--- OA_place: publisher OA_type: hybrid _id: '19280' 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. acknowledged_ssus: - _id: M-Shop - _id: NanoFab 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.' article_number: '063601' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: M. full_name: Zens, M. last_name: Zens - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka orcid: 0009-0005-0878-3032 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Przemyslaw D full_name: Zielinski, Przemyslaw D id: e198fcc4-f6e0-11ea-865d-b6a256760ee8 last_name: Zielinski - first_name: H. S. full_name: Dhar, H. S. last_name: Dhar - first_name: D. O. full_name: Krimer, D. O. last_name: Krimer - first_name: S. full_name: Rotter, S. last_name: Rotter - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Redchenko E, Zens M, Zemlicka M, et al. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 2025;134(6). doi:10.1103/PhysRevLett.134.063601 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. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.063601 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.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.063601. ieee: E. Redchenko et al., “Observation of collapse and revival in a superconducting atomic frequency comb,” Physical Review Letters, vol. 134, no. 6. American Physical Society, 2025. 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. mla: Redchenko, Elena, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” Physical Review Letters, vol. 134, no. 6, 063601, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.063601. 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). corr_author: '1' date_created: 2025-03-02T23:01:52Z date_published: 2025-02-14T00:00:00Z date_updated: 2026-10-18T22:31:17Z day: '14' ddc: - '530' department: - _id: JoFi doi: 10.1103/PhysRevLett.134.063601 ec_funded: 1 external_id: arxiv: - '2310.04200' isi: - '001454696700003' pmid: - '40021171' file: - access_level: open_access checksum: 633d6c5ddd9b805da22c5839d3d48df6 content_type: application/pdf creator: dernst date_created: 2025-03-04T10:40:50Z date_updated: 2025-03-04T10:40:50Z file_id: '19291' file_name: 2025_PhysReviewLetters_Redchenko.pdf file_size: 2080408 relation: main_file success: 1 file_date_updated: 2025-03-04T10:40:50Z fulldoi: https://doi.org/10.1103/PhysRevLett.134.063601 has_accepted_license: '1' intvolume: ' 134' isi: 1 issue: '6' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 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 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '19533' relation: dissertation_contains status: public scopus_import: '1' status: public title: Observation of collapse and revival in a superconducting atomic frequency comb tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 134 year: '2025' ... --- OA_place: publisher _id: '20212' abstract: - lang: eng 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. " acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 citation: ama: Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:10.15479/AT-ISTA-20212 apa: Miranda, O. (2025). Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20212 chicago: Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20212. ieee: O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025. ista: Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. mla: Miranda, Osvaldo. Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20212. short: O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-22T14:07:00Z date_published: 2025-08-22T00:00:00Z date_updated: 2026-10-02T12:16:56Z day: '22' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/AT-ISTA-20212 doi_confirm: '1' file: - access_level: closed checksum: 3331f76bbef74ff4908e2d2c9262045c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: omiranda date_created: 2025-08-26T09:03:50Z date_updated: 2026-08-26T22:30:02Z embargo_to: open_access file_id: '20230' file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.docx file_size: 32887334 relation: source_file - access_level: open_access checksum: 02509d50cff8e35c5bcbf71e8d658176 content_type: application/pdf creator: omiranda date_created: 2025-08-26T09:05:55Z date_updated: 2026-08-26T22:30:02Z embargo: 2026-08-26 file_id: '20231' file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf file_size: 28636240 relation: main_file file_date_updated: 2026-08-26T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20212 has_accepted_license: '1' keyword: - Pten - mtor - cortical development - MADM - Mapk language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '119' project: - _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d grant_number: '26253' name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development publication_identifier: isbn: - 978-3-99078-063-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17425' relation: part_of_dissertation status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Unraveling the role of Pten in cortical stem cell lineage progression using MADM type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20117' abstract: - lang: eng 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. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Yiqun full_name: Wang, Yiqun id: 82F537F2-B517-11E9-84D7-6433E6697425 last_name: Wang citation: ama: Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:10.15479/AT-ISTA-20117 apa: Wang, Y. (2025). The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20117 chicago: Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20117. ieee: Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025. ista: Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. mla: Wang, Yiqun. The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20117. short: Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-04T15:24:21Z date_published: 2025-08-04T00:00:00Z date_updated: 2026-10-02T12:33:36Z day: '04' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-20117 doi_confirm: '1' file: - access_level: closed checksum: 36b87c17d12c7bf5955d6d812acb8d77 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: yiqwang date_created: 2025-08-22T08:22:10Z date_updated: 2026-09-03T22:30:03Z embargo_to: open_access file_id: '20209' file_name: 2025_Wang_Yiqun_Thesis.docx file_size: 25798848 relation: source_file - access_level: open_access checksum: 8d7a2383f66377da675d379ec30ea0fe content_type: application/pdf creator: yiqwang date_created: 2025-08-22T10:32:30Z date_updated: 2026-09-03T22:30:03Z embargo: 2026-09-03 file_id: '20211' file_name: 2025_Wang_Yiqun_Thesis.pdf file_size: 12628313 relation: main_file file_date_updated: 2026-09-03T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20117 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '108' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18063' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: The role of dynamin related protein 2A in cytokinin regulated plant growth and development type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20187' 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. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: LifeSc 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)." article_number: e70396 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Frédérique full_name: Tellier, Frédérique last_name: Tellier - first_name: Adrijana full_name: Smoljan, Adrijana id: cced8a85-223e-11ed-af04-b0596c55053b last_name: Smoljan - first_name: Hana full_name: Rakusova, Hana id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA last_name: Rakusova - first_name: Petr full_name: Valošek, Petr id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87 last_name: Valošek - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jean Denis full_name: Faure, Jean Denis last_name: Faure - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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. Plant Journal. 2025;123(3). doi:10.1111/tpj.70396 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. Plant Journal. Wiley. https://doi.org/10.1111/tpj.70396 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.” Plant Journal. Wiley, 2025. https://doi.org/10.1111/tpj.70396. ieee: D. Babic et al., “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” Plant Journal, vol. 123, no. 3. Wiley, 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.” Plant Journal, vol. 123, no. 3, e70396, Wiley, 2025, doi:10.1111/tpj.70396. 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). corr_author: '1' date_created: 2025-08-17T22:01:36Z date_published: 2025-08-01T00:00:00Z date_updated: 2026-10-18T22:31:20Z day: '01' ddc: - '580' department: - _id: EvBe - _id: JiFr - _id: GradSch doi: 10.1111/tpj.70396 external_id: isi: - '001547884300001' pmid: - '40782342' file: - access_level: open_access checksum: 1cdc3341d2d23101abca72521f1f23cb content_type: application/pdf creator: dernst date_created: 2025-09-01T14:09:31Z date_updated: 2025-09-01T14:09:31Z file_id: '20264' file_name: 2025_PlantJournal_Babic.pdf file_size: 5791111 relation: main_file success: 1 file_date_updated: 2025-09-01T14:09:31Z fulldoi: https://doi.org/10.1111/tpj.70396 has_accepted_license: '1' intvolume: ' 123' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis publication: Plant Journal publication_identifier: eissn: - 1365-313X issn: - 0960-7412 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '20362' relation: dissertation_contains status: public scopus_import: '1' status: public title: Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2025' ... --- OA_place: publisher _id: '20362' 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." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic citation: ama: Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:10.15479/AT-ISTA-20362 apa: Babic, D. (2025). Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20362 chicago: Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20362. ieee: 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. mla: Babic, David. Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20362. short: D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-17T13:28:01Z date_published: 2025-09-18T00:00:00Z date_updated: 2026-10-16T07:59:32Z day: '18' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: EvBe doi: 10.15479/AT-ISTA-20362 doi_confirm: '1' file: - access_level: open_access checksum: 5ecf274281a54a41e0288bc79edf7492 content_type: application/pdf creator: dbabic date_created: 2025-09-24T13:43:14Z date_updated: 2026-09-25T22:30:02Z embargo: 2026-09-25 file_id: '20388' file_name: 2025_David_Babic_Thesis.pdf file_size: 7501548 relation: main_file - access_level: closed checksum: 2703e548390de0a1af7a707137e8ab3b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dbabic date_created: 2025-09-24T13:43:14Z date_updated: 2026-09-25T22:30:02Z embargo_to: open_access file_id: '20389' file_name: Thesis_Babic_draft.docx file_size: 23206052 relation: source_file file_date_updated: 2026-09-25T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20362 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '116' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20187' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository _id: '21427' 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. acknowledgement: "European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360" article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Erik full_name: Sahai, Erik last_name: Sahai - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. doi:10.1101/2025.05.20.655037 apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., & Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. https://doi.org/10.1101/2025.05.20.655037 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.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.20.655037. ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” bioRxiv. . 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, 10.1101/2025.05.20.655037. mla: Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” BioRxiv, doi:10.1101/2025.05.20.655037. short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-03-11T08:40:06Z date_published: 2025-09-25T00:00:00Z date_updated: 2026-10-18T22:31:19Z day: '25' ddc: - '539' - '570' department: - _id: GradSch - _id: EdHa - _id: MiSi - _id: NanoFab - _id: AnSa doi: 10.1101/2025.05.20.655037 fulldoi: https://doi.org/10.1101/2025.05.20.655037 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.20.655037 month: '09' oa: 1 oa_version: Preprint project: - _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd grant_number: '101071793' name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces' - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication: bioRxiv publication_status: draft related_material: record: - id: '21439' relation: research_data status: public - id: '22963' relation: later_version status: public - id: '21423' relation: dissertation_contains status: public status: public title: Substrate heterogeneity promotes cancer cell dissemination through interface roughening tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20393' abstract: - lang: eng 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. " acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi orcid: 0000-0001-6060-4795 citation: ama: Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:10.15479/AT-ISTA-20393 apa: Kishi, K. (2025). Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20393 chicago: Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20393. ieee: 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. Regulation of Notochord and Floor Plate Size during Mouse Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20393. short: K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-25T10:08:10Z date_published: 2025-09-24T00:00:00Z date_updated: 2026-10-16T08:31:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi - _id: EdHa doi: 10.15479/AT-ISTA-20393 doi_confirm: '1' file: - access_level: closed checksum: 6bb5a7ce318dc3f7bd165f2523e77b89 content_type: application/x-zip-compressed creator: kkishi date_created: 2025-09-30T14:33:17Z date_updated: 2026-09-30T22:30:04Z embargo_to: open_access file_id: '20413' file_name: 2025-Kishi-Kasumi-Thesis.zip file_size: 41847994 relation: source_file - access_level: open_access checksum: 88349b9177e1dcbe1242cd3884b36fdb content_type: application/pdf creator: kkishi date_created: 2025-09-30T14:33:22Z date_updated: 2026-09-30T22:30:04Z embargo: 2026-09-30 file_id: '20414' file_name: 2025-Kishi-Kasumi-Thesis.pdf file_size: 55747072 relation: main_file file_date_updated: 2026-09-30T22:30:04Z fulldoi: https://doi.org/10.15479/AT-ISTA-20393 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18481' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Regulation of notochord and floor plate size during mouse development tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20364' abstract: - lang: eng 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. " acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "Plant Facility,\r\nProtein Service Facility" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini citation: ama: Giannini C. Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. 2025. doi:10.15479/AT-ISTA-20364 apa: Giannini, C. (2025). Nuclear and cell surface auxin signaling in A. thaliana developmental transitions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20364 chicago: Giannini, Caterina. “Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20364. ieee: 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. Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20364. short: C. Giannini, Nuclear and Cell Surface Auxin Signaling in A. Thaliana Developmental Transitions, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-19T12:23:38Z date_published: 2025-09-19T00:00:00Z date_updated: 2026-10-16T08:24:09Z day: '19' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: MaLo doi: 10.15479/AT-ISTA-20364 doi_confirm: '1' file: - access_level: open_access checksum: 536ba1701453b0b2346be14c046b2911 content_type: application/pdf creator: cgiannin date_created: 2025-09-24T14:46:34Z date_updated: 2026-09-30T22:30:03Z embargo: 2026-09-30 file_id: '20390' file_name: 2025_Giannini_Caterina_Thesis...pdf file_size: 14278965 relation: main_file - access_level: closed checksum: 192f55262f2da2ea0a59d9c23a1b8573 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cgiannin