[{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"Synapseek: Meta-learning synaptic plasticity rules","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9633","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2024-10-13T22:30:04Z","day":"12","abstract":[{"lang":"eng","text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n"}],"date_created":"2023-10-12T14:13:25Z","supervisor":[{"orcid":"0000-0003-3295-6181","last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"author":[{"last_name":"Confavreux","first_name":"Basile J","full_name":"Confavreux, Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E"}],"page":"148","doi":"10.15479/at:ista:14422","_id":"14422","project":[{"call_identifier":"H2020","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"type":"dissertation","citation":{"mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>.","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023."},"ddc":["610"],"oa":1,"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"TiVo"}],"month":"10","date_published":"2023-10-12T00:00:00Z","publication_status":"published","date_updated":"2026-06-18T19:55:49Z","publisher":"Institute of Science and Technology Austria","ec_funded":1,"degree_awarded":"PhD","status":"public","year":"2023","corr_author":"1","has_accepted_license":"1","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2024-10-13T22:30:04Z","creator":"cchlebak","checksum":"7f636555eae7803323df287672fd13ed","file_size":30599717,"content_type":"application/pdf","access_level":"open_access","file_id":"14424","file_name":"Confavreux_Thesis_2A.pdf","embargo":"2024-10-12","date_created":"2023-10-12T14:53:50Z","relation":"main_file"},{"embargo_to":"open_access","checksum":"725e85946db92290a4583a0de9779e1b","file_size":68406739,"content_type":"application/x-zip-compressed","access_level":"closed","creator":"cchlebak","date_updated":"2024-10-13T22:30:04Z","relation":"source_file","date_created":"2023-10-18T07:38:34Z","file_name":"Confavreux Thesis.zip","file_id":"14440"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"}},{"volume":19,"file_date_updated":"2023-10-04T11:13:28Z","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"13081","relation":"dissertation_contains"}]},"title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2023-04-16T22:01:09Z","day":"01","abstract":[{"text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.","lang":"eng"}],"isi":1,"scopus_import":"1","pmid":1,"page":"1050-1058","author":[{"last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Bocanegra, Laura"},{"last_name":"Singh","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958","first_name":"Amrita","full_name":"Singh, Amrita"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0001-7896-7762","last_name":"Zagórski","full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"quality_controlled":"1","project":[{"grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_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","grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"_id":"12837","doi":"10.1038/s41567-023-01977-w","type":"journal_article","publication":"Nature Physics","intvolume":"        19","ddc":["570"],"external_id":{"isi":["000964029300003"],"pmid":["37456593"]},"citation":{"apa":"Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., &#38; Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>","ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. <i>Nature Physics</i>. 2023;19:1050-1058. doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1050–1058, 2023.","mla":"Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1050–58, doi:<a href=\"https://doi.org/10.1038/s41567-023-01977-w\">10.1038/s41567-023-01977-w</a>.","chicago":"Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-01977-w\">https://doi.org/10.1038/s41567-023-01977-w</a>.","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","ista":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 19, 1050–1058."},"acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","oa":1,"department":[{"_id":"EdHa"},{"_id":"AnKi"}],"article_processing_charge":"No","date_updated":"2026-06-29T22:30:17Z","publication_status":"published","date_published":"2023-07-01T00:00:00Z","month":"07","article_type":"original","ec_funded":1,"publisher":"Springer Nature","year":"2023","status":"public","has_accepted_license":"1","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","file":[{"date_updated":"2023-10-04T11:13:28Z","content_type":"application/pdf","access_level":"open_access","checksum":"858225a4205b74406e5045006cdd853f","file_size":5532285,"creator":"dernst","success":1,"file_id":"14392","date_created":"2023-10-04T11:13:28Z","file_name":"2023_NaturePhysics_Boncanegra.pdf","relation":"main_file"}]},{"month":"05","date_published":"2023-05-05T00:00:00Z","publication_status":"published","date_updated":"2025-06-12T06:56:58Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2663-337X"]},"file":[{"date_updated":"2024-05-06T22:30:03Z","content_type":"application/pdf","file_size":31434230,"access_level":"open_access","checksum":"59b0303dc483f40a96a610a90aab7ee9","creator":"aschauer","file_id":"12907","date_created":"2023-05-05T13:01:14Z","embargo":"2024-05-05","file_name":"Thesis_Schauer_final.pdf","relation":"main_file"},{"file_id":"12908","file_name":"Thesis_Schauer_final.docx","date_created":"2023-05-05T13:04:15Z","relation":"source_file","date_updated":"2024-05-06T22:30:03Z","creator":"aschauer","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":43809109,"checksum":"25f54e12479b6adaabd129a20568e6c1","embargo_to":"open_access"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","degree_awarded":"PhD","year":"2023","status":"public","has_accepted_license":"1","corr_author":"1","supervisor":[{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2024-05-06T22:30:03Z","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7888","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8966"}]},"day":"05","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"date_created":"2023-05-05T08:48:20Z","type":"dissertation","citation":{"ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria."