[{"type":"preprint","project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"article_processing_charge":"No","oa_version":"Preprint","doi":"10.48550/ARXIV.2203.17143","_id":"14597","abstract":[{"lang":"eng","text":"Phase-field models such as the Allen-Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen-Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow.\r\nIn the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: As long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen-Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε1/2).\r\nOur approach is based on the gradient flow structure of the Allen-Cahn equation and its limiting motion: Building on the recent concept of \"gradient flow calibrations\" for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen-Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen-Cahn operator or additional convergence hypotheses for the energy at positive times."}],"arxiv":1,"publication":"arXiv","status":"public","article_number":"2203.17143","date_updated":"2026-08-12T09:15:49Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>.","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, 2203.17143, doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>.","ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow,” <i>arXiv</i>. .","apa":"Fischer, J. L., &#38; Marveggio, A. (n.d.). Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>","ista":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv, 2203.17143.","short":"J.L. Fischer, A. Marveggio, ArXiv (n.d.)."},"department":[{"_id":"JuFi"}],"corr_author":"1","external_id":{"arxiv":["2203.17143"]},"publication_status":"draft","related_material":{"record":[{"status":"public","id":"14587","relation":"dissertation_contains"},{"status":"public","id":"17481","relation":"later_version"}]},"date_published":"2022-03-31T00:00:00Z","title":"Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.17143"}],"day":"31","year":"2022","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio","full_name":"Marveggio, Alice"}],"date_created":"2023-11-23T09:30:02Z","month":"03","language":[{"iso":"eng"}],"ec_funded":1},{"file_date_updated":"2023-01-27T10:36:50Z","day":"01","volume":149,"month":"11","language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","_id":"12231","abstract":[{"text":"Ventral tail bending, which is transient but pronounced, is found in many chordate embryos and constitutes an interesting model of how tissue interactions control embryo shape. Here, we identify one key upstream regulator of ventral tail bending in embryos of the ascidian Ciona. We show that during the early tailbud stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates. We further show that interfering with the function of the BMP ligand Admp led to pMLC localizing to the basal instead of the apical side of ventral epidermal cells and a reduced number of boat cells. Finally, we show that cutting ventral epidermal midline cells at their apex using an ultraviolet laser relaxed ventral tail bending. Based on these results, we propose a previously unreported function for Admp in localizing pMLC to the apical side of ventral epidermal cells, which causes the tail to bend ventrally by resisting antero-posterior notochord extension at the ventral side of the tail.","lang":"eng"}],"doi":"10.1242/dev.200215","type":"journal_article","publication":"Development","acknowledgement":"iona intestinalis adults were provided by Dr Yutaka Satou (Kyoto University) and Dr Manabu Yoshida (the University of Tokyo) with support from the National Bio-Resource Project of AMED, Japan. We thank Dr Hidehiko Hashimoto and Dr Yuji Mizotani for technical information about 1P-myosin antibody staining. We thank Dr Kaoru Imai and Dr Yutaka Satou for valuable discussion about Admp and for the DNA construct of Bmp2/4 under the Dlx.b upstream sequence. We thank Ms Maki Kogure for constructing the FUSION360 of the intercalating epidermal cell.\r\nThis work was supported by funding from the Japan Society for the Promotion of Science (JP16H01451, JP21H00440). Open Access funding provided by Keio University: Keio Gijuku Daigaku.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_updated":"2026-08-12T09:59:24Z","citation":{"short":"Y.S. Kogure, H. Muraoka, W.C. Koizumi, R. Gelin-alessi, B.G. Godard, K. Oka, C.-P.J. Heisenberg, K. Hotta, Development 149 (2022).","ista":"Kogure YS, Muraoka H, Koizumi WC, Gelin-alessi R, Godard BG, Oka K, Heisenberg C-PJ, Hotta K. 2022. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. Development. 149(21), dev200215.","apa":"Kogure, Y. S., Muraoka, H., Koizumi, W. C., Gelin-alessi, R., Godard, B. G., Oka, K., … Hotta, K. (2022). Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>","ieee":"Y. S. Kogure <i>et al.</i>, “Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona,” <i>Development</i>, vol. 149, no. 21. Company of Biologists, 2022.","ama":"Kogure YS, Muraoka H, Koizumi WC, et al. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. 2022;149(21). doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>","mla":"Kogure, Yuki S., et al. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>, vol. 149, no. 21, dev200215, Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>.","chicago":"Kogure, Yuki S., Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi, Benoit G Godard, Kotaro Oka, Carl-Philipp J Heisenberg, and Kohji Hotta. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>. Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>."},"date_published":"2022-11-01T00:00:00Z","article_type":"original","scopus_import":"1","title":"Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona","issue":"21","publisher":"Company of Biologists","author":[{"last_name":"Kogure","full_name":"Kogure, Yuki S.","first_name":"Yuki S."},{"first_name":"Hiromochi","full_name":"Muraoka, Hiromochi","last_name":"Muraoka"},{"first_name":"Wataru C.","last_name":"Koizumi","full_name":"Koizumi, Wataru C."},{"first_name":"Raphaël","full_name":"Gelin-alessi, Raphaël","last_name":"Gelin-alessi"},{"id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G","full_name":"Godard, Benoit G","last_name":"Godard"},{"last_name":"Oka","full_name":"Oka, Kotaro","first_name":"Kotaro"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hotta, Kohji","last_name":"Hotta","first_name":"Kohji"}],"keyword":["Developmental Biology","Molecular Biology"],"year":"2022","intvolume":"       149","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"pmid":1,"date_created":"2023-01-16T09:50:12Z","isi":1,"quality_controlled":"1","ddc":["570"],"file":[{"creator":"dernst","checksum":"871b9c58eb79b9e60752de25a46938d6","file_size":9160451,"relation":"main_file","date_created":"2023-01-27T10:36:50Z","success":1,"content_type":"application/pdf","file_name":"2022_Development_Kogure.pdf","date_updated":"2023-01-27T10:36:50Z","access_level":"open_access","file_id":"12423"}],"status":"public","article_number":"dev200215","tmp":{"short":"CC BY (4.0)","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)"},"publication_status":"published","corr_author":"1","external_id":{"pmid":["36227591"],"isi":["000903991700002"]},"has_accepted_license":"1","department":[{"_id":"CaHe"}]},{"type":"journal_article","article_processing_charge":"No","oa_version":"Published Version","_id":"12245","abstract":[{"lang":"eng","text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state."}],"doi":"10.1242/dev.200474","publication":"Development","date_updated":"2026-08-12T09:59:40Z","acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. Company of Biologists, 2022.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>.","chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>.","ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>"},"file_date_updated":"2023-01-30T08:35:44Z","day":"01","volume":149,"month":"10","language":[{"iso":"eng"}],"file":[{"file_size":9348839,"creator":"dernst","checksum":"d7c29b74e9e4032308228cc704a30e88","relation":"main_file","file_name":"2022_Development_Soto.pdf","success":1,"content_type":"application/pdf","date_created":"2023-01-30T08:35:44Z","file_id":"12438","access_level":"open_access","date_updated":"2023-01-30T08:35:44Z"}],"tmp":{"short":"CC BY (4.0)","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)"},"status":"public","article_number":"dev200474","has_accepted_license":"1","department":[{"_id":"AnKi"}],"publication_status":"published","external_id":{"isi":["000918161000003"],"pmid":["36189829"]},"related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"date_published":"2022-10-01T00:00:00Z","title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","issue":"19","scopus_import":"1","article_type":"original","keyword":["Developmental Biology","Molecular Biology"],"year":"2022","intvolume":"       149","publisher":"Company of Biologists","author":[{"first_name":"Ximena","full_name":"Soto, Ximena","last_name":"Soto"},{"first_name":"Joshua","full_name":"Burton, Joshua","last_name":"Burton"},{"first_name":"Cerys S.","last_name":"Manning","full_name":"Manning, Cerys S."},{"last_name":"Minchington","full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"last_name":"Lea","full_name":"Lea, Robert","first_name":"Robert"},{"full_name":"Lee, Jessica","last_name":"Lee","first_name":"Jessica"},{"full_name":"Kursawe, Jochen","last_name":"Kursawe","first_name":"Jochen"},{"first_name":"Magnus","full_name":"Rattray, Magnus","last_name":"Rattray"},{"first_name":"Nancy","full_name":"Papalopulu, Nancy","last_name":"Papalopulu"}],"quality_controlled":"1","isi":1,"date_created":"2023-01-16T09:53:17Z","ddc":["570"],"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"pmid":1},{"intvolume":"        34","year":"2022","author":[{"full_name":"Nauman, Muhammad","last_name":"Nauman","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad"},{"last_name":"Hussain","full_name":"Hussain, Tayyaba","first_name":"Tayyaba"},{"first_name":"Joonyoung","last_name":"Choi","full_name":"Choi, Joonyoung"},{"full_name":"Lee, Nara","last_name":"Lee","first_name":"Nara"},{"full_name":"Choi, Young Jai","last_name":"Choi","first_name":"Young Jai"},{"last_name":"Kang","full_name":"Kang, Woun","first_name":"Woun"},{"last_name":"Jo","full_name":"Jo, Younjung","first_name":"Younjung"}],"publisher":"IOP Publishing","ddc":["530"],"isi":1,"quality_controlled":"1","date_created":"2022-02-06T23:01:31Z","pmid":1,"publication_identifier":{"eissn":["1361-648X"]},"date_published":"2022-01-20T00:00:00Z","issue":"13","title":"Low-field