[{"month":"02","ec_funded":1,"project":[{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"}],"issue":"6","date_updated":"2026-10-18T22:31:17Z","publication_status":"published","status":"public","OA_place":"publisher","date_created":"2025-03-02T23:01:52Z","OA_type":"hybrid","external_id":{"arxiv":["2310.04200"],"isi":["001454696700003"],"pmid":["40021171"]},"quality_controlled":"1","intvolume":"       134","doi":"10.1103/PhysRevLett.134.063601","author":[{"full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zens, M.","first_name":"M.","last_name":"Zens"},{"full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","last_name":"Zemlicka"},{"last_name":"Peruzzo","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"full_name":"Sett, Riya","first_name":"Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7641-8348"},{"full_name":"Zielinski, Przemyslaw D","first_name":"Przemyslaw D","id":"e198fcc4-f6e0-11ea-865d-b6a256760ee8","last_name":"Zielinski"},{"first_name":"H. S.","full_name":"Dhar, H. S.","last_name":"Dhar"},{"last_name":"Krimer","full_name":"Krimer, D. O.","first_name":"D. O."},{"last_name":"Rotter","full_name":"Rotter, S.","first_name":"S."},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"citation":{"ista":"Redchenko E, Zens M, Zemlicka M, Peruzzo M, Hassani F, Sett R, Zielinski PD, Dhar HS, Krimer DO, Rotter S, Fink JM. 2025. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 134(6), 063601.","short":"E. Redchenko, M. Zens, M. Zemlicka, M. Peruzzo, F. Hassani, R. Sett, P.D. Zielinski, H.S. Dhar, D.O. Krimer, S. Rotter, J.M. Fink, Physical Review Letters 134 (2025).","apa":"Redchenko, E., Zens, M., Zemlicka, M., Peruzzo, M., Hassani, F., Sett, R., … Fink, J. M. (2025). Observation of collapse and revival in a superconducting atomic frequency comb. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">https://doi.org/10.1103/PhysRevLett.134.063601</a>","ama":"Redchenko E, Zens M, Zemlicka M, et al. Observation of collapse and revival in a superconducting atomic frequency comb. <i>Physical Review Letters</i>. 2025;134(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">10.1103/PhysRevLett.134.063601</a>","ieee":"E. Redchenko <i>et al.</i>, “Observation of collapse and revival in a superconducting atomic frequency comb,” <i>Physical Review Letters</i>, vol. 134, no. 6. American Physical Society, 2025.","chicago":"Redchenko, Elena, M. Zens, Martin Zemlicka, Matilda Peruzzo, Farid Hassani, Riya Sett, Przemyslaw D Zielinski, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">https://doi.org/10.1103/PhysRevLett.134.063601</a>.","mla":"Redchenko, Elena, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” <i>Physical Review Letters</i>, vol. 134, no. 6, 063601, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">10.1103/PhysRevLett.134.063601</a>."},"ddc":["530"],"file_date_updated":"2025-03-04T10:40:50Z","department":[{"_id":"JoFi"}],"article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics."}],"has_accepted_license":"1","publisher":"American Physical Society","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19533"}]},"fulldoi":"https://doi.org/10.1103/PhysRevLett.134.063601","date_published":"2025-02-14T00:00:00Z","oa":1,"isi":1,"title":"Observation of collapse and revival in a superconducting atomic frequency comb","article_number":"063601","day":"14","publication":"Physical Review Letters","volume":134,"type":"journal_article","file":[{"success":1,"date_created":"2025-03-04T10:40:50Z","relation":"main_file","file_name":"2025_PhysReviewLetters_Redchenko.pdf","file_id":"19291","date_updated":"2025-03-04T10:40:50Z","content_type":"application/pdf","access_level":"open_access","checksum":"633d6c5ddd9b805da22c5839d3d48df6","creator":"dernst","file_size":2080408}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"acknowledgement":"The authors thank G. Arnold and R. Sahu for the discussions, L. Drmic for software development, the MIBA workshop and the ISTA nanofabrication facility for technical support, and VTT Technical Research Centre of Finland for providing us TWPAs for follow-up measurements. This work was supported by the Austrian Science Fund (FWF) [Grant DOI: 10.55776/F71] through BeyondC (F7105) and IST Austria. E. S. R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J. M. F. and M. Ž. acknowledge support from the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant.","pmid":1,"oa_version":"Published Version","_id":"19280","arxiv":1,"year":"2025","article_type":"original"},{"supervisor":[{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"keyword":["Pten","mtor","cortical development","MADM","Mapk"],"_id":"20212","oa_version":"Published Version","year":"2025","acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"type":"dissertation","file":[{"relation":"source_file","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx","file_id":"20230","date_updated":"2026-08-26T22:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"3331f76bbef74ff4908e2d2c9262045c","access_level":"closed","creator":"omiranda","file_size":32887334,"embargo_to":"open_access","date_created":"2025-08-26T09:03:50Z"},{"creator":"omiranda","file_size":28636240,"embargo":"2026-08-26","content_type":"application/pdf","checksum":"02509d50cff8e35c5bcbf71e8d658176","access_level":"open_access","file_id":"20231","date_updated":"2026-08-26T22:30:02Z","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","relation":"main_file","date_created":"2025-08-26T09:05:55Z"}],"alternative_title":["ISTA Thesis"],"day":"22","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM","degree_awarded":"PhD","oa":1,"fulldoi":"https://doi.org/10.15479/AT-ISTA-20212","date_published":"2025-08-22T00:00:00Z","page":"119","corr_author":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"17425","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-063-3"]},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","article_processing_charge":"No","abstract":[{"text":"Cortical development has been studied for many decades and with each passing year, we learn \r\nmore about the processes that govern the tightly regulated developmental program. Up until \r\nrecently, the field has struggled to gain reliable access to progenitors at the single-cell level, \r\nlimiting the resolution at which we can study cortical development in vivo. Therefore, much of \r\nthe data we have on mammalian cortical development is at the cell population level. The \r\nsubsequent pages of this thesis describe novel elements of cortical development in mice; \r\nacquired using a candidate gene approach in conjunction with Mosaic Analysis with Double \r\nMarkers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview \r\nof the state of the field, describe the methodology used to quantify morphological \r\ncharacteristics of neurons and glia, and delve into the role of Phosphatase and tensin \r\nhomologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse \r\ncortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells \r\nare mutated, to study population-level changes, we can bypass the early postnatal lethality \r\nreported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to \r\ninduce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor \r\nlevel. Pten-mutant neuron populations within the mosaics were significantly expanded. In the \r\nlatter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance \r\nof astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate \r\nPten mosaics within a series of distinct knockout tissues to test for the interactions between \r\nPten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey \r\nof Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical \r\neffectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results \r\ndemonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage \r\nprogression. ","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"file_date_updated":"2026-08-26T22:30:02Z","ddc":["570"],"citation":{"mla":"Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>.","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>","apa":"Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage progression using MADM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025.","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria.","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025."},"author":[{"last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo","first_name":"Osvaldo"}],"doi":"10.15479/AT-ISTA-20212","doi_confirm":"1","date_created":"2025-08-22T14:07:00Z","OA_place":"publisher","status":"public","publication_status":"published","date_updated":"2026-10-02T12:16:56Z","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253"}],"month":"08"},{"alternative_title":["ISTA Thesis"],"day":"04","title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","page":"108","corr_author":"1","related_material":{"record":[{"status":"public","id":"18063","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","oa":1,"date_published":"2025-08-04T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20117","year":"2025","oa_version":"Published Version","_id":"20117","supervisor":[{"first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","file":[{"date_created":"2025-08-22T08:22:10Z","file_name":"2025_Wang_Yiqun_Thesis.docx","relation":"source_file","file_id":"20209","date_updated":"2026-09-03T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"36b87c17d12c7bf5955d6d812acb8d77","creator":"yiqwang","embargo_to":"open_access","file_size":25798848},{"checksum":"8d7a2383f66377da675d379ec30ea0fe","access_level":"open_access","content_type":"application/pdf","embargo":"2026-09-03","file_size":12628313,"creator":"yiqwang","file_name":"2025_Wang_Yiqun_Thesis.pdf","relation":"main_file","date_updated":"2026-09-03T22:30:03Z","file_id":"20211","date_created":"2025-08-22T10:32:30Z"}],"acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"date_created":"2025-08-04T15:24:21Z","OA_place":"publisher","status":"public","doi_confirm":"1","month":"08","publication_status":"published","date_updated":"2026-10-02T12:33:36Z","abstract":[{"text":"Auxin