},"ddc":["570"],"page":"190","author":[{"last_name":"Schauer","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra"}],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"doi":"10.15479/at:ista:12891","_id":"12891"},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2023-12-13T23:30:03Z","content_type":"application/pdf","checksum":"d800e06252eaefba28531fa9440f23f0","access_level":"open_access","file_size":5244581,"creator":"alisjak","file_id":"13204","embargo":"2023-12-12","date_created":"2023-07-10T08:48:40Z","file_name":"2023_PNAS_Wang.pdf","relation":"main_file"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2023","issue":"25","status":"public","has_accepted_license":"1","date_published":"2023-06-12T00:00:00Z","month":"06","article_type":"original","publication_status":"published","date_updated":"2023-12-13T23:30:04Z","publisher":"National Academy of Sciences","oa":1,"article_processing_charge":"No","department":[{"_id":"JiFr"}],"article_number":"e2221313120","type":"journal_article","publication":"Proceedings of the National Academy of Sciences of the United States of America","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","citation":{"ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023.","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>"},"external_id":{"isi":["001030689600003"],"pmid":["37307446"]},"ddc":["570"],"intvolume":"       120","quality_controlled":"1","author":[{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"last_name":"Yuan","first_name":"Zhi","full_name":"Yuan, Zhi"},{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"first_name":"Huixin","full_name":"Xiao, Huixin","last_name":"Xiao"},{"full_name":"Wan, Lu","first_name":"Lu","last_name":"Wan"},{"first_name":"Lanxin","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li"},{"first_name":"Yan","full_name":"Guo, Yan","last_name":"Guo"},{"last_name":"Gong","first_name":"Zhizhong","full_name":"Gong, Zhizhong"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Jing","full_name":"Zhang, Jing","last_name":"Zhang"}],"doi":"10.1073/pnas.2221313120","_id":"13201","scopus_import":"1","isi":1,"pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","language":[{"iso":"eng"}],"file_date_updated":"2023-12-13T23:30:03Z","volume":120,"day":"12","abstract":[{"text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability.","lang":"eng"}],"date_created":"2023-07-09T22:01:12Z"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-14T09:50:54Z","publication_status":"published","month":"05","date_published":"2023-05-23T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"article_processing_charge":"No","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version","file":[{"embargo_to":"open_access","creator":"lbocaneg","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":25615534,"checksum":"74f3f89e59a0189bee53ebfad9c1b9af","date_updated":"2024-06-01T22:30:04Z","relation":"source_file","file_name":"Thesis_final_LauraBocanegra.docx","date_created":"2023-05-25T06:32:12Z","file_id":"13089"},{"embargo":"2024-05-31","date_created":"2023-05-25T06:32:16Z","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","relation":"main_file","file_id":"13090","access_level":"open_access","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","file_size":12386046,"content_type":"application/pdf","creator":"lbocaneg","date_updated":"2024-06-01T22:30:04Z"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","has_accepted_license":"1","corr_author":"1","year":"2023","status":"public","degree_awarded":"PhD","supervisor":[{"full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"date_created":"2023-05-23T19:10:42Z","abstract":[{"text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling.  Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.","lang":"eng"}],"day":"23","file_date_updated":"2024-06-01T22:30:04Z","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9349"},{"status":"public","relation":"part_of_dissertation","id":"12837"}]},"title":"Epithelial dynamics during mouse neural tube development","ddc":["570"],"citation":{"short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>","apa":"Bocanegra, L. (2023). <i>Epithelial dynamics during mouse neural tube development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","mla":"Bocanegra, Laura. <i>Epithelial Dynamics during Mouse Neural Tube Development</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>."},"type":"dissertation","_id":"13081","doi":"10.15479/at:ista:13081","author":[{"full_name":"Bocanegra, Laura","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","last_name":"Bocanegra"}],"page":"93"},{"file_date_updated":"2024-11-30T23:30:03Z","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"13125","status":"public"},{"relation":"part_of_dissertation","id":"11471","status":"public"},{"relation":"part_of_dissertation","id":"9760","status":"public"}]},"title":"Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems","date_created":"2023-11-28T10:58:13Z","day":"30","abstract":[{"text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation.","lang":"eng"}],"supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"}],"page":"142","author":[{"full_name":"Sack, Stefan","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","last_name":"Sack"}],"project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IMB PhD Nomination Fellowship - Stefan Sack"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"_id":"14622","doi":"10.15479/at:ista:14622","type":"dissertation","ddc":["530"],"citation":{"mla":"Sack, Stefan. <i>Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>.","ieee":"S. Sack, “Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","ama":"Sack S. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>","apa":"Sack, S. (2023). <i>Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","ista":"Sack S. 2023. Improving variational quantum algorithms : Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","short":"S. Sack, Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms : Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>."},"oa":1,"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"article_processing_charge":"No","publication_status":"published","date_updated":"2026-04-07T13:53:47Z","month":"11","date_published":"2023-11-30T00:00:00Z","ec_funded":1,"publisher":"Institute of Science and Technology Austria","year":"2023","status":"public","degree_awarded":"PhD","has_accepted_license":"1","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"file":[{"file_id":"14635","file_name":"PhD_Thesis.pdf","date_created":"2023-11-30T15:53:10Z","embargo":"2024-11-30","relation":"main_file","date_updated":"2024-11-30T23:30:03Z","creator":"ssack","file_size":11947523,"checksum":"068fd3570506ec42b2faa390de784bc4","content_type":"application/pdf","access_level":"open_access"},{"file_name":"PhD Thesis (1).zip","date_created":"2023-11-30T15:54:11Z","relation":"source_file","file_id":"14636","creator":"ssack","content_type":"application/zip","access_level":"closed","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_size":18422964,"embargo_to":"open_access","date_updated":"2024-11-30T23:30:03Z"}]},{"page":"151","author":[{"last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"_id":"14323","doi":"10.15479/at:ista:14323","type":"dissertation","ddc":["570"],"citation":{"short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2025-03-13T23:30:05Z","related_material":{"record":[{"status":"public","id":"7883","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","date_created":"2023-09-13T10:07:18Z","day":"13","abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"supervisor":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998"}],"year":"2023","status":"public","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version","file":[{"date_updated":"2025-03-13T23:30:05Z","access_level":"open_access","content_type":"application/pdf","file_size":10147911,"checksum":"bd83596869c814b24aeff7077d031c0e","creator":"kkuzmicz","file_id":"14324","embargo":"2025-03-13","date_created":"2023-09-13T09:52:52Z","file_name":"PhDThesis_KK_final_pdfA.pdf","relation":"main_file"},{"file_name":"thesis_KK_final_corrections_092023.docx","date_created":"2023-09-13T09:53:29Z","relation":"source_file","file_id":"14325","creator":"kkuzmicz","file_size":103980668,"checksum":"aa2757ae4c3478041fd7e62c587d3e4d","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access","date_updated":"2025-03-13T23:30:05Z"}],"alternative_title":["ISTA Thesis"],"oa":1,"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"article_processing_charge":"No","date_updated":"2026-04-14T09:50:54Z","publication_status":"published","month":"09","date_published":"2023-09-13T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publisher":"Institute of Science and Technology Austria"},{"citation":{"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.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","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>.","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>.","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","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>","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>"},"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). ","ddc":["530"],"external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"arxiv":1,"intvolume":"       107","publication":"Physical Review A","type":"journal_article","doi":"10.1103/physreva.107.062404","_id":"13125","project":[{"call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"quality_controlled":"1","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","full_name":"Sack, Stefan","last_name":"Sack","orcid":"0000-0001-5400-8508"},{"last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A"},{"first_name":"Richard","full_name":"Kueng, Richard","last_name":"Kueng"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"}],"scopus_import":"1","isi":1,"day":"02","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"date_created":"2023-06-07T06:57:32Z","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","related_material":{"record":[{"id":"17208","relation":"dissertation_contains","status":"public"},{"status":"public","id":"14622","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file_date_updated":"2023-06-13T07:28:36Z","volume":107,"file":[{"success":1,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":2524611,"checksum":"0d71423888eeccaa60d8f41197f26306","date_updated":"2023-06-13T07:28:36Z","relation":"main_file","file_name":"2023_PhysRevA_Sack.pdf","date_created":"2023-06-13T07:28:36Z","file_id":"13131"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","corr_author":"1","has_accepted_license":"1","year":"2023","issue":"6","status":"public","publisher":"American Physical