magnetic anisotropy of Sr2IrO4","article_type":"original","scopus_import":"1","department":[{"_id":"KiMo"}],"has_accepted_license":"1","publication_status":"published","external_id":{"pmid":["34986467"],"isi":["000775191800001"]},"file":[{"relation":"main_file","checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","creator":"cchlebak","file_size":1742414,"date_updated":"2022-02-07T10:35:28Z","access_level":"open_access","file_id":"10741","date_created":"2022-02-07T10:35:28Z","success":1,"content_type":"application/pdf","file_name":"2022_JPhysCondensMatter_Nauman.pdf"}],"tmp":{"short":"CC BY (4.0)","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)"},"article_number":"135802","status":"public","volume":34,"day":"20","month":"01","language":[{"iso":"eng"}],"file_date_updated":"2022-02-07T10:35:28Z","date_updated":"2026-08-12T14:03:01Z","oa":1,"acknowledgement":"YJ was supported by the National Research Foundation of Korea (NRF) (Grant Nos. NRF-2018K2A9A1A06069211 and NRF-2019R1A2C1089017). The work at Yonsei was supported by the NRF (Grant Nos. NRF-2017R1A5A-1014862 (SRC program: vdWMRC center), NRF-2019R1A2C2002601, and NRF-2021R1A2C1006375). WK acknowledges the support by the NRF (Grant Nos. 2018R1D1A1B07050087, 2018R1A6A1A03025340).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of Physics: Condensed Matter</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>","chicago":"Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>.","mla":"Nauman, Muhammad, et al. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>, vol. 34, no. 13, 135802, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>.","apa":"Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., &#38; Jo, Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>","ista":"Nauman M, Hussain T, Choi J, Lee N, Choi YJ, Kang W, Jo Y. 2022. Low-field magnetic anisotropy of Sr2IrO4. Journal of Physics: Condensed Matter. 34(13), 135802.","short":"M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal of Physics: Condensed Matter 34 (2022).","ieee":"M. Nauman <i>et al.</i>, “Low-field magnetic anisotropy of Sr2IrO4,” <i>Journal of Physics: Condensed Matter</i>, vol. 34, no. 13. IOP Publishing, 2022."},"type":"journal_article","abstract":[{"lang":"eng","text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of its strong spin–orbit coupling and crystal field effect. In this paper, we present a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for different sample orientations using torque magnetometry measurements in the low-magnetic-field region before the isospins are completely ordered. Dominant in-plane anisotropy was identified at low fields, confirming the b axis as an easy magnetization axis. Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange interaction affecting the OOP interaction. The effect of interlayer exchange interaction results in additional anisotropic terms owing to the tilting of the isospins. The results are relevant for understanding OOP magnetic anisotropy and provide a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic exchange interactions. This study provides insight into the understanding of bulk magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies."}],"_id":"10735","doi":"10.1088/1361-648X/ac484d","oa_version":"Published Version","article_processing_charge":"No","publication":"Journal of Physics: Condensed Matter"},{"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"has_accepted_license":"1","corr_author":"1","publication_status":"submitted","tmp":{"short":"CC BY (4.0)","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)"},"alternative_title":["LIPIcs"],"status":"public","file":[{"content_type":"application/pdf","file_name":"window 1.pdf","date_created":"2022-07-27T09:30:30Z","file_id":"11661","date_updated":"2022-07-27T09:30:30Z","access_level":"open_access","creator":"scultrer","checksum":"95903f9d1649e8e437a967b6f2f64730","file_size":564836,"relation":"main_file"}],"ddc":["510"],"date_created":"2022-07-27T09:31:15Z","quality_controlled":"1","ec_funded":1,"year":"2022","author":[{"first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","last_name":"Biswas"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","related_material":{"record":[{"relation":"dissertation_contains","id":"15094","status":"public"},{"id":"13182","relation":"later_version","status":"public"}]},"date_published":"2022-07-25T00:00:00Z","citation":{"ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>."},"date_updated":"2026-08-13T09:41:58Z","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"LIPIcs","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","grant_number":"Z00342","call_identifier":"FWF"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"type":"journal_article","_id":"11660","abstract":[{"lang":"eng","text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. "}],"article_processing_charge":"No","oa_version":"Submitted Version","language":[{"iso":"eng"}],"month":"07","day":"25","file_date_updated":"2022-07-27T09:30:30Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","date_updated":"2026-08-14T09:33:45Z","citation":{"ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022."