is essential for many aspects of plant growth and development, from \r\nembryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and \r\ngradients, which are important for regulating various plant development process, including \r\nembryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is \r\nmediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The \r\nregulation of PIN proteins is a key convergence of crosstalk between auxin and other \r\nhormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis \r\nroots, preferentially the dephosphorylated PIN1, and the process is independent of \r\ntranscription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization \r\nof PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis \r\n(Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 \r\ndegradation through regulating the phosphorylation of PIN1 or trafficking components is \r\nunknown. Here, we demonstrate that dynamin related protein DRP2s are required for the \r\ncytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite \r\nthe reported redundancy of DRP2A and DRP2B in gametophyte development, we found that \r\nCK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a \r\nor drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of \r\nDRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma \r\nmembrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin \r\nreceptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly \r\ncycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we \r\ninvestigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in \r\ncytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN \r\ntrafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of \r\nendocytosis accessory protein DRP2A. ","lang":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2026-09-03T22:30:03Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","author":[{"id":"82F537F2-B517-11E9-84D7-6433E6697425","last_name":"Wang","full_name":"Wang, Yiqun","first_name":"Yiqun"}],"doi":"10.15479/AT-ISTA-20117","citation":{"ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>."},"ddc":["580"]},{"PlanS_conform":"1","acknowledgement":"We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"type":"journal_article","file":[{"date_updated":"2025-09-01T14:09:31Z","file_id":"20264","file_name":"2025_PlantJournal_Babic.pdf","relation":"main_file","file_size":5791111,"creator":"dernst","access_level":"open_access","checksum":"1cdc3341d2d23101abca72521f1f23cb","content_type":"application/pdf","success":1,"date_created":"2025-09-01T14:09:31Z"}],"volume":123,"article_type":"original","oa_version":"Published Version","_id":"20187","year":"2025","oa":1,"isi":1,"fulldoi":"https://doi.org/10.1111/tpj.70396","date_published":"2025-08-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20362"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"scopus_import":"1","publication":"Plant Journal","day":"01","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","article_number":"e70396","citation":{"short":"D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025).","ista":"Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396.","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>.","ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","apa":"Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>","ama":"Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>","chicago":"Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>."},"ddc":["580"],"author":[{"last_name":"Babic","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","full_name":"Babic, David","first_name":"David"},{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed"},{"first_name":"Lukas","full_name":"Fiedler, Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","first_name":"Linlin","full_name":"Qi, Linlin"},{"last_name":"Tellier","full_name":"Tellier, Frédérique","first_name":"Frédérique"},{"id":"cced8a85-223e-11ed-af04-b0596c55053b","last_name":"Smoljan","first_name":"Adrijana","full_name":"Smoljan, Adrijana"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","last_name":"Rakusova","full_name":"Rakusova, Hana","first_name":"Hana"},{"last_name":"Valošek","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr","first_name":"Petr"},{"first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"last_name":"Faure","full_name":"Faure, Jean Denis","first_name":"Jean Denis"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"intvolume":"       123","doi":"10.1111/tpj.70396","has_accepted_license":"1","publisher":"Wiley","abstract":[{"lang":"eng","text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development."}],"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-09-01T14:09:31Z","department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"publication_status":"published","issue":"3","date_updated":"2026-10-18T22:31:20Z","project":[{"grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"}],"month":"08","quality_controlled":"1","external_id":{"isi":["001547884300001"],"pmid":["40782342"]},"date_created":"2025-08-17T22:01:36Z","OA_type":"hybrid","status":"public","OA_place":"publisher"},{"file":[{"checksum":"5ecf274281a54a41e0288bc79edf7492","access_level":"open_access","content_type":"application/pdf","embargo":"2026-09-25","file_size":7501548,"creator":"dbabic","relation":"main_file","file_name":"2025_David_Babic_Thesis.pdf","date_updated":"2026-09-25T22:30:02Z","file_id":"20388","date_created":"2025-09-24T13:43:14Z"},{"date_created":"2025-09-24T13:43:14Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"2703e548390de0a1af7a707137e8ab3b","creator":"dbabic","embargo_to":"open_access","file_size":23206052,"relation":"source_file","file_name":"Thesis_Babic_draft.docx","file_id":"20389","date_updated":"2026-09-25T22:30:02Z"}],"type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"_id":"20362","oa_version":"Published Version","year":"2025","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20187"}]},"corr_author":"1","page":"116","fulldoi":"https://doi.org/10.15479/AT-ISTA-20362","date_published":"2025-09-18T00:00:00Z","oa":1,"degree_awarded":"PhD","title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","alternative_title":["ISTA Thesis"],"day":"18","doi":"10.15479/AT-ISTA-20362","author":[{"first_name":"David","full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","last_name":"Babic"}],"ddc":["580"],"citation":{"short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>","apa":"Babic, D. (2025). <i>Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>.","mla":"Babic, David. <i>Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>."},"file_date_updated":"2026-09-25T22:30:02Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"abstract":[{"lang":"eng","text":"Arabidopsis embryo has long served as a model system for understanding how plant body \r\npatterning and axis establishment arise. Previous work established that auxin flows, directed \r\nby polar transport and reinforced by local biosynthesis, underpin axes formation, while recent \r\nstudies suggest that maternal tissue, membrane composition and surface receptor signaling add \r\nfurther regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which \r\nguide plant embryonic and post-embryonic development. We review methodological advances \r\nthat allow the embryo to be imaged and studied. These tools offer exciting venues for future \r\naddressing of outstanding research questions. Furthermore, we dissect the contribution of \r\nmaternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments \r\nlowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens \r\nthe initial apical maximum. The resulting deficit dampens downstream embryonic auxin \r\nbiosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided \r\nauxin controls auxin flows in the embryos on a larger scale than previously understood. \r\nIntriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases \r\nTMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be \r\npreferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK \r\nactivity arrests embryos, affects seedling development and persists into adult growth, \r\nsuggesting that maternal effect could shape development beyond fertilization and early \r\nembryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane \r\ncomposition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid \r\nmetabolism triggers widespread patterning errors. \r\nTogether, these results reposition early plant patterning as a hierarchical cascade that begins \r\nwith maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated \r\nby maternal receptor signaling and could ultimately be gated by the biophysical properties of \r\nthe membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking \r\ninto a single narrative, this thesis helps shifting the approach of viewing the embryo as an \r\nautonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal \r\ncontext."}],"article_processing_charge":"No","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","month":"09","date_updated":"2026-10-16T07:59:32Z","publication_status":"published","OA_place":"publisher","status":"public","date_created":"2025-09-17T13:28:01Z","doi_confirm":"1"},{"acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","language":[{"iso":"eng"}],"type":"preprint","year":"2025","oa_version":"Preprint","_id":"21427","oa":1,"date_published":"2025-09-25T00:00:00Z","fulldoi":"https://doi.org/10.1101/2025.05.20.655037","corr_author":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"21439"},{"relation":"later_version","id":"22963","status":"public"},{"id":"21423","relation":"dissertation_contains","status":"public"}]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"bioRxiv","day":"25","title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","citation":{"ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. ."