date_created: 2025-09-24T14:46:35Z date_updated: 2026-09-30T22:30:03Z embargo_to: open_access file_id: '20391' file_name: 2025_Giannini_Caterina_Thesis...docx file_size: 24499022 relation: source_file file_date_updated: 2026-09-30T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20364 has_accepted_license: '1' keyword: - Auxin Signaling - Plant Development language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '151' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '19399' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Nuclear and cell surface auxin signaling in A. thaliana developmental transitions type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '19399' abstract: - lang: eng 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. acknowledged_ssus: - _id: Bio - _id: LifeSc 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).' article_processing_charge: No author: - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Yongfan full_name: Yu, Yongfan last_name: Yu - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Meng full_name: Chen, Meng last_name: Chen - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Maria Mar full_name: Marques-Bueno, Maria Mar last_name: Marques-Bueno - first_name: Zainab full_name: Quddoos, Zainab id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466 last_name: Quddoos - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Yvon full_name: Jaillais, Yvon last_name: Jaillais - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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. bioRxiv. doi:10.1101/2022.11.30.518503 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. bioRxiv. https://doi.org/10.1101/2022.11.30.518503 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.” BioRxiv, n.d. https://doi.org/10.1101/2022.11.30.518503. ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” bioRxiv. . 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, 10.1101/2022.11.30.518503. mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” BioRxiv, doi:10.1101/2022.11.30.518503. 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.). corr_author: '1' das_tickbox: '1' date_created: 2025-03-13T08:36:48Z date_published: 2025-02-20T00:00:00Z date_updated: 2026-10-18T22:31:21Z day: '20' ddc: - '580' department: - _id: JiFr - _id: XiFe doi: 10.1101/2022.11.30.518503 ec_funded: 1 fulldoi: https://doi.org/10.1101/2022.11.30.518503 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2022.11.30.518503 month: '02' oa: 1 oa_version: Published Version project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26060676-B435-11E9-9278-68D0E5697425 grant_number: ALTF 985-2016 name: Cell surface receptor complexes for auxin signaling in plants publication: bioRxiv publication_status: draft related_material: record: - id: '20656' relation: later_version status: public - id: '19395' relation: dissertation_contains status: public - id: '20364' relation: dissertation_contains status: public status: public title: ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20415' acknowledged_ssus: - _id: LifeSc - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 citation: ama: Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:10.15479/AT-ISTA-20415 apa: Lee, S. (2025). Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20415 chicago: Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20415. ieee: 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. Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20415. short: S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-01T09:04:00Z date_published: 2025-10-01T00:00:00Z date_updated: 2026-10-16T09:31:49Z day: '01' ddc: - '540' degree_awarded: PhD department: - _id: GradSch - _id: MaIb doi: 10.15479/AT-ISTA-20415 file: - access_level: closed checksum: fa6d5946feb37b678ee1c6dffb4fa167 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: slee date_created: 2025-10-03T12:29:43Z date_updated: 2026-10-03T22:30:02Z embargo_to: open_access file_id: '20420' file_name: 2025_Lee_Seungho_Thesis.docx file_size: 88706648 relation: source_file - access_level: open_access checksum: c5ba6d464113ad0c5812a9d24b539b86 content_type: application/pdf creator: slee date_created: 2025-10-03T12:29:25Z date_updated: 2026-10-03T22:30:02Z embargo: 2026-10-03 file_id: '20421' file_name: 2025_Lee_Seungho_Thesis__.pdf file_size: 14587276 relation: main_file file_date_updated: 2026-10-03T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20415 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '144' project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12237' relation: part_of_dissertation status: public - id: '15357' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Loredana full_name: Protesescu, Loredana last_name: Protesescu - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 title: Nanoparticle-based precursors toward advanced crystalline inorganic solids type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: repository OA_type: green _id: '22026' 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 article_type: original arxiv: 1 author: - first_name: Andreia full_name: Chapouto, Andreia last_name: Chapouto - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: ama: 'Chapouto A, Killip R, Vişan M. Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. Duke Mathematical Journal. 2024;173(7):1227-1267. doi:10.1215/00127094-2023-0035' apa: 'Chapouto, A., Killip, R., & Vişan, M. (2024). Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2023-0035' chicago: 'Chapouto, Andreia, Rowan Killip, and Monica Vişan. “Bounded Solutions of KdV: Uniqueness and the Loss of Almost Periodicity.” Duke Mathematical Journal. Duke University Press, 2024. https://doi.org/10.1215/00127094-2023-0035.' ieee: 'A. Chapouto, R. Killip, and M. Vişan, “Bounded solutions of KdV: Uniqueness and the loss of almost periodicity,” Duke Mathematical Journal, vol. 173, no. 7. Duke University Press, pp. 1227–1267, 2024.' 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.' mla: 'Chapouto, Andreia, et al. “Bounded Solutions of KdV: Uniqueness and the Loss of Almost Periodicity.” Duke Mathematical Journal, vol. 173, no. 7, Duke University Press, 2024, pp. 1227–67, doi:10.1215/00127094-2023-0035.' short: A. Chapouto, R. Killip, M. Vişan, Duke Mathematical Journal 173 (2024) 1227–1267. das_tickbox: '1' date_created: 2026-06-19T07:34:05Z date_published: 2024-05-15T00:00:00Z date_updated: 2026-06-22T10:32:25Z day: '15' doi: 10.1215/00127094-2023-0035 extern: '1' external_id: arxiv: - '2209.07501' fulldoi: https://doi.org/10.1215/00127094-2023-0035 intvolume: ' 173' issue: '7' keyword: - Almost-periodic solutions - Korteweg–de Vries - unconditional uniqueness language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2209.07501 month: '05' oa: 1 oa_version: Preprint page: 1227-1267 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Bounded solutions of KdV: Uniqueness and the loss of almost periodicity' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 173 year: '2024' ... --- _id: '12875' 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. acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: LifeSc - _id: PreCl 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. " article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Thomas full_name: Krausgruber, Thomas last_name: Krausgruber - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Martin full_name: Schrammel, Martin id: f13e7cae-e8bd-11ed-841a-96dedf69f46d last_name: Schrammel - first_name: Natalie Y full_name: Özgen, Natalie Y id: e68ece33-f6e0-11ea-865d-ae1031dcc090 last_name: Özgen - first_name: Alexis full_name: Ivec, Alexis id: 1d144691-e8be-11ed-9b33-bdd3077fad4c last_name: Ivec - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009 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. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009 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.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009. ieee: G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024. 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. mla: Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009. 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. corr_author: '1' date_created: 2023-04-27T09:41:48Z date_published: 2024-01-17T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '17' ddc: - '570' department: - _id: SiHi - _id: RySh doi: 10.1016/j.neuron.2023.11.009 external_id: isi: - '001163937900001' pmid: - '38096816' file: - access_level: open_access checksum: 32b3788f7085cf44a84108d8faaff3ce content_type: application/pdf creator: dernst date_created: 2024-02-06T13:56:15Z date_updated: 2024-02-06T13:56:15Z file_id: '14944' file_name: 2024_Neuron_Cheung.pdf file_size: 5942467 relation: main_file success: 1 file_date_updated: 2024-02-06T13:56:15Z fulldoi: https://doi.org/10.1016/j.neuron.2023.11.009 has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 230-246.e11 pmid: 1 project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/the-pedigree-of-brain-cells/ scopus_import: '1' status: public title: Multipotent progenitors instruct ontogeny of the superior colliculus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2024' ... --- OA_place: repository OA_type: green _id: '20838' 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." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Pierre full_name: Berger, Pierre last_name: Berger - first_name: Nicolaz full_name: Gourmelon, Nicolaz last_name: Gourmelon - first_name: Mathieu full_name: Helfter, Mathieu id: 7d296fbe-e2c6-11ee-84d3-d5c2945f9a57 last_name: Helfter citation: ama: Berger P, Gourmelon N, Helfter M. Every diffeomorphism is a total renormalization of a close to identity map. Inventiones mathematicae. 2024;239(2):431-468. doi:10.1007/s00222-024-01305-w apa: Berger, P., Gourmelon, N., & Helfter, M. (2024). Every diffeomorphism is a total renormalization of a close to identity map. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-024-01305-w chicago: Berger, Pierre, Nicolaz Gourmelon, and Mathieu Helfter. “Every Diffeomorphism Is a Total Renormalization of a Close to Identity Map.” Inventiones Mathematicae. Springer Nature, 2024. https://doi.org/10.1007/s00222-024-01305-w. ieee: P. Berger, N. Gourmelon, and M. Helfter, “Every diffeomorphism is a total renormalization of a close to identity map,” Inventiones mathematicae, vol. 239, no. 2. Springer Nature, pp. 431–468, 2024. 