},"page":"575-581","article_processing_charge":"No","oa_version":"Submitted Version","doi":"10.1038/s41586-022-05187-x","_id":"12291","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development"}],"type":"journal_article","publication":"Nature","day":"15","volume":609,"language":[{"iso":"eng"}],"month":"09","file_date_updated":"2023-11-02T17:12:37Z","external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"corr_author":"1","publication_status":"published","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"file":[{"file_size":79774945,"checksum":"a6055c606aefb900bf62ae3e7d15f921","creator":"amally","relation":"main_file","date_created":"2023-11-02T17:12:37Z","file_name":"Friml Nature 2022_merged.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-11-02T17:12:37Z","file_id":"14483"}],"status":"public","publisher":"Springer Nature","author":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"full_name":"Monzer, Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328"},{"last_name":"Živanović","full_name":"Živanović, Branka D.","first_name":"Branka D."},{"full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","full_name":"Randuch, Marek","last_name":"Randuch"},{"last_name":"Rýdza","full_name":"Rýdza, Nikola","first_name":"Nikola"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova","full_name":"Teplova, Anastasiia"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"first_name":"Hana","full_name":"Rakusová, Hana","last_name":"Rakusová"}],"year":"2022","intvolume":"       609","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"ec_funded":1,"pmid":1,"quality_controlled":"1","isi":1,"date_created":"2023-01-16T10:04:48Z","ddc":["580"],"date_published":"2022-09-15T00:00:00Z","related_material":{"record":[{"id":"20364","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"19395","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"article_type":"original","scopus_import":"1","issue":"7927","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization"},{"file_date_updated":"2022-05-17T15:19:39Z","month":"05","language":[{"iso":"eng"}],"degree_awarded":"PhD","day":"12","supervisor":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"oa_version":"Published Version","article_processing_charge":"No","doi":"10.15479/at:ista:11362","_id":"11362","abstract":[{"lang":"eng","text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks."}],"citation":{"apa":"Lechner, M. (2022). <i>Learning verifiable representations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","ama":"Lechner M. Learning verifiable representations. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>.","mla":"Lechner, Mathias. <i>Learning Verifiable Representations</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>."},"page":"124","date_updated":"2026-08-19T09:28:05Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Learning verifiable representations","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11366"},{"relation":"part_of_dissertation","id":"7808","status":"public"},{"id":"10666","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10667"},{"status":"public","relation":"part_of_dissertation","id":"10665"}]},"date_published":"2022-05-12T00:00:00Z","date_created":"2022-05-12T07:14:01Z","ddc":["004"],"ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-017-6"]},"year":"2022","keyword":["neural networks","verification","machine learning"],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"status":"public","file":[{"date_created":"2022-05-13T12:33:26Z","content_type":"application/zip","file_name":"src.zip","access_level":"closed","date_updated":"2022-05-13T12:49:00Z","file_id":"11378","creator":"mlechner","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","file_size":13210143,"relation":"source_file"},{"access_level":"open_access","date_updated":"2022-05-17T15:19:39Z","file_id":"11382","date_created":"2022-05-16T08:02:28Z","file_name":"thesis_main-a2.pdf","content_type":"application/pdf","relation":"main_file","file_size":2732536,"checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","creator":"mlechner"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","corr_author":"1"},{"issue":"3","title":"Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.07287"}],"date_published":"2022-03-26T00:00:00Z","researchdata_availability":"no","isi":1,"quality_controlled":"1","date_created":"2022-02-20T23:01:30Z","publication_identifier":{"issn":["0001-8708"],"eissn":["1090-2082"]},"supplementarymaterial":"no","intvolume":"       398","das_tickbox":"0","year":"2022","author":[{"first_name":"Yang","last_name":"Cao","full_name":"Cao, Yang"},{"id":"21f1b52f-2fd1-11eb-a347-a4cdb9b18a51","first_name":"Zhizhong","full_name":"Huang, Zhizhong","last_name":"Huang"}],"publisher":"Elsevier","article_number":"108236","status":"public","arxiv":1,"department":[{"_id":"TiBr"}],"corr_author":"1","external_id":{"arxiv":["2003.07287"],"isi":["000792517300014"]},"publication_status":"published","month":"03","language":[{"iso":"eng"}],"volume":398,"day":"26","publication":"Advances in Mathematics","type":"journal_article","abstract":[{"lang":"eng","text":"We establish the Hardy-Littlewood property (à la Borovoi-Rudnick) for Zariski open subsets in affine quadrics of the form q(x1,...,xn)=m, where q is a non-degenerate integral quadratic form in  n>3 variables and m is a non-zero integer. This gives asymptotic formulas for the density of integral points taking coprime polynomial values, which is a quantitative version of the arithmetic purity of strong approximation property off infinity for affine quadrics."