},"ddc":["539","570"],"author":[{"first_name":"Zuzana","full_name":"Dunajova, Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan"},{"id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","last_name":"Majek","first_name":"Juraj","full_name":"Majek, Juraj"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"last_name":"Sahai","full_name":"Sahai, Erik","first_name":"Erik"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1101/2025.05.20.655037","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo."}],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.20.655037","open_access":"1"}],"department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"publication_status":"draft","date_updated":"2026-10-18T22:31:19Z","project":[{"name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"},{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"month":"09","das_tickbox":"1","date_created":"2026-03-11T08:40:06Z","OA_place":"repository","status":"public"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","article_processing_charge":"No","abstract":[{"text":"During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a key role in \r\npatterning the tissues of the extending body. This requires precise coordination between the \r\nsize of the source of Shh production and the embryo body. Shh is produced by the notochord, \r\nas well as floorplate of the neural tube. In this thesis, we investigated how the sizes of the \r\nnotochord and floorplate are regulated and how they impact the developing mouse embryo.  \r\nTo measure the size and shape of the developing mouse notochord and the cell behaviours \r\nwithin this organ, we performed high-resolution measurements in cleared embryos between \r\nE8.5 and E10.5 of development. Strikingly, our data revealed that the notochord maintains a \r\nconstant cross-sectional area throughout the trunk over time as it lengthens by cell \r\nproliferation. We show that this is achieved by a feedback between the notochord cell \r\nproliferation rate and both the cross-sectional area of the trunk notochord and elongation of \r\nthe embryo. Using live imaging, we further show that notochord cells undergo posteriorly\r\ndirected active cell migration and that this cell migration contributes to maintaining the \r\nstructural integrity of the notochord. Our results show a complex coordination of cell \r\nbehaviours that allow for robust notochord morphogenesis during mouse development and \r\nthe maintenance of a defined Shh source size.  \r\nShh produced by the notochord induces a secondary Shh-producing domain, the floor plate. \r\nHow the notochord and floor plate contribute to the formation of the Shh gradient in the \r\nneural tube and to the regulation of the floor plate size is poorly understood. Our theoretical \r\nand experimental analysis indicates that only the initial levels of notochord-derived Shh \r\ninfluence the size of the floor plate, and the floor plate is insensitive to its own production of \r\nShh. After its initial establishment, the floor plate expands by tissue growth, leading to scaling \r\nof the Shh gradient amplitude with tissue size.   \r\nAltogether, we show that the mechanisms regulating the sizes of the notochord and \r\nfloorplate in mouse development help to achieve size robustness of these tissues. Our data \r\ndemonstrate that the initial establishment of the Shh gradient in the neural tube is strongly \r\ndependent on the notochord and suggest that the robustness of notochord morphogenesis \r\nis essential for pattern formation. Later in development, the floor plate size and the Shh \r\ngradient are coupled to neural tube growth. Our findings provide new insights on how pattern \r\nformation, tissue growth and morphogenesis interact to ensure reproducible developmental \r\noutcomes. ","lang":"eng"}],"file_date_updated":"2026-09-30T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"citation":{"short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria.","mla":"Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>.","chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>.","apa":"Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025.","ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>"},"ddc":["570"],"author":[{"first_name":"Kasumi","full_name":"Kishi, Kasumi","last_name":"Kishi","orcid":"0000-0001-6060-4795","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT-ISTA-20393","doi_confirm":"1","date_created":"2025-09-25T10:08:10Z","OA_place":"publisher","status":"public","publication_status":"published","date_updated":"2026-10-16T08:31:16Z","month":"09","supervisor":[{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"}],"year":"2025","oa_version":"Published Version","_id":"20393","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"type":"dissertation","file":[{"creator":"kkishi","embargo_to":"open_access","file_size":41847994,"content_type":"application/x-zip-compressed","access_level":"closed","checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","file_id":"20413","date_updated":"2026-09-30T22:30:04Z","relation":"source_file","file_name":"2025-Kishi-Kasumi-Thesis.zip","date_created":"2025-09-30T14:33:17Z"},{"file_size":55747072,"creator":"kkishi","access_level":"open_access","checksum":"88349b9177e1dcbe1242cd3884b36fdb","content_type":"application/pdf","embargo":"2026-09-30","date_updated":"2026-09-30T22:30:04Z","file_id":"20414","file_name":"2025-Kishi-Kasumi-Thesis.pdf","relation":"main_file","date_created":"2025-09-30T14:33:22Z"}],"alternative_title":["ISTA Thesis"],"day":"24","title":"Regulation of notochord and floor plate size during mouse development","degree_awarded":"PhD","oa":1,"date_published":"2025-09-24T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20393","corr_author":"1","page":"102","related_material":{"record":[{"id":"18481","relation":"part_of_dissertation","status":"public"}]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]}},{"doi_confirm":"1","OA_place":"publisher","status":"public","date_created":"2025-09-19T12:23:38Z","date_updated":"2026-10-16T08:24:09Z","publication_status":"published","month":"09","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-09-30T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"article_processing_charge":"No","abstract":[{"text":"Auxin is a central regulator of plant growth and development, orchestrating processes from \r\nembryogenesis to senescence through a complex network of biosynthesis, transport, and \r\nsignaling pathways.  \r\nIn Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB \r\nreceptors, which promote degradation of AUX/IAA repressors to enable ARF transcription \r\nfactors-driven transcriptional reprogramming. Parallel to this well-established nuclear \r\nmechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell \r\nsurface, most notably through ABP1 and TMKs. Despite decades of research, the integration \r\nof these pathways and their links to fundamental cellular processes remains not fully \r\nunderstood.  \r\nIn this study, we uncover a new role for TIR1/AFB signaling in rapidly activating \r\nmacroautophagy during developmental reprogramming. Auxin induces autophagy via \r\nTIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and \r\ntranscriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit \r\ndelayed meristem differentiation, impaired lateral root progression, and reduced shoot \r\norganogenesis, demonstrating its necessity for timely developmental transitions. \r\nWe also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing \r\nbiochemical and mass photometry evidence for auxin-dependent complex formation. We show \r\nthat ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 \r\nproteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. \r\nThis pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent \r\nROP activation. \r\nThese findings establish an integrated framework in which nuclear TIR1/AFB signaling and \r\ncell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic \r\nremodelling, and transporter regulation, thereby ensuring robust developmental plasticity in \r\nArabidopsis thaliana. ","lang":"eng"}],"citation":{"short":"C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025.","ista":"Giannini C. 2025. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria.","mla":"Giannini, Caterina. <i>Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>.","chicago":"Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>.","ama":"Giannini C. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20364\">10.15479/AT-ISTA-20364</a>","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025.","apa":"Giannini, C. (2025). <i>Nuclear and cell surface auxin signaling in A. thaliana developmental transitions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20364\">https://doi.org/10.15479/AT-ISTA-20364</a>"},"ddc":["580"],"doi":"10.15479/AT-ISTA-20364","author":[{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","first_name":"Caterina","full_name":"Giannini, Caterina"}],"title":"Nuclear and cell surface auxin signaling in A. thaliana developmental transitions","day":"19","alternative_title":["ISTA Thesis"],"date_published":"2025-09-19T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20364","oa":1,"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","corr_author":"1","page":"151","related_material":{"record":[{"status":"public","id":"12291","relation":"part_of_dissertation"},{"id":"19399","relation":"part_of_dissertation","status":"public"}]},"keyword":["Auxin Signaling","Plant Development"],"supervisor":[{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2025","oa_version":"Published Version","_id":"20364","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"acknowledgement":"Plant Facility,\r\nProtein Service Facility","type":"dissertation","file":[{"date_created":"2025-09-24T14:46:34Z","file_name":"2025_Giannini_Caterina_Thesis...pdf","relation":"main_file","date_updated":"2026-09-30T22:30:03Z","file_id":"20390","checksum":"536ba1701453b0b2346be14c046b2911","access_level":"open_access","embargo":"2026-09-30","content_type":"application/pdf","file_size":14278965,"creator":"cgiannin"},{"date_created":"2025-09-24T14:46:35Z","file_size":24499022,"embargo_to":"open_access","creator":"cgiannin","checksum":"192f55262f2da2ea0a59d9c23a1b8573","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-09-30T22:30:03Z","file_id":"20391","file_name":"2025_Giannini_Caterina_Thesis...docx","relation":"source_file"}]},{"year":"2025","oa_version":"Published Version","_id":"19399","type":"preprint","acknowledgement":"We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova for help with manuscript preparation; J. Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at ISTA for their excellent service and assistance. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant 32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural Science Foundation of China (32321001).","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"day":"20","title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","publication":"bioRxiv","related_material":{"record":[{"status":"public","relation":"later_version","id":"20656"},{"relation":"dissertation_contains","id":"19395","status":"public"},{"status":"public","relation":"dissertation_contains","id":"20364"}]},"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_published":"2025-02-20T00:00:00Z","fulldoi":"https://doi.org/10.1101/2022.11.30.518503","article_processing_charge":"No","abstract":[{"text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.11.30.518503"}],"department":[{"_id":"JiFr"},{"_id":"XiFe"}],"author":[{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia"},{"first_name":"Lukas","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","full_name":"Zou, Minxia","first_name":"Minxia"},{"last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","full_name":"Giannini, Caterina"},{"full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer"},{"full_name":"Vladimirtsev, Dmitrii","first_name":"Dmitrii","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","last_name":"Vladimirtsev"},{"last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","full_name":"Randuch, Marek"},{"first_name":"Yongfan","full_name":"Yu, Yongfan","last_name":"Yu"},{"last_name":"Gelová","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","full_name":"Gelová, Zuzana"},{"first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"first_name":"Jakub","full_name":"Hajny, Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Meng","first_name":"Meng"},{"full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"first_name":"Lukas","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lanxin","full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marques-Bueno, Maria Mar","first_name":"Maria Mar","last_name":"Marques-Bueno"},{"first_name":"Zainab","full_name":"Quddoos, Zainab","id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","last_name":"Quddoos"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","full_name":"Molnar, Gergely","first_name":"Gergely"},{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich","first_name":"Ivan","full_name":"Kulich, Ivan"},{"first_name":"Yvon","full_name":"Jaillais, Yvon","last_name":"Jaillais"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1101/2022.11.30.518503","citation":{"ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv, <a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais, J. Friml, BioRxiv (n.d.).","mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>.","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” <i>bioRxiv</i>. ."},"ddc":["580"],"OA_type":"green","das_tickbox":"1","date_created":"2025-03-13T08:36:48Z","status":"public","OA_place":"repository","project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"name":"Cell surface receptor complexes for auxin signaling in plants","grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425"}],"month":"02","ec_funded":1,"publication_status":"draft","date_updated":"2026-10-18T22:31:21Z"},{"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file_date_updated":"2026-10-03T22:30:02Z","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"citation":{"short":"S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025.","ista":"Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria.","mla":"Lee, Seungho. <i>Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>.","ieee":"S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025.","apa":"Lee, S. (2025). <i>Nanoparticle-based precursors toward advanced crystalline inorganic solids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>","ama":"Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20415\">10.15479/AT-ISTA-20415</a>","chicago":"Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20415\">https://doi.org/10.15479/AT-ISTA-20415</a>."},"ddc":["540"],"author":[{"full_name":"Lee, Seungho","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","last_name":"Lee"}],"doi":"10.15479/AT-ISTA-20415","date_created":"2025-10-01T09:04:00Z","OA_place":"publisher","status":"public","publication_status":"published","date_updated":"2026-10-16T09:31:49Z","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"month":"10","supervisor":[{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"last_name":"Protesescu","first_name":"Loredana","full_name":"Protesescu, Loredana"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"}],"year":"2025","_id":"20415","oa_version":"Published Version","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"type":"dissertation","file":[{"date_created":"2025-10-03T12:29:43Z","file_id":"20420","date_updated":"2026-10-03T22:30:02Z","relation":"source_file","file_name":"2025_Lee_Seungho_Thesis.docx","creator":"slee","embargo_to":"open_access","file_size":88706648,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"fa6d5946feb37b678ee1c6dffb4fa167"},{"relation":"main_file","file_name":"2025_Lee_Seungho_Thesis__.pdf","file_id":"20421","date_updated":"2026-10-03T22:30:02Z","content_type":"application/pdf","embargo":"2026-10-03","checksum":"c5ba6d464113ad0c5812a9d24b539b86","access_level":"open_access","creator":"slee","file_size":14587276,"date_created":"2025-10-03T12:29:25Z"}],"alternative_title":["ISTA Thesis"],"day":"01","title":"Nanoparticle-based precursors toward advanced crystalline inorganic solids","oa":1,"degree_awarded":"PhD","date_published":"2025-10-01T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20415","related_material":{"record":[{"relation":"part_of_dissertation","id":"12237","status":"public"},{"status":"public","id":"15357","relation":"part_of_dissertation"}]},"corr_author":"1","page":"144","publication_identifier":{"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"abstract":[{"lang":"eng","text":"We address two pressing questions in the theory of the Korteweg–de Vries (KdV) equation. First, we show the uniqueness of solutions to KdV that are merely bounded, without any further decay, regularity, periodicity, or almost periodicity assumptions. The second question, emphasized by Deift, regards whether almost periodic initial data leads to almost periodic solutions to KdV. Building on the new observation that this is false for the Airy equation, we construct an example of almost periodic initial data whose KdV evolution remains bounded, but fails to be almost periodic at a later time. Our uniqueness result ensures that the solution constructed is the unique development of this initial data."}],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.07501","open_access":"1"}],"extern":"1","publisher":"Duke University Press","author":[{"first_name":"Andreia","full_name":"Chapouto, Andreia","last_name":"Chapouto"},{"last_name":"Killip","full_name":"Killip, Rowan","first_name":"Rowan"},{"id":"056daca0-b8d1-11f0-964f-f91054abf8ca","last_name":"Visan","full_name":"Visan, Monica","first_name":"Monica"}],"intvolume":"       173","doi":"10.1215/00127094-2023-0035","citation":{"chicago":"Chapouto, Andreia, Rowan Killip, and Monica Vişan. “Bounded Solutions of KdV: Uniqueness and the Loss of Almost Periodicity.” <i>Duke Mathematical Journal</i>. Duke University Press, 2024. <a href=\"https://doi.org/10.1215/00127094-2023-0035\">https://doi.org/10.1215/00127094-2023-0035</a>.","apa":"Chapouto, A., Killip, R., &#38; Vişan, M. (2024). Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2023-0035\">https://doi.org/10.1215/00127094-2023-0035</a>","ieee":"A. Chapouto, R. Killip, and M. Vişan, “Bounded solutions of KdV: Uniqueness and the loss of almost periodicity,” <i>Duke Mathematical Journal</i>, vol. 173, no. 7. Duke University Press, pp. 1227–1267, 2024.","ama":"Chapouto A, Killip R, Vişan M. Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. <i>Duke Mathematical Journal</i>. 2024;173(7):1227-1267. doi:<a href=\"https://doi.org/10.1215/00127094-2023-0035\">10.1215/00127094-2023-0035</a>","mla":"Chapouto, Andreia, et al. “Bounded Solutions of KdV: Uniqueness and the Loss of Almost Periodicity.” <i>Duke Mathematical Journal</i>, vol. 173, no. 7, Duke University Press, 2024, pp. 1227–67, doi:<a href=\"https://doi.org/10.1215/00127094-2023-0035\">10.1215/00127094-2023-0035</a>.","ista":"Chapouto A, Killip R, Vişan M. 2024. Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. Duke Mathematical Journal. 173(7), 1227–1267.","short":"A. Chapouto, R. Killip, M. Vişan, Duke Mathematical Journal 173 (2024) 1227–1267."