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. mla: Berger, Pierre, et al. “Every Diffeomorphism Is a Total Renormalization of a Close to Identity Map.” Inventiones Mathematicae, vol. 239, no. 2, Springer Nature, 2024, pp. 431–68, doi:10.1007/s00222-024-01305-w. short: P. Berger, N. Gourmelon, M. Helfter, Inventiones Mathematicae 239 (2024) 431–468. date_created: 2025-12-19T10:15:13Z date_published: 2024-12-19T00:00:00Z date_updated: 2025-12-29T12:03:10Z day: '19' doi: 10.1007/s00222-024-01305-w extern: '1' external_id: arxiv: - '2210.09064' fulldoi: https://doi.org/10.1007/s00222-024-01305-w intvolume: ' 239' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2210.09064 month: '12' oa: 1 oa_version: Preprint page: 431-468 publication: Inventiones mathematicae publication_identifier: eissn: - 1432-1297 issn: - 0020-9910 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Every diffeomorphism is a total renormalization of a close to identity map type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 239 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20961' 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Yulong full_name: Jin, Yulong last_name: Jin - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Juntian full_name: Wu, Juntian last_name: Wu - first_name: Armin full_name: Kiani, Armin last_name: Kiani - first_name: Rui full_name: Zhao, Rui last_name: Zhao - first_name: Ivan full_name: Huc, Ivan last_name: Huc - first_name: Sijbren full_name: Otto, Sijbren last_name: Otto citation: ama: Jin Y, Mandal PK, Wu J, et al. Light-mediated interconversion between a foldamer and a self-replicator. Journal of the American Chemical Society. 2024;146(49):33395-33402. doi:10.1021/jacs.4c09114 apa: Jin, Y., Mandal, P. K., 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. American Chemical Society. https://doi.org/10.1021/jacs.4c09114 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.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.4c09114. ieee: Y. Jin et al., “Light-mediated interconversion between a foldamer and a self-replicator,” Journal of the American Chemical Society, vol. 146, no. 49. American Chemical Society, pp. 33395–33402, 2024. 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. mla: Jin, Yulong, et al. “Light-Mediated Interconversion between a Foldamer and a Self-Replicator.” Journal of the American Chemical Society, vol. 146, no. 49, American Chemical Society, 2024, pp. 33395–402, doi:10.1021/jacs.4c09114. 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. date_created: 2026-01-08T07:05:57Z date_published: 2024-11-26T00:00:00Z date_updated: 2026-01-19T11:03:31Z day: '26' ddc: - '540' doi: 10.1021/jacs.4c09114 extern: '1' external_id: pmid: - '39590511' fulldoi: https://doi.org/10.1021/jacs.4c09114 has_accepted_license: '1' intvolume: ' 146' issue: '49' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/jacs.4c09114 month: '11' oa: 1 oa_version: Published Version page: 33395-33402 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Light-mediated interconversion between a foldamer and a self-replicator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20962' abstract: - lang: eng 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ankush full_name: Sood, Ankush last_name: Sood - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Jim full_name: Ottelé, Jim last_name: Ottelé - first_name: Juntian full_name: Wu, Juntian last_name: Wu - first_name: Marcel full_name: Eleveld, Marcel last_name: Eleveld - first_name: Joydev full_name: Hatai, Joydev last_name: Hatai - first_name: Charalampos G. full_name: Pappas, Charalampos G. last_name: Pappas - first_name: Ivan full_name: Huc, Ivan last_name: Huc - first_name: Sijbren full_name: Otto, Sijbren last_name: Otto citation: 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. Journal of the American Chemical Society. 2024;146(49):33386-33394. doi:10.1021/jacs.4c09111 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. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.4c09111 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.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.4c09111. ieee: A. Sood et al., “Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry,” Journal of the American Chemical Society, vol. 146, no. 49. American Chemical Society, pp. 33386–33394, 2024. 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.” Journal of the American Chemical Society, vol. 146, no. 49, American Chemical Society, 2024, pp. 33386–94, doi:10.1021/jacs.4c09111. 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. date_created: 2026-01-08T07:06:27Z date_published: 2024-11-26T00:00:00Z date_updated: 2026-01-19T10:57:53Z day: '26' doi: 10.1021/jacs.4c09111 extern: '1' external_id: pmid: - '39590110' fulldoi: https://doi.org/10.1021/jacs.4c09111 has_accepted_license: '1' intvolume: ' 146' issue: '49' keyword: - Fibers - Foldamers - Macrocycles - Monomers - Peptides - Proteins language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/jacs.4c09111 month: '11' oa: 1 oa_version: Published Version page: 33386-33394 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20967' 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sunbum full_name: Kwon, Sunbum last_name: Kwon - first_name: Vasily full_name: Morozov, Vasily last_name: Morozov - first_name: Lingfei full_name: Wang, Lingfei last_name: Wang - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Stéphane full_name: Chaignepain, Stéphane last_name: Chaignepain - first_name: Céline full_name: Douat, Céline last_name: Douat - first_name: Ivan full_name: Huc, Ivan last_name: Huc citation: ama: Kwon S, Morozov V, Wang L, et al. Interrogating the potential of helical aromatic foldamers for protein recognition. Organic & Biomolecular Chemistry. 