}],"_id":"10765","doi":"10.1016/j.aim.2022.108236","article_processing_charge":"No","oa_version":"Preprint","citation":{"mla":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>, vol. 398, no. 3, 108236, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>.","chicago":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>.","ama":"Cao Y, Huang Z. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. 2022;398(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>","ieee":"Y. Cao and Z. Huang, “Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics,” <i>Advances in Mathematics</i>, vol. 398, no. 3. Elsevier, 2022.","short":"Y. Cao, Z. Huang, Advances in Mathematics 398 (2022).","apa":"Cao, Y., &#38; Huang, Z. (2022). Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>","ista":"Cao Y, Huang Z. 2022. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. Advances in Mathematics. 398(3), 108236."},"date_updated":"2026-08-19T13:00:41Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We are grateful to Mikhail Borovoi, Zeev Rudnick and Olivier Wienberg for their interest in our\r\nwork. We would like to address our gratitude to Ulrich Derenthal for his generous support at Leibniz Universitat Hannover. We are in debt to Tim Browning for an enlightening discussion and to the anonymous referees for critical comments, which lead to overall improvements of various preliminary versions of this paper. Part of this work was carried out and reported during a visit to the University of Science and Technology of China. We thank Yongqi Liang for offering warm hospitality. The first author was supported by a Humboldt-Forschungsstipendium. The second author was supported by grant DE 1646/4-2 of the Deutsche Forschungsgemeinschaft."},{"department":[{"_id":"TiBr"}],"corr_author":"1","external_id":{"isi":["000844789100001"],"arxiv":["2104.14946"]},"publication_status":"published","status":"public","arxiv":1,"researchdata_availability":"no","quality_controlled":"1","isi":1,"date_created":"2024-05-28T13:39:26Z","publication_identifier":{"eissn":["1730-6264"],"issn":["0065-1036"]},"supplementarymaterial":"no","intvolume":"       204","das_tickbox":"0","year":"2022","author":[{"orcid":"0000-0002-1812-2810","last_name":"Shute","full_name":"Shute, Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L"}],"publisher":"Institute of Mathematics","issue":"4","title":"On the leading constant in the Manin-type conjecture for Campana points","scopus_import":"1","article_type":"original","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2104.14946","open_access":"1"}],"related_material":{"record":[{"id":"12077","relation":"earlier_version","status":"public"}]},"date_published":"2022-08-22T00:00:00Z","page":"317-346","citation":{"mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>Acta Arithmetica</i>, vol. 204, no. 4, Institute of Mathematics, 2022, pp. 317–46, doi:<a href=\"https://doi.org/10.4064/aa210430-1-7\">10.4064/aa210430-1-7</a>.","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>Acta Arithmetica</i>. Institute of Mathematics, 2022. <a href=\"https://doi.org/10.4064/aa210430-1-7\">https://doi.org/10.4064/aa210430-1-7</a>.","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>Acta Arithmetica</i>. 2022;204(4):317-346. doi:<a href=\"https://doi.org/10.4064/aa210430-1-7\">10.4064/aa210430-1-7</a>","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>Acta Arithmetica</i>, vol. 204, no. 4. Institute of Mathematics, pp. 317–346, 2022.","short":"A.L. Shute, Acta Arithmetica 204 (2022) 317–346.","ista":"Shute AL. 2022. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 204(4), 317–346.","apa":"Shute, A. L. (2022). On the leading constant in the Manin-type conjecture for Campana points. <i>Acta Arithmetica</i>. Institute of Mathematics. <a href=\"https://doi.org/10.4064/aa210430-1-7\">https://doi.org/10.4064/aa210430-1-7</a>"},"date_updated":"2026-08-19T12:54:59Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"publication":"Acta Arithmetica","type":"journal_article","_id":"17058","abstract":[{"text":"We compare the Manin-type conjecture for Campana points recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado with an alternative prediction of Browning and Van Valckenborgh in the special case of the orbifold (P1,D), where D=1/2[0]+1/2[1]+1/2[∞]. We find that the two predicted leading constants do not agree, and we discuss whether thin sets could explain this discrepancy. Motivated by this, we provide a counterexample to the Manin-type conjecture for Campana points, by considering orbifolds corresponding to squareful values of binary quadratic forms.","lang":"eng"}],"doi":"10.4064/aa210430-1-7","article_processing_charge":"No","oa_version":"Preprint","language":[{"iso":"eng"}],"month":"08","volume":204,"day":"22"},{"publication":"Physical Review Materials","type":"journal_article","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"_id":"12109","abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"doi":"10.1103/PhysRevMaterials.6.125605","article_processing_charge":"No","oa_version":"Preprint","citation":{"ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022."