Society","ec_funded":1,"month":"06","date_published":"2023-06-02T00:00:00Z","article_type":"original","date_updated":"2026-06-29T22:30:17Z","publication_status":"published","article_processing_charge":"No","department":[{"_id":"MaSe"}],"article_number":"062404","oa":1},{"corr_author":"1","has_accepted_license":"1","status":"public","year":"2023","degree_awarded":"MS","oa_version":"Published Version","file":[{"creator":"cchlebak","access_level":"closed","checksum":"453caf851d75c3478c10ed09bd242a91","file_size":15501411,"content_type":"application/x-zip-compressed","embargo_to":"open_access","date_updated":"2024-02-26T23:30:03Z","file_name":"documents-export-2023-08-24.zip","date_created":"2023-08-24T13:02:49Z","relation":"source_file","file_id":"14227"},{"relation":"main_file","file_name":"thesis_pdf_a.pdf","date_created":"2023-08-24T13:03:42Z","embargo":"2024-02-25","file_id":"14228","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","checksum":"7349d29963d6695e555e171748648d9a","file_size":6854783,"date_updated":"2024-02-26T23:30:03Z"}],"alternative_title":["ISTA Master's Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2791-4585"]},"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"article_processing_charge":"No","oa":1,"publisher":"Institute of Science and Technology Austria","publication_status":"published","date_updated":"2026-04-07T14:02:30Z","date_published":"2023-08-24T00:00:00Z","month":"08","_id":"14226","doi":"10.15479/at:ista:14226","author":[{"orcid":"0000-0002-6862-208X","last_name":"Stephenson","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"}],"page":"43","ddc":["500"],"citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","apa":"Stephenson, E. R. (2023). <i>Generalizing medial axes with homology switches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>","mla":"Stephenson, Elizabeth R. <i>Generalizing Medial Axes with Homology Switches</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023."},"type":"dissertation","date_created":"2023-08-24T13:01:18Z","day":"24","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"file_date_updated":"2024-02-26T23:30:03Z","language":[{"iso":"eng"}],"title":"Generalizing medial axes with homology switches","supervisor":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}]},{"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:14697","_id":"14697","author":[{"last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","first_name":"Julian A"}],"page":"226","citation":{"ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","mla":"Stopp, Julian A. <i>Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria."},"ddc":["570"],"type":"dissertation","abstract":[{"text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies.","lang":"eng"}],"day":"20","date_created":"2023-12-18T19:14:28Z","file_date_updated":"2024-12-20T23:30:04Z","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","related_material":{"record":[{"status":"public","id":"14360","relation":"part_of_dissertation"},{"status":"public","id":"12272","relation":"part_of_dissertation"},{"id":"6328","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7885","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14274","status":"public"}]},"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"}],"corr_author":"1","has_accepted_license":"1","degree_awarded":"PhD","status":"public","year":"2023","file":[{"date_updated":"2024-12-20T23:30:04Z","creator":"jstopp","content_type":"application/pdf","access_level":"open_access","file_size":51585778,"checksum":"457927165d5d556305d3086f6b83e5c7","file_id":"14699","file_name":"Thesis.pdf","embargo":"2024-12-20","date_created":"2023-12-20T09:35:34Z","relation":"main_file"},{"date_updated":"2024-12-20T23:30:04Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950,"creator":"jstopp","file_id":"14700","relation":"source_file","date_created":"2023-12-20T09:35:35Z","file_name":"Thesis.docx"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-038-1"]},"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"article_processing_charge":"No","oa":1,"ec_funded":1,"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"12","date_published":"2023-12-20T00:00:00Z","date_updated":"2026-06-18T17:34:48Z","publication_status":"published"},{"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","related_material":{"record":[{"id":"10077","relation":"earlier_version","status":"public"}]},"language":[{"iso":"eng"}],"file_date_updated":"2024-06-02T22:30:03Z","volume":43,"day":"29","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"date_created":"2023-12-10T23:00:58Z","scopus_import":"1","isi":1,"pmid":1,"quality_controlled":"1","author":[{"full_name":"Nardin, Michele","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","last_name":"Nardin"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Savin, Cristina","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin"}],"page":"8140-8156","doi":"10.1523/JNEUROSCI.0194-23.2023","_id":"14656","project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"type":"journal_article","publication":"The Journal of Neuroscience","citation":{"apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156."