},"das_tickbox":"1","date_created":"2026-06-19T07:34:05Z","OA_type":"green","status":"public","OA_place":"repository","quality_controlled":"1","external_id":{"arxiv":["2209.07501"]},"month":"05","publication_status":"published","issue":"7","date_updated":"2026-06-22T10:32:25Z","_id":"22026","oa_version":"Preprint","year":"2024","arxiv":1,"article_type":"original","keyword":["Almost-periodic solutions","Korteweg–de Vries","unconditional uniqueness"],"type":"journal_article","volume":173,"language":[{"iso":"eng"}],"day":"15","title":"Bounded solutions of KdV: Uniqueness and the loss of almost periodicity","publication":"Duke Mathematical Journal","page":"1227-1267","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0012-7094"]},"scopus_import":"1","oa":1,"fulldoi":"https://doi.org/10.1215/00127094-2023-0035","date_published":"2024-05-15T00:00:00Z"},{"citation":{"mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. 2024;112(2):230-246.e11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>","ieee":"G. T. Cheung <i>et al.</i>, “Multipotent progenitors instruct ontogeny of the superior colliculus,” <i>Neuron</i>, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11."},"ddc":["570"],"author":[{"last_name":"Cheung","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","full_name":"Cheung, Giselle T"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948"},{"last_name":"Krausgruber","first_name":"Thomas","full_name":"Krausgruber, Thomas"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"first_name":"Martin","full_name":"Schrammel, Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","last_name":"Schrammel"},{"id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","last_name":"Özgen","full_name":"Özgen, Natalie Y","first_name":"Natalie Y"},{"last_name":"Ivec","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","full_name":"Ivec, Alexis","first_name":"Alexis"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"intvolume":"       112","doi":"10.1016/j.neuron.2023.11.009","publisher":"Elsevier","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny."}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"SiHi"},{"_id":"RySh"}],"file_date_updated":"2024-02-06T13:56:15Z","publication_status":"published","issue":"2","date_updated":"2025-12-30T10:54:12Z","project":[{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"month":"01","quality_controlled":"1","external_id":{"isi":["001163937900001"],"pmid":["38096816"]},"date_created":"2023-04-27T09:41:48Z","status":"public","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","pmid":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"type":"journal_article","file":[{"file_name":"2024_Neuron_Cheung.pdf","relation":"main_file","file_id":"14944","date_updated":"2024-02-06T13:56:15Z","content_type":"application/pdf","access_level":"open_access","checksum":"32b3788f7085cf44a84108d8faaff3ce","creator":"dernst","file_size":5942467,"success":1,"date_created":"2024-02-06T13:56:15Z"}],"volume":112,"article_type":"original","oa_version":"Published Version","_id":"12875","year":"2024","oa":1,"isi":1,"fulldoi":"https://doi.org/10.1016/j.neuron.2023.11.009","date_published":"2024-01-17T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"page":"230-246.e11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0896-6273"]},"scopus_import":"1","publication":"Neuron","day":"17","title":"Multipotent progenitors instruct ontogeny of the superior colliculus"},{"volume":239,"type":"journal_article","language":[{"iso":"eng"}],"arxiv":1,"year":"2024","oa_version":"Preprint","_id":"20838","article_type":"original","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"page":"431-468","date_published":"2024-12-19T00:00:00Z","fulldoi":"https://doi.org/10.1007/s00222-024-01305-w","oa":1,"title":"Every diffeomorphism is a total renormalization of a close to identity map","day":"19","publication":"Inventiones mathematicae","doi":"10.1007/s00222-024-01305-w","intvolume":"       239","author":[{"first_name":"Pierre","full_name":"Berger, Pierre","last_name":"Berger"},{"last_name":"Gourmelon","first_name":"Nicolaz","full_name":"Gourmelon, Nicolaz"},{"last_name":"Helfter","id":"7d296fbe-e2c6-11ee-84d3-d5c2945f9a57","full_name":"Helfter, Mathieu","first_name":"Mathieu"}],"citation":{"ista":"Berger P, Gourmelon N, Helfter M. 2024. Every diffeomorphism is a total renormalization of a close to identity map. Inventiones mathematicae. 239(2), 431–468.","short":"P. Berger, N. Gourmelon, M. Helfter, Inventiones Mathematicae 239 (2024) 431–468.","mla":"Berger, Pierre, et al. “Every Diffeomorphism Is a Total Renormalization of a Close to Identity Map.” <i>Inventiones Mathematicae</i>, vol. 239, no. 2, Springer Nature, 2024, pp. 431–68, doi:<a href=\"https://doi.org/10.1007/s00222-024-01305-w\">10.1007/s00222-024-01305-w</a>.","ama":"Berger P, Gourmelon N, Helfter M. Every diffeomorphism is a total renormalization of a close to identity map. <i>Inventiones mathematicae</i>. 2024;239(2):431-468. doi:<a href=\"https://doi.org/10.1007/s00222-024-01305-w\">10.1007/s00222-024-01305-w</a>","apa":"Berger, P., Gourmelon, N., &#38; Helfter, M. (2024). Every diffeomorphism is a total renormalization of a close to identity map. <i>Inventiones Mathematicae</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00222-024-01305-w\">https://doi.org/10.1007/s00222-024-01305-w</a>","ieee":"P. Berger, N. Gourmelon, and M. Helfter, “Every diffeomorphism is a total renormalization of a close to identity map,” <i>Inventiones mathematicae</i>, vol. 239, no. 2. Springer Nature, pp. 431–468, 2024.","chicago":"Berger, Pierre, Nicolaz Gourmelon, and Mathieu Helfter. “Every Diffeomorphism Is a Total Renormalization of a Close to Identity Map.” <i>Inventiones Mathematicae</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00222-024-01305-w\">https://doi.org/10.1007/s00222-024-01305-w</a>."},"extern":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.09064","open_access":"1"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"For any 1 ≤ r ≤ ∞, we show that every diffeomorphism of a manifold of the form\r\nR/Z × M is a total renormalization of a Cr-close to identity map. In other words, for\r\nevery diffeomorphism f of R/Z×M, there exists a map g arbitrarily close to identity\r\nsuch that the first return map of g to a domain is conjugate to f and moreover the\r\norbit of this domain is equal to R/Z×M. This enables us to localize near the identity\r\nthe existence of many properties in dynamical systems, such as being Bernoulli for a\r\nsmooth volume form."}],"publisher":"Springer Nature","month":"12","date_updated":"2025-12-29T12:03:10Z","issue":"2","publication_status":"published","OA_place":"repository","status":"public","OA_type":"green","date_created":"2025-12-19T10:15:13Z","external_id":{"arxiv":["2210.09064"]},"quality_controlled":"1"},{"intvolume":"       146","doi":"10.1021/jacs.4c09114","author":[{"last_name":"Jin","first_name":"Yulong","full_name":"Jin, Yulong"},{"id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X","last_name":"Mandal","full_name":"Mandal, Pradeep K","first_name":"Pradeep K"},{"first_name":"Juntian","full_name":"Wu, Juntian","last_name":"Wu"},{"full_name":"Kiani, Armin","first_name":"Armin","last_name":"Kiani"},{"first_name":"Rui","full_name":"Zhao, Rui","last_name":"Zhao"},{"last_name":"Huc","first_name":"Ivan","full_name":"Huc, Ivan"},{"first_name":"Sijbren","full_name":"Otto, Sijbren","last_name":"Otto"}],"citation":{"mla":"Jin, Yulong, et al. “Light-Mediated Interconversion between a Foldamer and a Self-Replicator.” <i>Journal of the American Chemical Society</i>, vol. 146, no. 49, American Chemical Society, 2024, pp. 33395–402, doi:<a href=\"https://doi.org/10.1021/jacs.4c09114\">10.1021/jacs.4c09114</a>.","chicago":"Jin, Yulong, Pradeep K Mandal, Juntian Wu, Armin Kiani, Rui Zhao, Ivan Huc, and Sijbren Otto. “Light-Mediated Interconversion between a Foldamer and a Self-Replicator.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/jacs.4c09114\">https://doi.org/10.1021/jacs.4c09114</a>.","ama":"Jin Y, Mandal PK, Wu J, et al. Light-mediated interconversion between a foldamer and a self-replicator. <i>Journal of the American Chemical Society</i>. 2024;146(49):33395-33402. doi:<a href=\"https://doi.org/10.1021/jacs.4c09114\">10.1021/jacs.4c09114</a>","apa":"Jin, Y., Mandal, P. K., Wu, J., Kiani, A., Zhao, R., Huc, I., &#38; Otto, S. (2024). Light-mediated interconversion between a foldamer and a self-replicator. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.4c09114\">https://doi.org/10.1021/jacs.4c09114</a>","ieee":"Y. Jin <i>et al.</i>, “Light-mediated interconversion between a foldamer and a self-replicator,” <i>Journal of the American Chemical Society</i>, vol. 146, no. 49. American Chemical Society, pp. 33395–33402, 2024.","short":"Y. Jin, P.K. Mandal, J. Wu, A. Kiani, R. Zhao, I. Huc, S. Otto, Journal of the American Chemical Society 146 (2024) 33395–33402.","ista":"Jin Y, Mandal PK, Wu J, Kiani A, Zhao R, Huc I, Otto S. 2024. Light-mediated interconversion between a foldamer and a self-replicator. Journal of the American Chemical Society. 146(49), 33395–33402."},"ddc":["540"],"extern":"1","article_processing_charge":"Yes (in subscription journal)","main_file_link":[{"url":"https://doi.org/10.1021/jacs.4c09114","open_access":"1"}],"abstract":[{"lang":"eng","text":"Self-replicating molecules and well-defined folded macromolecules are of great significance in the emergence and evolution of life. How they may interconnect and affect each other remains largely elusive. Here, we demonstrate an abiotic system where a single building block can oligomerize to yield either a self-replicating molecule or a foldamer. Specifically, agitation of a disulfide-based dynamic combinatorial library at moderately elevated pH channels it selectively into a self-replicating hexamer assembled into fibers, after passing through a period where a 15-subunit macrocyclic foldamer existed transiently. Without mechanoagitation or at lower pH, the formation of hexamer fiber is suppressed, resulting in the accumulation of the 15mer foldamer. Foldamer and self-replicator can be interconverted in response to external stimuli, including agitation and a change in pH. Furthermore, upon the addition of a photoacid, the pH of the medium can be controlled by irradiation, driving the switching between replicator and foldamer and allowing a dissipative out-of-equilibrium state to be accessed, using light as a source of energy."