2024;22(48):9342-9347. doi:10.1039/d4ob01436g apa: Kwon, S., Morozov, V., Wang, L., Mandal, P. K., Chaignepain, S., Douat, C., & Huc, I. (2024). Interrogating the potential of helical aromatic foldamers for protein recognition. Organic & Biomolecular Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/d4ob01436g 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.” Organic & Biomolecular Chemistry. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4ob01436g. ieee: S. Kwon et al., “Interrogating the potential of helical aromatic foldamers for protein recognition,” Organic & Biomolecular Chemistry, vol. 22, no. 48. Royal Society of Chemistry, pp. 9342–9347, 2024. 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 & Biomolecular Chemistry. 22(48), 9342–9347. mla: Kwon, Sunbum, et al. “Interrogating the Potential of Helical Aromatic Foldamers for Protein Recognition.” Organic & Biomolecular Chemistry, vol. 22, no. 48, Royal Society of Chemistry, 2024, pp. 9342–47, doi:10.1039/d4ob01436g. short: S. Kwon, V. Morozov, L. Wang, P.K. Mandal, S. Chaignepain, C. Douat, I. Huc, Organic & Biomolecular Chemistry 22 (2024) 9342–9347. date_created: 2026-01-11T14:32:23Z date_published: 2024-10-30T00:00:00Z date_updated: 2026-01-20T06:56:44Z day: '30' doi: 10.1039/d4ob01436g extern: '1' external_id: pmid: - '39501876' fulldoi: https://doi.org/10.1039/d4ob01436g has_accepted_license: '1' intvolume: ' 22' issue: '48' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1039/D4OB01436G month: '10' oa: 1 oa_version: Published Version page: 9342-9347 pmid: 1 publication: Organic & Biomolecular Chemistry publication_identifier: eissn: - 1477-0539 issn: - 1477-0520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Interrogating the potential of helical aromatic foldamers for protein recognition tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21064' 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. 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.' article_number: '92' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Ivo full_name: Labbe, Ivo last_name: Labbe - first_name: Jenny E. full_name: Greene, 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 - first_name: Andy D. full_name: Goulding, Andy D. last_name: Goulding - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Pascal A. full_name: Oesch, Pascal A. last_name: Oesch - first_name: Hakim full_name: Atek, Hakim last_name: Atek - first_name: Gabriel full_name: Brammer, Gabriel last_name: Brammer - first_name: Iryna full_name: Chemerynska, Iryna last_name: Chemerynska - first_name: Dan full_name: Coe, Dan last_name: Coe - first_name: Sam E. full_name: Cutler, Sam E. last_name: Cutler - first_name: Pratika full_name: Dayal, Pratika last_name: Dayal - first_name: Robert full_name: Feldmann, Robert last_name: Feldmann - first_name: Marijn full_name: Franx, Marijn last_name: Franx - first_name: Karl full_name: Glazebrook, Karl last_name: Glazebrook - first_name: Joel full_name: Leja, Joel last_name: Leja - first_name: Michael full_name: Maseda, Michael last_name: Maseda - first_name: Danilo full_name: Marchesini, Danilo last_name: Marchesini - first_name: Themiya full_name: Nanayakkara, Themiya last_name: Nanayakkara - first_name: Erica J. full_name: Nelson, Erica J. last_name: Nelson - first_name: Richard full_name: Pan, Richard last_name: Pan - first_name: Casey full_name: Papovich, Casey last_name: Papovich - first_name: Sedona H. full_name: Price, Sedona H. last_name: Price - first_name: Katherine A. full_name: Suess, Katherine A. last_name: Suess - first_name: Bingjie 冰洁 full_name: Wang, Bingjie 冰洁 last_name: Wang - first_name: John R. full_name: Weaver, John R. last_name: Weaver - first_name: Katherine E. full_name: Whitaker, Katherine E. last_name: Whitaker - first_name: Christina C. full_name: Williams, Christina C. last_name: Williams - first_name: Adi full_name: Zitrin, Adi last_name: Zitrin citation: ama: 'Labbe I, Greene JE, Bezanson R, et al. UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA. The Astrophysical Journal. 2024;978. doi:10.3847/1538-4357/ad3551' 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 < z < 7 with JWST and ALMA. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad3551' 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 < z < 7 with JWST and ALMA.” The Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad3551.' ieee: 'I. Labbe et al., “UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA,” The Astrophysical Journal, vol. 978. IOP Publishing, 2024.' 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 < z < 7 with JWST and ALMA. The Astrophysical Journal. 978, 92.' mla: 'Labbe, Ivo, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 < z < 7 with JWST and ALMA.” The Astrophysical Journal, vol. 978, 92, IOP Publishing, 2024, doi:10.3847/1538-4357/ad3551.' 