},"acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","external_id":{"isi":["001148071000005"],"pmid":["37758476"]},"ddc":["570"],"intvolume":"        43","oa":1,"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"month":"11","article_type":"original","date_published":"2023-11-29T00:00:00Z","date_updated":"2025-09-09T13:37:51Z","publication_status":"published","publisher":"Society for Neuroscience","ec_funded":1,"year":"2023","status":"public","issue":"48","has_accepted_license":"1","publication_identifier":{"eissn":["1529-2401"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","file_name":"2023_JourNeuroscience_Nardin.pdf","date_created":"2023-12-11T11:30:37Z","embargo":"2024-06-01","file_id":"14674","creator":"dernst","access_level":"open_access","checksum":"e2503c8f84be1050e28f64320f1d5bd2","content_type":"application/pdf","file_size":2280632,"date_updated":"2024-06-02T22:30:03Z"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"article_processing_charge":"Yes (via OA deal)","article_number":"5644","department":[{"_id":"MiSi"}],"oa":1,"publisher":"Springer Nature","publication_status":"published","date_updated":"2026-06-29T22:30:19Z","date_published":"2023-09-13T00:00:00Z","article_type":"original","month":"09","has_accepted_license":"1","year":"2023","status":"public","oa_version":"Published Version","file":[{"file_id":"14365","relation":"main_file","date_created":"2023-09-25T08:22:58Z","file_name":"2023_NatureComm_Sitarska.pdf","date_updated":"2023-09-25T08:22:58Z","success":1,"checksum":"ad670e3b3c64fc585675948370f6b149","content_type":"application/pdf","access_level":"open_access","file_size":2725421,"creator":"dernst"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-24T22:01:10Z","abstract":[{"text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.","lang":"eng"}],"day":"13","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"14697","relation":"dissertation_contains","status":"public"}]},"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","volume":14,"file_date_updated":"2023-09-25T08:22:58Z","pmid":1,"scopus_import":"1","isi":1,"_id":"14360","doi":"10.1038/s41467-023-41173-1","quality_controlled":"1","author":[{"last_name":"Sitarska","full_name":"Sitarska, Ewa","first_name":"Ewa"},{"full_name":"Almeida, Silvia Dias","first_name":"Silvia Dias","last_name":"Almeida"},{"last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold","first_name":"Marianne Sandvold"},{"first_name":"Julian A","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp"},{"full_name":"Czuchnowski, Jakub","first_name":"Jakub","last_name":"Czuchnowski"},{"last_name":"Siggel","first_name":"Marc","full_name":"Siggel, Marc"},{"last_name":"Roessner","first_name":"Rita","full_name":"Roessner, Rita"},{"full_name":"Tschanz, Aline","first_name":"Aline","last_name":"Tschanz"},{"first_name":"Christer","full_name":"Ejsing, Christer","last_name":"Ejsing"},{"first_name":"Yannick","full_name":"Schwab, Yannick","last_name":"Schwab"},{"last_name":"Kosinski","full_name":"Kosinski, Jan","first_name":"Jan"},{"first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Kreshuk","first_name":"Anna","full_name":"Kreshuk, Anna"},{"full_name":"Erzberger, Anna","first_name":"Anna","last_name":"Erzberger"},{"first_name":"Alba","full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz"}],"ddc":["570"],"external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"citation":{"apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644."},"acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","intvolume":"        14","publication":"Nature Communications","type":"journal_article"},{"publisher":"Springer Nature","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"ec_funded":1,"date_updated":"2026-06-29T22:30:23Z","publication_status":"published","date_published":"2023-04-01T00:00:00Z","month":"04","article_type":"original","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"oa":1,"oa_version":"Published Version","file":[{"relation":"main_file","date_created":"2023-10-04T11:40:51Z","file_name":"2023_NatureNeuroscience_Gupta.pdf","file_id":"14395","success":1,"checksum":"a33d91e398e548f34003170e10988368","content_type":"application/pdf","file_size":6144866,"access_level":"open_access","creator":"dernst","date_updated":"2023-10-04T11:40:51Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","corr_author":"1","status":"public","year":"2023","pmid":1,"scopus_import":"1","isi":1,"date_created":"2023-01-23T14:14:19Z","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"}],"day":"01","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"12370"},{"id":"18574","relation":"dissertation_contains","status":"public"}]},"title":"Panoramic visual statistics shape retina-wide organization of receptive fields","volume":26,"file_date_updated":"2023-10-04T11:40:51Z","ddc":["570"],"external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"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).","citation":{"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.","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>.","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.","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>.","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>"},"intvolume":"        26","publication":"Nature Neuroscience","type":"journal_article","_id":"12349","doi":"10.1038/s41593-023-01280-0","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"full_name":"Gupta, Divyansh","first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","last_name":"Gupta"},{"last_name":"Mlynarski","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sumser","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L","full_name":"Sumser, Anton L"},{"orcid":"0000-0003-2012-9947","last_name":"Symonova","full_name":"Symonova, Olga","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","first_name":"Jan","full_name":"Svaton, Jan","last_name":"Svaton","orcid":"0000-0002-6198-2939"},{"orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"page":"606-614"},{"file":[{"file_id":"14068","relation":"main_file","file_name":"2023_EvLetters_Mrnjavac.pdf","date_created":"2023-08-16T11:43:33Z","date_updated":"2023-08-16T11:43:33Z","success":1,"creator":"dernst","file_size":2592189,"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2056-3744"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","has_accepted_license":"1","year":"2023","issue":"1","status":"public","publisher":"Oxford University Press","ec_funded":1,"date_published":"2023-02-01T00:00:00Z","month":"02","article_type":"original","date_updated":"2026-06-29T22:30:24Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","article_number":"qrac004","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"oa":1,"citation":{"ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>."