}],"publisher":"American Chemical Society","has_accepted_license":"1","month":"11","issue":"49","date_updated":"2026-01-19T11:03:31Z","publication_status":"published","OA_place":"publisher","status":"public","date_created":"2026-01-08T07:05:57Z","OA_type":"hybrid","external_id":{"pmid":["39590511"]},"quality_controlled":"1","volume":146,"type":"journal_article","language":[{"iso":"eng"}],"PlanS_conform":"1","pmid":1,"_id":"20961","oa_version":"Published Version","year":"2024","article_type":"original","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"33395-33402","fulldoi":"https://doi.org/10.1021/jacs.4c09114","date_published":"2024-11-26T00:00:00Z","oa":1,"title":"Light-mediated interconversion between a foldamer and a self-replicator","day":"26","publication":"Journal of the American Chemical Society"},{"article_type":"original","keyword":["Fibers","Foldamers","Macrocycles","Monomers","Peptides","Proteins"],"year":"2024","_id":"20962","oa_version":"Published Version","pmid":1,"PlanS_conform":"1","language":[{"iso":"eng"}],"type":"journal_article","volume":146,"publication":"Journal of the American Chemical Society","day":"26","title":"Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry","oa":1,"date_published":"2024-11-26T00:00:00Z","fulldoi":"https://doi.org/10.1021/jacs.4c09111","page":"33386-33394","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"scopus_import":"1","has_accepted_license":"1","publisher":"American Chemical Society","abstract":[{"text":"Systems chemistry has emerged as a useful paradigm to access structures and phenomena typically exhibited by living systems, including complex molecular systems such as self-replicators and foldamers. As we progress further toward the noncovalent synthesis of life-like systems, and eventually life itself, it is necessary to gain control over assembly pathways. Dissipative chemical fueling has enabled access to stable populations of (self-assembled) structures that would normally form only transiently. Here, we report a synthetic dynamic combinatorial library, made from a single structurally simple building block, from which a self-replicator and a foldamer can emerge along two distinct and competing pathways through an inter- or intramolecular assembly process, respectively. A fueled chemical reaction cycle is then set up to generate the foldamer transiently, in the presence of the self-replicator. The partitioning of the building block between the folding and self-replication pathways and the duration of the fueled reaction cycles are controlled by adjusting the amount of the chemical fuel. An out-of-equilibrium steady state involving the two assemblies could also be achieved by using a continuous stirred tank reactor with inflow and outflow of material. This work connects the domains of folding and self-replication in synthetic systems through dissipative out-of-equilibrium chemistry. It demonstrates that foldamers and self-replicators, formed from the same building block, can stably coexist if the system is continuously supplied with energy, while at equilibrium, the Gibbs phase rule prohibits such coexistence.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","main_file_link":[{"url":"https://doi.org/10.1021/jacs.4c09111","open_access":"1"}],"extern":"1","citation":{"short":"A. Sood, P.K. Mandal, J. Ottelé, J. Wu, M. Eleveld, J. Hatai, C.G. Pappas, I. Huc, S. Otto, Journal of the American Chemical Society 146 (2024) 33386–33394.","ista":"Sood A, Mandal PK, Ottelé J, Wu J, Eleveld M, Hatai J, Pappas CG, Huc I, Otto S. 2024. Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry. Journal of the American Chemical Society. 146(49), 33386–33394.","mla":"Sood, Ankush, et al. “Simultaneous Formation of a Foldamer and a Self-Replicator by out-of-Equilibrium Dynamic Covalent Chemistry.” <i>Journal of the American Chemical Society</i>, vol. 146, no. 49, American Chemical Society, 2024, pp. 33386–94, doi:<a href=\"https://doi.org/10.1021/jacs.4c09111\">10.1021/jacs.4c09111</a>.","ieee":"A. Sood <i>et al.</i>, “Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry,” <i>Journal of the American Chemical Society</i>, vol. 146, no. 49. American Chemical Society, pp. 33386–33394, 2024.","apa":"Sood, A., Mandal, P. K., Ottelé, J., Wu, J., Eleveld, M., Hatai, J., … Otto, S. (2024). Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.4c09111\">https://doi.org/10.1021/jacs.4c09111</a>","ama":"Sood A, Mandal PK, Ottelé J, et al. Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry. <i>Journal of the American Chemical Society</i>. 2024;146(49):33386-33394. doi:<a href=\"https://doi.org/10.1021/jacs.4c09111\">10.1021/jacs.4c09111</a>","chicago":"Sood, Ankush, Pradeep K Mandal, Jim Ottelé, Juntian Wu, Marcel Eleveld, Joydev Hatai, Charalampos G. Pappas, Ivan Huc, and Sijbren Otto. “Simultaneous Formation of a Foldamer and a Self-Replicator by out-of-Equilibrium Dynamic Covalent Chemistry.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/jacs.4c09111\">https://doi.org/10.1021/jacs.4c09111</a>."},"author":[{"last_name":"Sood","full_name":"Sood, Ankush","first_name":"Ankush"},{"full_name":"Mandal, Pradeep K","first_name":"Pradeep K","last_name":"Mandal","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X"},{"full_name":"Ottelé, Jim","first_name":"Jim","last_name":"Ottelé"},{"last_name":"Wu","full_name":"Wu, Juntian","first_name":"Juntian"},{"last_name":"Eleveld","full_name":"Eleveld, Marcel","first_name":"Marcel"},{"last_name":"Hatai","first_name":"Joydev","full_name":"Hatai, Joydev"},{"last_name":"Pappas","first_name":"Charalampos G.","full_name":"Pappas, Charalampos G."},{"last_name":"Huc","first_name":"Ivan","full_name":"Huc, Ivan"},{"first_name":"Sijbren","full_name":"Otto, Sijbren","last_name":"Otto"}],"doi":"10.1021/jacs.4c09111","intvolume":"       146","quality_controlled":"1","external_id":{"pmid":["39590110"]},"OA_type":"hybrid","date_created":"2026-01-08T07:06:27Z","OA_place":"publisher","status":"public","publication_status":"published","date_updated":"2026-01-19T10:57:53Z","issue":"49","month":"11"},{"publication_status":"published","date_updated":"2026-01-20T06:56:44Z","issue":"48","month":"10","quality_controlled":"1","external_id":{"pmid":["39501876"]},"OA_type":"hybrid","date_created":"2026-01-11T14:32:23Z","status":"public","OA_place":"publisher","citation":{"chicago":"Kwon, Sunbum, Vasily Morozov, Lingfei Wang, Pradeep K Mandal, Stéphane Chaignepain, Céline Douat, and Ivan Huc. “Interrogating the Potential of Helical Aromatic Foldamers for Protein Recognition.” <i>Organic &#38; Biomolecular Chemistry</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d4ob01436g\">https://doi.org/10.1039/d4ob01436g</a>.","apa":"Kwon, S., Morozov, V., Wang, L., Mandal, P. K., Chaignepain, S., Douat, C., &#38; Huc, I. (2024). Interrogating the potential of helical aromatic foldamers for protein recognition. <i>Organic &#38; Biomolecular Chemistry</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4ob01436g\">https://doi.org/10.1039/d4ob01436g</a>","ieee":"S. Kwon <i>et al.</i>, “Interrogating the potential of helical aromatic foldamers for protein recognition,” <i>Organic &#38; Biomolecular Chemistry</i>, vol. 22, no. 48. Royal Society of Chemistry, pp. 9342–9347, 2024.","ama":"Kwon S, Morozov V, Wang L, et al. Interrogating the potential of helical aromatic foldamers for protein recognition. <i>Organic &#38; Biomolecular Chemistry</i>. 2024;22(48):9342-9347. doi:<a href=\"https://doi.org/10.1039/d4ob01436g\">10.1039/d4ob01436g</a>","mla":"Kwon, Sunbum, et al. “Interrogating the Potential of Helical Aromatic Foldamers for Protein Recognition.” <i>Organic &#38; Biomolecular Chemistry</i>, vol. 22, no. 48, Royal Society of Chemistry, 2024, pp. 9342–47, doi:<a href=\"https://doi.org/10.1039/d4ob01436g\">10.1039/d4ob01436g</a>.","ista":"Kwon S, Morozov V, Wang L, Mandal PK, Chaignepain S, Douat C, Huc I. 2024. Interrogating the potential of helical aromatic foldamers for protein recognition. Organic &#38; Biomolecular Chemistry. 22(48), 9342–9347.","short":"S. Kwon, V. Morozov, L. Wang, P.K. Mandal, S. Chaignepain, C. Douat, I. Huc, Organic &#38; Biomolecular Chemistry 22 (2024) 9342–9347."},"author":[{"first_name":"Sunbum","full_name":"Kwon, Sunbum","last_name":"Kwon"},{"last_name":"Morozov","full_name":"Morozov, Vasily","first_name":"Vasily"},{"last_name":"Wang","full_name":"Wang, Lingfei","first_name":"Lingfei"},{"full_name":"Mandal, Pradeep K","first_name":"Pradeep K","last_name":"Mandal","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X"},{"full_name":"Chaignepain, Stéphane","first_name":"Stéphane","last_name":"Chaignepain"},{"last_name":"Douat","first_name":"Céline","full_name":"Douat, Céline"},{"first_name":"Ivan","full_name":"Huc, Ivan","last_name":"Huc"}],"doi":"10.1039/d4ob01436g","intvolume":"        22","publisher":"Royal Society of Chemistry","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/3.0/","abstract":[{"lang":"eng","text":"A biotinylated helical aromatic oligoamide foldamer equivalent in size to a 24mer peptide was designed without any prejudice other than to display various polar and hydrophobic side chains at its surface. It was synthesized on solid phase, its P- and M-helical conformers were separated by HPLC on a chiral stationary phase, and the solid state structure of a non-biotinylated analogue was elucidated by X-ray crystallography. Pull-down experiments from a yeast cell lysate using the foldamer as a bait followed by proteomic analysis revealed potential protein binding partners. Three of these proteins were recombinantly expressed. Biolayer interferometry showed submicromolar binding demonstrating the potential of a given foldamer to have affinity for certain proteins in the absence of design considerations. Yet, binding selectivity was low in all three cases since both P- and M-conformers bound to the proteins with similar affinities."