_name":"Eeckhout, D","first_name":"D"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"last_name":"Yperman","full_name":"Yperman, K","first_name":"K"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"N","last_name":"Vang","full_name":"Vang, N"},{"last_name":"Yan","full_name":"Yan, X","first_name":"X"},{"last_name":"Hwang","full_name":"Hwang, I","first_name":"I"},{"last_name":"Heese","full_name":"Heese, A","first_name":"A"},{"first_name":"G","full_name":"De Jaeger, G","last_name":"De Jaeger"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"last_name":"Pan","full_name":"Pan, J","first_name":"J"},{"full_name":"Bednarek, SY","last_name":"Bednarek","first_name":"SY"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"isi":1,"_id":"10841","date_updated":"2025-05-14T11:06:15Z","date_published":"2022-06-01T00:00:00Z","publication_status":"published","pmid":1,"project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"article_processing_charge":"No","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"volume":34,"fulldoi":"https://doi.org/10.1093/plcell/koac071"}]