},"date_updated":"2026-08-21T12:03:48Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"month":"12","language":[{"iso":"eng"}],"volume":6,"day":"29","article_number":"125605","status":"public","arxiv":1,"department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"publication_status":"published","external_id":{"arxiv":["2209.01889"],"isi":["000908384800001"]},"corr_author":"1","issue":"12","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","article_type":"original","scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"related_material":{"record":[{"status":"public","id":"20203","relation":"dissertation_contains"},{"status":"for_moderation","id":"22684","relation":"dissertation_contains"}]},"date_published":"2022-12-29T00:00:00Z","date_created":"2023-01-08T23:00:53Z","isi":1,"quality_controlled":"1","ec_funded":1,"publication_identifier":{"eissn":["2475-9953"]},"intvolume":"         6","year":"2022","author":[{"orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix","last_name":"Pertl","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"},{"id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A"},{"orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B"},{"first_name":"Tobias","last_name":"Cramer","full_name":"Cramer, Tobias"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176"}],"publisher":"American Physical Society"},{"file_date_updated":"2023-04-20T22:30:03Z","degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"04","day":"20","supervisor":[{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"_id":"11196","doi":"10.15479/at:ista:11196","abstract":[{"lang":"eng","text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n"}],"oa_version":"Published Version","article_processing_charge":"No","project":[{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497","call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"type":"dissertation","page":"132","citation":{"short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","apa":"Kim, O. (2022). <i>Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>","mla":"Kim, Olena. <i>Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>.","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_updated":"2026-06-18T10:49:27Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","date_published":"2022-04-20T00:00:00Z","related_material":{"record":[{"id":"7473","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"11222","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"date_created":"2022-04-20T09:47:12Z","OA_place":"publisher","author":[{"full_name":"Kim, Olena","orcid":"0000-0003-2344-1039","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"}],"publisher":"Institute of Science and Technology Austria","year":"2022","status":"public","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"alternative_title":["ISTA Thesis"],"file":[{"file_name":"Olena_KIM_thesis_final.pdf","content_type":"application/pdf","date_created":"2022-04-20T14:21:56Z","file_id":"11220","date_updated":"2023-04-20T22:30:03Z","access_level":"open_access","embargo":"2023-04-19","file_size":21273537,"creator":"okim","checksum":"1616a8bf6f13a57c892dac873dcd0936","relation":"main_file"},{"date_created":"2022-04-20T14:22:56Z","content_type":"application/x-zip-compressed","file_name":"KIM_thesis_final.zip","date_updated":"2023-04-20T22:30:03Z","access_level":"closed","embargo_to":"open_access","file_id":"11221","creator":"okim","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","file_size":59248569,"relation":"source_file"}],"publication_status":"published","corr_author":"1","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"has_accepted_license":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","date_updated":"2026-04-07T14:30:39Z","citation":{"chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>.","mla":"Artner, Christina. <i>Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>.","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022."},"page":"128","article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"_id":"11879","doi":"10.15479/at:ista:11879","type":"dissertation","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"supervisor":[{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"day":"17","month":"08","language":[{"iso":"eng"}],"degree_awarded":"PhD","file_date_updated":"2023-09-09T22:30:03Z","publication_status":"published","corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file":[{"creator":"cartner","checksum":"a2c2fdc28002538840490bfa6a08b2cb","embargo":"2023-09-08","file_size":11113608,"relation":"main_file","date_created":"2022-08-17T12:08:49Z","content_type":"application/pdf","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","date_updated":"2023-09-09T22:30:03Z","access_level":"open_access","file_id":"11907"},{"relation":"source_file","file_size":19097730,"checksum":"66b461c074b815fbe63481b3f46a9f43","creator":"cartner","file_id":"11908","embargo_to":"open_access","access_level":"closed","date_updated":"2023-09-09T22:30:03Z","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","content_type":"application/octet-stream","date_created":"2022-08-17T12:08:59Z"}],"status":"public","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","full_name":"Artner, Christina"}],"OA_place":"publisher","year":"2022","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"date_created":"2022-08-17T07:58:53Z","ddc":["580"],"date_published":"2022-08-17T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature"},{"publisher":"Elsevier","author":[{"last_name":"Villa","full_name":"Villa, Carlo