},"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).","ddc":["570"],"external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"intvolume":"         7","type":"journal_article","publication":"Evolution Letters","doi":"10.1093/evlett/qrac004","_id":"12521","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"}],"quality_controlled":"1","author":[{"last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea","first_name":"Andrea"},{"orcid":"0000-0002-6246-1465","last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"pmid":1,"scopus_import":"1","isi":1,"day":"01","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"}],"date_created":"2023-02-06T13:59:12Z","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"18531","status":"public"}]},"file_date_updated":"2023-08-16T11:43:33Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"volume":7},{"type":"research_data","ddc":["571"],"citation":{"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.","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>.","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>.","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>.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023)."},"author":[{"last_name":"Gupta","orcid":"0000-0001-7400-6665","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","first_name":"Divyansh","full_name":"Gupta, Divyansh"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","full_name":"Sumser, Anton L","first_name":"Anton L","last_name":"Sumser","orcid":"0000-0002-4792-1881"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","last_name":"Jösch"}],"project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"},{"name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"_id":"12370","doi":"10.15479/AT:ISTA:12370","file_date_updated":"2023-01-26T10:51:34Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12349"},{"relation":"used_in_publication","id":"18574","status":"public"}]},"title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields","date_created":"2023-01-25T12:45:18Z","day":"26","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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F"},{"first_name":"Jan","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","last_name":"Svaton","contributor_type":"researcher"}],"date_updated":"2026-06-29T22:30:24Z","month":"01","date_published":"2023-01-26T00:00:00Z","ec_funded":1,"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"oa":1,"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"article_processing_charge":"No"},{"scopus_import":"1","isi":1,"pmid":1,"related_material":{"record":[{"id":"18871","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","DOAJ_listed":"1","volume":14,"file_date_updated":"2023-07-10T10:10:54Z","date_created":"2023-07-09T22:01:11Z","day":"24","abstract":[{"lang":"eng","text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks."}],"type":"journal_article","publication":"Nature Communications","ddc":["000"],"external_id":{"isi":["001018100800002"],"arxiv":["2210.12443"],"pmid":["37355691"]},"citation":{"apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., &#38; Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>, vol. 14, 3784, Nature Research, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>.","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” <i>Nature Communications</i>, vol. 14. Nature Research, 2023.","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>. Nature Research, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784."},"acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","intvolume":"        14","arxiv":1,"quality_controlled":"1","author":[{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu","first_name":"Liu","last_name":"Qiu","orcid":"0000-0003-4345-4267"},{"full_name":"Sahu, Rishabh","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","last_name":"Sahu"},{"last_name":"Hease","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J","first_name":"William J"},{"full_name":"Arnold, Georg M","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","last_name":"Arnold"},{"first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"_id":"13200","doi":"10.1038/s41467-023-39493-3","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"date_updated":"2026-06-29T22:30:26Z","publication_status":"published","APC_amount":"6228 EUR","article_type":"original","month":"06","date_published":"2023-06-24T00:00:00Z","publisher":"Nature Research","ec_funded":1,"oa":1,"article_processing_charge":"Yes","department":[{"_id":"JoFi"}],"article_number":"3784","publication_identifier":{"eissn":["2041-1723"]},"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"13206","relation":"main_file","date_created":"2023-07-10T10:10:54Z","file_name":"2023_NatureComms_Qiu.pdf","date_updated":"2023-07-10T10:10:54Z","success":1,"access_level":"open_access","file_size":1349134,"checksum":"ec7ccd2c08f90d59cab302fd0d7776a4","content_type":"application/pdf","creator":"alisjak"}],"OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"year":"2023","status":"public","corr_author":"1","has_accepted_license":"1"},{"article_processing_charge":"No","department":[{"_id":"JoFi"}],"oa":1,"ec_funded":1,"month":"10","date_published":"2023-10-25T00:00:00Z","date_updated":"2026-06-29T22:30:26Z","publication_status":"draft","corr_author":"1","status":"public","year":"2023","oa_version":"Preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The