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). date_created: 2026-01-28T15:26:12Z date_published: 2024-12-26T00:00:00Z date_updated: 2026-02-10T06:49:49Z day: '26' ddc: - '520' department: - _id: JoMa doi: 10.3847/1538-4357/ad3551 external_id: arxiv: - '2306.07320' file: - access_level: open_access checksum: 825c35ebd26e292c8a5c2bffac327854 content_type: application/pdf creator: dernst date_created: 2026-02-10T06:44:24Z date_updated: 2026-02-10T06:44:24Z file_id: '21201' file_name: 2024_AstrophysicalJourn_Labbe.pdf file_size: 5041924 relation: main_file success: 1 file_date_updated: 2026-02-10T06:44:24Z fulldoi: https://doi.org/10.3847/1538-4357/ad3551 has_accepted_license: '1' intvolume: ' 978' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 978 year: '2024' ... --- OA_place: repository OA_type: green _id: '21304' abstract: - lang: eng text: No description provided. article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral citation: ama: 'Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024. doi:10.5281/ZENODO.13934991' apa: 'Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples. Zenodo. https://doi.org/10.5281/ZENODO.13934991' chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.13934991.' ieee: 'M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo, 2024.' ista: 'Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples, Zenodo, 10.5281/ZENODO.13934991.' mla: 'Santana de Freitas Amaral, Miguel. Archaeal_membranes : Code and Examples. Zenodo, 2024, doi:10.5281/ZENODO.13934991.' short: M. Santana de Freitas Amaral, (2024). corr_author: '1' date_created: 2026-02-17T12:52:26Z date_published: 2024-10-15T00:00:00Z date_updated: 2026-02-23T11:49:05Z day: '15' department: - _id: AnSa doi: 10.5281/ZENODO.13934991 fulldoi: https://doi.org/10.5281/ZENODO.13934991 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.13934991 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '21251' relation: used_for_analysis_in status: public status: public title: 'archaeal_membranes : code and examples' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21528' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Gaurav full_name: Arya, Gaurav last_name: Arya - first_name: William F. full_name: Li, William F. last_name: Li - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić - first_name: Steven G. full_name: Johnson, Steven G. last_name: Johnson - first_name: Zin full_name: Lin, Zin last_name: Lin citation: 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. ACS Photonics. 2024;11(5):2077-2087. doi:10.1021/acsphotonics.4c00259 apa: Arya, G., Li, W. F., Roques-Carmes, C., Soljačić, M., Johnson, S. G., & Lin, Z. (2024). End-to-end optimization of metasurfaces for imaging with compressed sensing. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.4c00259 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.” ACS Photonics. American Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00259. 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,” ACS Photonics, vol. 11, no. 5. American Chemical Society, pp. 2077–2087, 2024. 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.” ACS Photonics, vol. 11, no. 5, American Chemical Society, 2024, pp. 2077–87, doi:10.1021/acsphotonics.4c00259. short: G. Arya, W.F. Li, C. Roques-Carmes, M. Soljačić, S.G. Johnson, Z. Lin, ACS Photonics 11 (2024) 2077–2087. date_created: 2026-03-30T12:22:47Z date_published: 2024-04-23T00:00:00Z date_updated: 2026-04-27T09:03:21Z day: '23' ddc: - '530' doi: 10.1021/acsphotonics.4c00259 extern: '1' external_id: arxiv: - '2201.12348' fulldoi: https://doi.org/10.1021/acsphotonics.4c00259 intvolume: ' 11' issue: '5' keyword: - end-to-end - optimization - metasurface - imaging - compressed sensing language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2201.12348 month: '04' oa: 1 oa_version: Preprint page: 2077-2087 publication: ACS Photonics publication_identifier: eissn: - 2330-4022 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: End-to-end optimization of metasurfaces for imaging with compressed sensing type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 11 year: '2024' ... --- OA_place: repository OA_type: green _id: '21529' abstract: - lang: eng 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.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Nicholas full_name: Rivera, Nicholas last_name: Rivera - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. ACS Photonics. 2024;11(8):3401-3411. doi:10.1021/acsphotonics.4c00908 apa: Karnieli, A., Roques-Carmes, C., Rivera, N., & Fan, S. (2024). Strong coupling and single-photon nonlinearity in free-electron quantum optics. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.4c00908 chicago: Karnieli, Aviv, Charles Roques-Carmes, Nicholas Rivera, and Shanhui Fan. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” ACS Photonics. American Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00908. ieee: A. Karnieli, C. Roques-Carmes, N. Rivera, and S. Fan, “Strong coupling and single-photon nonlinearity in free-electron quantum optics,” ACS Photonics, vol. 11, no. 8. American Chemical Society, pp. 3401–3411, 2024. 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. mla: Karnieli, Aviv, et al. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” ACS Photonics, vol. 11, no. 8, American Chemical Society, 2024, pp. 3401–11, doi:10.1021/acsphotonics.4c00908. short: A. Karnieli, C. Roques-Carmes, N. Rivera, S. Fan, ACS Photonics 11 (2024) 3401–3411. date_created: 2026-03-30T12:22:47Z date_published: 2024-07-29T00:00:00Z date_updated: 2026-04-27T10:30:37Z day: '29' ddc: - '530' doi: 10.1021/acsphotonics.4c00908 extern: '1' external_id: arxiv: - '2403.13071' fulldoi: https://doi.org/10.1021/acsphotonics.4c00908 intvolume: ' 11' issue: '8' keyword: - quantum optics - free electrons - single photon nonlinearity - electron-photon interaction language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2403.13071 month: '07' oa: 1 oa_version: Preprint page: 3401-3411 publication: ACS Photonics publication_identifier: eissn: - 2330-4022 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Strong coupling and single-photon nonlinearity in free-electron quantum optics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2024' ...