Emanuele","first_name":"Carlo Emanuele"},{"last_name":"Cheroni","full_name":"Cheroni, Cristina","first_name":"Cristina"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096"},{"last_name":"López-Tóbon","full_name":"López-Tóbon, Alejandro","first_name":"Alejandro"},{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","first_name":"Bárbara","full_name":"Oliveira, Bárbara","last_name":"Oliveira"},{"last_name":"Sacco","full_name":"Sacco, Roberto","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yahya, Aysan Çerağ","last_name":"Yahya","first_name":"Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","last_name":"Morandell"},{"first_name":"Michele","full_name":"Gabriele, Michele","last_name":"Gabriele"},{"full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"first_name":"Mariano","last_name":"Gabitto","full_name":"Gabitto, Mariano"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"full_name":"Testa, Giuseppe","last_name":"Testa","first_name":"Giuseppe"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"year":"2022","intvolume":"        39","ec_funded":1,"publication_identifier":{"issn":["2211-1247"]},"pmid":1,"quality_controlled":"1","isi":1,"date_created":"2022-04-15T09:03:10Z","ddc":["570"],"date_published":"2022-04-05T00:00:00Z","related_material":{"record":[{"id":"18674","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18681"},{"status":"public","relation":"dissertation_contains","id":"12364"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_type":"original","scopus_import":"1","issue":"1","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","corr_author":"1","publication_status":"published","external_id":{"isi":["000785983900003"],"pmid":["35385734"]},"has_accepted_license":"1","department":[{"_id":"JoDa"},{"_id":"GaNo"}],"file":[{"relation":"main_file","checksum":"b4e8d68f0268dec499af333e6fd5d8e1","creator":"dernst","file_size":"7808644","access_level":"open_access","date_updated":"2022-04-15T09:06:25Z","file_id":"11164","date_created":"2022-04-15T09:06:25Z","success":1,"content_type":"application/pdf","file_name":"2022_CellReports_Villa.pdf"}],"article_number":"110615","status":"public","tmp":{"short":"CC BY (4.0)","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)"},"day":"05","volume":39,"language":[{"iso":"eng"}],"month":"04","file_date_updated":"2022-04-15T09:06:25Z","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com.","date_updated":"2026-08-22T22:30:07Z","citation":{"ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022."},"oa_version":"Published Version","article_processing_charge":"Yes","_id":"11160","abstract":[{"lang":"eng","text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling."}],"doi":"10.1016/j.celrep.2022.110615","project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"},{"name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205","call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","publication":"Cell Reports"},{"day":"19","degree_awarded":"PhD","month":"09","language":[{"iso":"eng"}],"file_date_updated":"2023-09-20T22:30:03Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T14:30:57Z","page":"152","citation":{"ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>.","mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>."},"doi":"10.15479/at:ista:12094","_id":"12364","abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","project":[{"name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","call_identifier":"FWF"}],"type":"dissertation","supervisor":[{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"}],"publisher":"Institute of Science and Technology Austria","year":"2022","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"ddc":["570"],"date_created":"2023-01-24T13:09:57Z","date_published":"2022-09-19T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"11160","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"3"}]},"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","publication_status":"published","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"has_accepted_license":"1","file":[{"access_level":"open_access","date_updated":"2023-09-20T22:30:03Z","file_id":"12365","date_created":"2023-01-24T13:15:45Z","file_name":"220923_Thesis_CDotter_Final.pdf","content_type":"application/pdf","relation":"main_file","embargo":"2023-09-19","file_size":20457465,"creator":"cchlebak","checksum":"896f4cac9adb6d3f26a6605772f4e1a3"},{"date_created":"2023-02-02T09:15:35Z","content_type":"application/x-zip-compressed","file_name":"latex_source_CDotter_Thesis_2022.zip","date_updated":"2023-09-20T22:30:03Z","access_level":"closed","embargo_to":"open_access","file_id":"12482","creator":"cchlebak","checksum":"ad01bb20da163be6893b7af832e58419","file_size":22433512,"relation":"source_file"}],"status":"public","alternative_title":["ISTA