rapid development of superconducting quantum hardware is expected to run into significant I/O restrictions due to the need for large-scale error correction in a cryogenic environment. Classical data centers rely on fiber-optic interconnects to remove similar networking bottlenecks and to allow for reconfigurable, software-defined infrastructures. In the same spirit, ultra-cold electro-optic links have been proposed and used to generate qubit control signals, or to replace cryogenic readout electronics. So far, the latter suffered from either low efficiency, low bandwidth and the need for additional microwave drives, or breaking of Cooper pairs and qubit states. In this work we realize electro-optic microwave photonics at millikelvin temperatures to implement a radio-over-fiber qubit readout that does not require any active or passive cryogenic microwave equipment. We demonstrate all-optical single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free readout scheme. Importantly, we do not observe any direct radiation impact on the qubit state as verified with high-fidelity quantum-non-demolition measurements despite the absence of shielding elements. This compatibility between superconducting circuits and telecom wavelength light is not only a prerequisite to establish modular quantum networks, it is also relevant for multiplexed readout of superconducting photon detectors and classical superconducting logic. Moreover, this experiment showcases the potential of electro-optic radiometry in harsh environments - an electronics-free sensing principle that extends into the THz regime with applications in radio astronomy, planetary missions and earth observation.","lang":"eng"}],"day":"25","date_created":"2025-01-29T11:11:34Z","title":"All-optical single-shot readout of a superconducting qubit","related_material":{"record":[{"status":"public","relation":"later_version","id":"19073"},{"status":"public","id":"18871","relation":"dissertation_contains"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.16817"}],"language":[{"iso":"eng"}],"doi":"10.48550/ARXIV.2310.16817","_id":"18953","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053"},{"_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a","grant_number":"101089099","name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"author":[{"last_name":"Arnold","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","full_name":"Arnold, Georg M"},{"orcid":"0009-0001-2346-5236","last_name":"Werner","full_name":"Werner, Thomas","first_name":"Thomas","id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7"},{"last_name":"Sahu","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","full_name":"Sahu, Rishabh"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","full_name":"Kapoor, Lucky","first_name":"Lucky","last_name":"Kapoor","orcid":"0000-0001-8319-2148"},{"orcid":"0000-0003-4345-4267","last_name":"Qiu","first_name":"Liu","full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"citation":{"mla":"Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","ieee":"G. M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, and J. M. Fink, “All-optical single-shot readout of a superconducting qubit,” <i>arXiv</i>. .","apa":"Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., &#38; Fink, J. M. (n.d.). All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>","ama":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>","ista":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">10.48550/ARXIV.2310.16817</a>.","chicago":"Arnold, Georg M, Thomas Werner, Rishabh Sahu, Lucky Kapoor, Liu Qiu, and Johannes M Fink. “All-Optical Single-Shot Readout of a Superconducting Qubit.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2310.16817\">https://doi.org/10.48550/ARXIV.2310.16817</a>.","short":"G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.)."},"acknowledgement":"We thank F. Hassani and M. Zemlicka for assistance\r\nwith qubit design and high power readout respectively,\r\nand P. Winkel and I. Pop at KIT for providing the JPA.\r\nThis work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG\r\nQUNNECT) and no. 101089099 (ERC CoG cQEO), the\r\nEuropean Union’s Horizon 2020 research and innovation\r\nprogram under grant agreement no. 899354 (FETopen\r\nSuperQuLAN) and the Austrian Science Fund (FWF)\r\nthrough BeyondC (grant no. F7105). L.Q. acknowledges\r\ngenerous support from the ISTFELLOW programme\r\nand G.A. is the recipient of a DOC fellowship of the\r\nAustrian Academy of Sciences at IST Austria.","external_id":{"arxiv":["2310.16817"]},"arxiv":1,"type":"preprint","publication":"arXiv"},{"has_accepted_license":"1","corr_author":"1","issue":"12","status":"public","year":"2023","oa_version":"Published Version","file":[{"file_id":"14727","date_created":"2024-01-02T11:39:38Z","file_name":"2023_MolecularBioEvo_Lasne.pdf","relation":"main_file","date_updated":"2024-01-02T11:39:38Z","file_size":8623505,"checksum":"47c1c72fb499f26ea52d216b242208c8","access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","department":[{"_id":"BeVi"}],"article_number":"msad245","oa":1,"publisher":"Oxford University Press","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","date_updated":"2026-06-29T22:30:29Z","article_type":"original","month":"12","date_published":"2023-12-01T00:00:00Z","_id":"14613","doi":"10.1093/molbev/msad245","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-1197-8616","last_name":"Lasne","first_name":"Clementine","full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237"},{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297","last_name":"Layana Franco"},{"full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001122489000003"],"pmid":["37988296"]},"ddc":["570"],"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).","citation":{"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>","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>.","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.","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>.