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/D4OB01436G"}],"article_processing_charge":"Yes (in subscription journal)","extern":"1","oa":1,"date_published":"2024-10-30T00:00:00Z","fulldoi":"https://doi.org/10.1039/d4ob01436g","page":"9342-9347","tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"scopus_import":"1","publication_identifier":{"issn":["1477-0520"],"eissn":["1477-0539"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Organic & Biomolecular Chemistry","day":"30","title":"Interrogating the potential of helical aromatic foldamers for protein recognition","pmid":1,"PlanS_conform":"1","language":[{"iso":"eng"}],"type":"journal_article","volume":22,"article_type":"original","year":"2024","_id":"20967","oa_version":"Published Version"},{"month":"12","publication_status":"published","date_updated":"2026-02-10T06:49:49Z","OA_type":"gold","date_created":"2026-01-28T15:26:12Z","OA_place":"publisher","status":"public","quality_controlled":"1","external_id":{"arxiv":["2306.07320"]},"author":[{"last_name":"Labbe","first_name":"Ivo","full_name":"Labbe, Ivo"},{"full_name":"Greene, Jenny E.","first_name":"Jenny E.","last_name":"Greene"},{"first_name":"Rachel","full_name":"Bezanson, Rachel","last_name":"Bezanson"},{"first_name":"Seiji","full_name":"Fujimoto, Seiji","last_name":"Fujimoto"},{"first_name":"Lukas J.","full_name":"Furtak, Lukas J.","last_name":"Furtak"},{"full_name":"Goulding, Andy D.","first_name":"Andy D.","last_name":"Goulding"},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"first_name":"Rohan P.","full_name":"Naidu, Rohan P.","last_name":"Naidu"},{"last_name":"Oesch","full_name":"Oesch, Pascal A.","first_name":"Pascal A."},{"last_name":"Atek","first_name":"Hakim","full_name":"Atek, Hakim"},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"last_name":"Chemerynska","full_name":"Chemerynska, Iryna","first_name":"Iryna"},{"last_name":"Coe","full_name":"Coe, Dan","first_name":"Dan"},{"last_name":"Cutler","full_name":"Cutler, Sam E.","first_name":"Sam E."},{"last_name":"Dayal","first_name":"Pratika","full_name":"Dayal, Pratika"},{"last_name":"Feldmann","full_name":"Feldmann, Robert","first_name":"Robert"},{"last_name":"Franx","first_name":"Marijn","full_name":"Franx, Marijn"},{"last_name":"Glazebrook","full_name":"Glazebrook, Karl","first_name":"Karl"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"last_name":"Maseda","full_name":"Maseda, Michael","first_name":"Michael"},{"full_name":"Marchesini, Danilo","first_name":"Danilo","last_name":"Marchesini"},{"last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya","first_name":"Themiya"},{"full_name":"Nelson, Erica J.","first_name":"Erica J.","last_name":"Nelson"},{"full_name":"Pan, Richard","first_name":"Richard","last_name":"Pan"},{"first_name":"Casey","full_name":"Papovich, Casey","last_name":"Papovich"},{"last_name":"Price","first_name":"Sedona H.","full_name":"Price, Sedona H."},{"last_name":"Suess","full_name":"Suess, Katherine A.","first_name":"Katherine A."},{"first_name":"Bingjie 冰洁","full_name":"Wang, Bingjie 冰洁","last_name":"Wang"},{"last_name":"Weaver","full_name":"Weaver, John R.","first_name":"John R."},{"first_name":"Katherine E.","full_name":"Whitaker, Katherine E.","last_name":"Whitaker"},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"},{"last_name":"Zitrin","full_name":"Zitrin, Adi","first_name":"Adi"}],"doi":"10.3847/1538-4357/ad3551","intvolume":"       978","ddc":["520"],"citation":{"apa":"Labbe, I., Greene, J. E., Bezanson, R., Fujimoto, S., Furtak, L. J., Goulding, A. D., … Zitrin, A. (2024). UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad3551\">https://doi.org/10.3847/1538-4357/ad3551</a>","ama":"Labbe I, Greene JE, Bezanson R, et al. UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. <i>The Astrophysical Journal</i>. 2024;978. doi:<a href=\"https://doi.org/10.3847/1538-4357/ad3551\">10.3847/1538-4357/ad3551</a>","ieee":"I. Labbe <i>et al.</i>, “UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA,” <i>The Astrophysical Journal</i>, vol. 978. IOP Publishing, 2024.","chicago":"Labbe, Ivo, Jenny E. Greene, Rachel Bezanson, Seiji Fujimoto, Lukas J. Furtak, Andy D. Goulding, Jorryt J Matthee, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 &#60; z &#60; 7 with JWST and ALMA.” <i>The Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad3551\">https://doi.org/10.3847/1538-4357/ad3551</a>.","mla":"Labbe, Ivo, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 &#60; z &#60; 7 with JWST and ALMA.” <i>The Astrophysical Journal</i>, vol. 978, 92, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad3551\">10.3847/1538-4357/ad3551</a>.","ista":"Labbe I, Greene JE, Bezanson R, Fujimoto S, Furtak LJ, Goulding AD, Matthee JJ, Naidu RP, Oesch PA, Atek H, Brammer G, Chemerynska I, Coe D, Cutler SE, Dayal P, Feldmann R, Franx M, Glazebrook K, Leja J, Maseda M, Marchesini D, Nanayakkara T, Nelson EJ, Pan R, Papovich C, Price SH, Suess KA, Wang B冰洁, Weaver JR, Whitaker KE, Williams CC, Zitrin A. 2024. UNCOVER: Candidate red active galactic nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. The Astrophysical Journal. 978, 92.","short":"I. Labbe, J.E. Greene, R. Bezanson, S. Fujimoto, L.J. Furtak, A.D. Goulding, J.J. Matthee, R.P. Naidu, P.A. Oesch, H. Atek, G. Brammer, I. Chemerynska, D. Coe, S.E. Cutler, P. Dayal, R. Feldmann, M. Franx, K. Glazebrook, J. Leja, M. Maseda, D. Marchesini, T. Nanayakkara, E.J. Nelson, R. Pan, C. Papovich, S.H. Price, K.A. Suess, B.冰洁 Wang, J.R. Weaver, K.E. Whitaker, C.C. Williams, A. Zitrin, The Astrophysical Journal 978 (2024)."},"abstract":[{"lang":"eng","text":"The James Webb Space Telescope (JWST) is revolutionizing our knowledge of z > 5 galaxies and their actively accreting black holes. Using the JWST Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam Observations before the Epoch of Reionization (UNCOVER) in the lensing field A2744, we report the identification of a sample of little red dots at 3 < zphot < 7 that likely contain highly reddened accreting supermassive black holes. Using a NIRCam-only selection to F444W < 27.7 mag, we find 26 sources over the ∼45 arcmin^2 field that are blue in F115W − F200W ∼ 0 (or βUV ∼ –2.0 for fλ ∝ λ^β), red in F200W − F444W = 1−4 (βopt ∼ +2.0), and are dominated by a point-source-like central component. Of the 20 sources with deep Atacama Large Millimeter/submillimeter Array (ALMA) 1.2 mm coverage, none are detected individually or in a stack. For the majority of the sample, spectral energy distribution fits to the JWST+ALMA observations prefer models with hot dust rather than obscured star formation to reproduce the red NIRCam colors and ALMA 1.2 mm nondetections. While compact dusty star formation cannot be ruled out, the combination of extremely small sizes (〈re〉 ≈ 50 pc after correction for magnification), red rest-frame optical slopes, and hot dust can be explained by reddened broad-line active galactic nuclei (AGNs). Our targets have faint M1450 ≈ −14 to −18 mag but inferred bolometric luminosities of Lbol = 10^43–10^46 erg s^−1, reflecting their obscured nature. If the candidates are confirmed as AGNs with upcoming UNCOVER spectroscopy, then we have found an abundant population of reddened luminous AGNs that are at least ten times more numerous than UV-luminous AGNs at the same intrinsic bolometric luminosity."}],"article_processing_charge":"Yes","file_date_updated":"2026-02-10T06:44:24Z","department":[{"_id":"JoMa"}],"has_accepted_license":"1","publisher":"IOP Publishing","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"oa":1,"date_published":"2024-12-26T00:00:00Z","fulldoi":"https://doi.org/10.3847/1538-4357/ad3551","day":"26","title":"UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA","article_number":"92","publication":"The Astrophysical Journal","type":"journal_article","file":[{"file_size":5041924,"creator":"dernst","access_level":"open_access","checksum":"825c35ebd26e292c8a5c2bffac327854","content_type":"application/pdf","date_updated":"2026-02-10T06:44:24Z","file_id":"21201","file_name":"2024_AstrophysicalJourn_Labbe.pdf","relation":"main_file","date_created":"2026-02-10T06:44:24Z","success":1}],"volume":978,"DOAJ_listed":"1","acknowledgement":"I.L. acknowledges support from Australian Research Council Future Fellowship FT220100798. J.E.G. and A.D.G acknowledge support from NSF/AAG grant #1007094, and J.E.G. also acknowledges support from NSF/AAG grant #1007052. L.J.F. and A.Z. acknowledge support by Grant No. 2020750 from the United States–Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (“ODIN”) and from the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. This paper makes use of the ALMA data: ADS/JAO. ALMA #2022.1.00073.S, 2018.1.00035.L, and 2013.1.00999.S. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation.","PlanS_conform":"1","language":[{"iso":"eng"}],"arxiv":1,"year":"2024","oa_version":"Published Version","_id":"21064","article_type":"original"},{"publisher":"Zenodo","has_accepted_license":"1","_id":"21304","oa_version":"Published Version","article_processing_charge":"No","abstract":[{"lang":"eng","text":"No description provided."