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","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."},"intvolume":"        40","type":"journal_article","publication":"Molecular Biology and Evolution","date_created":"2023-11-27T16:14:37Z","day":"01","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"14614","relation":"research_data","status":"public"},{"id":"19386","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","description":"News on ISTA webpage","url":"https://ista.ac.at/en/news/on-the-hunt/"}]},"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","volume":40,"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"file_date_updated":"2024-01-02T11:39:38Z","pmid":1,"scopus_import":"1","isi":1},{"publication_identifier":{"eissn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-06-06T07:31:20Z","file_size":1654389,"checksum":"a857df40f0882859c48a1ff1e2001ec2","content_type":"application/pdf","access_level":"open_access","creator":"dernst","success":1,"file_id":"13123","date_created":"2023-06-06T07:31:20Z","file_name":"2023_NaturePhysics_Redchenko.pdf","relation":"main_file"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","year":"2023","corr_author":"1","has_accepted_license":"1","date_published":"2023-05-24T00:00:00Z","article_type":"original","month":"05","publication_status":"published","date_updated":"2026-06-29T22:30:31Z","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"ec_funded":1,"oa":1,"article_processing_charge":"No","article_number":"2998","department":[{"_id":"JoFi"}],"publication":"Nature Communications","type":"journal_article","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.","citation":{"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>","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.","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>.","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>.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","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."},"external_id":{"arxiv":["2205.03293"],"pmid":["37225689"],"isi":["001001099700002"]},"ddc":["530"],"arxiv":1,"intvolume":"        14","quality_controlled":"1","author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko"},{"full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V.","last_name":"Poshakinskiy"},{"id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","first_name":"Riya","last_name":"Sett","orcid":"0000-0001-7641-8348"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka","orcid":"0009-0005-0878-3032"},{"full_name":"Poddubny, Alexander N.","first_name":"Alexander N.","last_name":"Poddubny"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"doi":"10.1038/s41467-023-38761-6","_id":"13117","project":[{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"scopus_import":"1","isi":1,"pmid":1,"title":"Tunable directional photon scattering from a pair of superconducting qubits","related_material":{"record":[{"id":"13124","relation":"research_data","status":"public"},{"id":"19533","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"file_date_updated":"2023-06-06T07:31:20Z","volume":14,"day":"24","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."}],"date_created":"2023-06-04T22:01:02Z"},{"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"related_material":{"record":[{"relation":"research_data","id":"14279","status":"public"},{"id":"14697","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19745"}]},"volume":8,"keyword":["General Medicine","Immunology"],"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"day":"01","date_created":"2023-09-06T08:07:51Z","scopus_import":"1","isi":1,"pmid":1,"quality_controlled":"1","author":[{"first_name":"Jonna H","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","last_name":"Alanko"},{"full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","last_name":"Ucar"},{"last_name":"Canigova","orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","full_name":"Canigova, Nikola"},{"last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan"},{"first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"}],"doi":"10.1126/sciimmunol.adc9584","_id":"14274","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020"},{"grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"Science Immunology","type":"journal_article","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","citation":{"ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584."},"ddc":["570"],"external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"intvolume":"         8","oa":1,"article_processing_charge":"No","article_number":"adc9584","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"month":"09","article_type":"original","date_published":"2023-09-01T00:00:00Z","publication_status":"published","date_updated":"2026-06-29T22:30:30Z","publisher":"American Association for the Advancement of Science","ec_funded":1,"status":"public","issue":"87","year":"2023","corr_author":"1","publication_identifier":{"issn":["2470-9468"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"}]