}],"main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.13934991","open_access":"1"}],"year":"2024","department":[{"_id":"AnSa"}],"citation":{"mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal_membranes : Code and Examples</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>.","ama":"Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>","ieee":"M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo, 2024.","apa":"Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.13934991\">https://doi.org/10.5281/ZENODO.13934991</a>","ista":"Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.13934991\">10.5281/ZENODO.13934991</a>.","short":"M. Santana de Freitas Amaral, (2024)."},"author":[{"last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel"}],"type":"research_data_reference","doi":"10.5281/ZENODO.13934991","date_created":"2026-02-17T12:52:26Z","OA_type":"green","day":"15","status":"public","OA_place":"repository","title":"archaeal_membranes : code and examples","oa":1,"fulldoi":"https://doi.org/10.5281/ZENODO.13934991","date_published":"2024-10-15T00:00:00Z","date_updated":"2026-02-23T11:49:05Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"21251"}]},"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10"},{"abstract":[{"lang":"eng","text":"We present a framework for the end-to-end optimization of metasurface imaging systems that reconstruct targets using compressed sensing, a technique for solving underdetermined imaging problems when the target object exhibits sparsity (e.g., the object can be described by a small number of nonzero values, but the positions of these values are unknown). We nest an iterative, unapproximated compressed sensing reconstruction algorithm into our end-to-end optimization pipeline, resulting in an interpretable, data-efficient method for maximally leveraging metaoptics to exploit object sparsity. We apply our framework to super-resolution imaging and high-resolution depth imaging with a phase-change material. In both situations, our end-to-end framework effectively optimizes metasurface structures for compressed sensing recovery, automatically balancing a number of complicated design considerations to select an imaging measurement matrix from a complex, physically constrained manifold with millions of dimensions. The optimized metasurface imaging systems are robust to noise, significantly improving over random scattering surfaces and approaching the ideal compressed sensing performance of a Gaussian matrix, showing how a physical metasurface system can demonstrably approach the mathematical limits of compressed sensing."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.12348"}],"article_processing_charge":"No","extern":"1","publisher":"American Chemical Society","author":[{"last_name":"Arya","first_name":"Gaurav","full_name":"Arya, Gaurav"},{"last_name":"Li","full_name":"Li, William F.","first_name":"William F."},{"id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","first_name":"Charles","full_name":"Roques-Carmes, Charles"},{"last_name":"Soljačić","first_name":"Marin","full_name":"Soljačić, Marin"},{"full_name":"Johnson, Steven G.","first_name":"Steven G.","last_name":"Johnson"},{"last_name":"Lin","first_name":"Zin","full_name":"Lin, Zin"}],"intvolume":"        11","doi":"10.1021/acsphotonics.4c00259","ddc":["530"],"citation":{"short":"G. Arya, W.F. Li, C. Roques-Carmes, M. Soljačić, S.G. Johnson, Z. Lin, ACS Photonics 11 (2024) 2077–2087.","ista":"Arya G, Li WF, Roques-Carmes C, Soljačić M, Johnson SG, Lin Z. 2024. End-to-end optimization of metasurfaces for imaging with compressed sensing. ACS Photonics. 11(5), 2077–2087.","mla":"Arya, Gaurav, et al. “End-to-End Optimization of Metasurfaces for Imaging with Compressed Sensing.” <i>ACS Photonics</i>, vol. 11, no. 5, American Chemical Society, 2024, pp. 2077–87, doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00259\">10.1021/acsphotonics.4c00259</a>.","ama":"Arya G, Li WF, Roques-Carmes C, Soljačić M, Johnson SG, Lin Z. End-to-end optimization of metasurfaces for imaging with compressed sensing. <i>ACS Photonics</i>. 2024;11(5):2077-2087. doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00259\">10.1021/acsphotonics.4c00259</a>","ieee":"G. Arya, W. F. Li, C. Roques-Carmes, M. Soljačić, S. G. Johnson, and Z. Lin, “End-to-end optimization of metasurfaces for imaging with compressed sensing,” <i>ACS Photonics</i>, vol. 11, no. 5. American Chemical Society, pp. 2077–2087, 2024.","apa":"Arya, G., Li, W. F., Roques-Carmes, C., Soljačić, M., Johnson, S. G., &#38; Lin, Z. (2024). End-to-end optimization of metasurfaces for imaging with compressed sensing. <i>ACS Photonics</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphotonics.4c00259\">https://doi.org/10.1021/acsphotonics.4c00259</a>","chicago":"Arya, Gaurav, William F. Li, Charles Roques-Carmes, Marin Soljačić, Steven G. Johnson, and Zin Lin. “End-to-End Optimization of Metasurfaces for Imaging with Compressed Sensing.” <i>ACS Photonics</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsphotonics.4c00259\">https://doi.org/10.1021/acsphotonics.4c00259</a>."},"date_created":"2026-03-30T12:22:47Z","OA_type":"green","OA_place":"repository","status":"public","quality_controlled":"1","external_id":{"arxiv":["2201.12348"]},"month":"04","publication_status":"published","issue":"5","date_updated":"2026-04-27T09:03:21Z","_id":"21528","oa_version":"Preprint","year":"2024","arxiv":1,"article_type":"original","keyword":["end-to-end","optimization","metasurface","imaging","compressed sensing"],"type":"journal_article","volume":11,"language":[{"iso":"eng"}],"day":"23","title":"End-to-end optimization of metasurfaces for imaging with compressed sensing","publication":"ACS Photonics","page":"2077-2087","publication_identifier":{"eissn":["2330-4022"]},"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"fulldoi":"https://doi.org/10.1021/acsphotonics.4c00259","date_published":"2024-04-23T00:00:00Z"},{"external_id":{"arxiv":["2403.13071"]},"quality_controlled":"1","OA_place":"repository","status":"public","OA_type":"green","date_created":"2026-03-30T12:22:47Z","date_updated":"2026-04-27T10:30:37Z","issue":"8","publication_status":"published","month":"07","publisher":"American Chemical Society","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.13071"}],"article_processing_charge":"No","abstract":[{"text":"A central challenge in the emerging field of free-electron quantum optics is to achieve strong quantum interaction and single-photon nonlinearity between a flying free electron and a photonic mode. Existing schemes are intrinsically limited by electron diffraction, which puts an upper bound on the interaction length and, therefore, on the strength of quantum coupling and nonlinearity. Here, we propose “free-electron fibers”: effectively one-dimensional photonic systems where free electrons copropagate with two guided modes. The first mode applies a ponderomotive trap to the free electron, removing the limitations due to electron diffraction. The second mode strongly couples to the guided free electron with an enhanced coupling that is orders of magnitude larger than previous designs. The extended interaction lengths enabled by our scheme allow for strong single-photon nonlinearities mediated by free electrons. We predict novel quantum effects in our system such as deterministic single-photon emission and nonlinear multimode dynamics. Our proposal paves the way toward the realization of heralded macroscopic nonclassical light generation, deterministic single-photon sources, and quantum gates controlled by free-electron–photon interactions.","lang":"eng"}],"citation":{"chicago":"Karnieli, Aviv, Charles Roques-Carmes, Nicholas Rivera, and Shanhui Fan. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” <i>ACS Photonics</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsphotonics.4c00908\">https://doi.org/10.1021/acsphotonics.4c00908</a>.","apa":"Karnieli, A., Roques-Carmes, C., Rivera, N., &#38; Fan, S. (2024). Strong coupling and single-photon nonlinearity in free-electron quantum optics. <i>ACS Photonics</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphotonics.4c00908\">https://doi.org/10.1021/acsphotonics.4c00908</a>","ieee":"A. Karnieli, C. Roques-Carmes, N. Rivera, and S. Fan, “Strong coupling and single-photon nonlinearity in free-electron quantum optics,” <i>ACS Photonics</i>, vol. 11, no. 8. American Chemical Society, pp. 3401–3411, 2024.","ama":"Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. <i>ACS Photonics</i>. 2024;11(8):3401-3411. doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00908\">10.1021/acsphotonics.4c00908</a>","mla":"Karnieli, Aviv, et al. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” <i>ACS Photonics</i>, vol. 11, no. 8, American Chemical Society, 2024, pp. 3401–11, doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00908\">10.1021/acsphotonics.4c00908</a>.","ista":"Karnieli A, Roques-Carmes C, Rivera N, Fan S. 2024. Strong coupling and single-photon nonlinearity in free-electron quantum optics. ACS Photonics. 11(8), 3401–3411.","short":"A. Karnieli, C. Roques-Carmes, N. Rivera, S. Fan, ACS Photonics 11 (2024) 3401–3411."},"ddc":["530"],"doi":"10.1021/acsphotonics.4c00908","intvolume":"        11","author":[{"last_name":"Karnieli","full_name":"Karnieli, Aviv","first_name":"Aviv"},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"first_name":"Nicholas","full_name":"Rivera, Nicholas","last_name":"Rivera"},{"full_name":"Fan, Shanhui","first_name":"Shanhui","last_name":"Fan"}],"publication":"ACS Photonics","title":"Strong coupling and single-photon nonlinearity in free-electron quantum optics","day":"29","date_published":"2024-07-29T00:00:00Z","fulldoi":"https://doi.org/10.1021/acsphotonics.4c00908","oa":1,"scopus_import":"1","publication_identifier":{"eissn":["2330-4022"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3401-3411","keyword":["quantum optics","free electrons","single photon nonlinearity","electron-photon interaction"],"article_type":"original","year":"2024","arxiv":1,"_id":"21529","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":11,"type":"journal_article"}]