Thesis"]},{"month":"05","language":[{"iso":"eng"}],"degree_awarded":"PhD","day":"16","file_date_updated":"2023-05-17T22:30:03Z","citation":{"ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","apa":"Jevtic, M. (2022). <i>Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>.","mla":"Jevtic, Marijo. <i>Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>"},"page":"108","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T14:31:19Z","supervisor":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","article_processing_charge":"No","doi":"10.15479/at:ista:11393","_id":"11393","abstract":[{"lang":"eng","text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits."}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"date_created":"2022-05-17T08:57:41Z","ddc":["570"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","author":[{"first_name":"Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","last_name":"Jevtic","full_name":"Jevtic, Marijo"}],"year":"2022","acknowledged_ssus":[{"_id":"EM-Fac"}],"title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","date_published":"2022-05-16T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"7391","status":"public"}]},"publication_status":"published","corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"RySh"}],"status":"public","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","file_size":56427603,"creator":"cchlebak","checksum":"8fc695d88020d70d231dad0e9f10b138","date_updated":"2023-05-17T22:30:03Z","access_level":"closed","file_id":"11395","embargo_to":"open_access","date_created":"2022-05-17T09:08:06Z","file_name":"MJ thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","creator":"cchlebak","checksum":"c1dd20a1aece521b3500607b00e463d6","embargo":"2023-05-16","file_size":4351981,"file_id":"11397","access_level":"open_access","date_updated":"2023-05-17T22:30:03Z","content_type":"application/pdf","file_name":"MJ_thesis_PDFA.pdf","date_created":"2022-05-17T12:09:25Z"}]},{"publication_status":"published","corr_author":"1","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"status":"public","alternative_title":["ISTA Thesis"],"file":[{"creator":"cchlebak","checksum":"39eabb1e006b41335f17f3b29af09648","embargo":"2022-12-28","file_size":56076868,"relation":"main_file","date_created":"2023-01-25T09:41:49Z","content_type":"application/pdf","file_name":"Final_Thesis_ES_Redchenko.pdf","access_level":"open_access","date_updated":"2023-01-26T23:30:44Z","file_id":"12367"}],"publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]},"ec_funded":1,"date_created":"2023-01-25T09:17:02Z","ddc":["530"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"}],"year":"2022","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"title":"Controllable states of superconducting Qubit ensembles","date_published":"2022-09-26T00:00:00Z","citation":{"ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>"},"page":"168","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_updated":"2026-04-07T14:22:39Z","supervisor":[{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"article_processing_charge":"No","oa_version":"Published Version","_id":"12366","doi":"10.15479/at:ista:12132","abstract":[{"text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n","lang":"eng"}],"type":"dissertation","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020"}],"month":"09","language":[{"iso":"eng"}],"degree_awarded":"PhD","day":"26","file_date_updated":"2023-01-26T23:30:44Z"},{"has_accepted_license":"1","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"publication_status":"published","corr_author":"1","external_id":{"pmid":["34990456"],"isi":["000971223700001"]},"tmp":{"short":"CC BY (4.0)","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)"},"status":"public","file":[{"file_name":"2022_PLOSBio_Belyaeva.pdf","content_type":"application/pdf","success":1,"date_created":"2022-01-12T13:50:04Z","file_id":"10615","date_updated":"2022-01-12T13:50:04Z","access_level":"open_access","file_size":5426932,"creator":"cchlebak","checksum":"f454212a5522a7818ba4b2892315c478","relation":"main_file"}],"isi":1,"quality_controlled":"1","date_created":"2022-01-12T10:18:17Z","ddc":["570"],"ec_funded":1,"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"pmid":1,"year":"2022","intvolume":"        20","publisher":"Public Library of Science","author":[{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera"},{"last_name":"Wachner","full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György"},{"orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi","last_name":"Emtenani","first_name":"Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","last_name":"Gridchyn"},{"full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","last_name":"Akhmanova","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M","last_name":"Linder","full_name":"Linder, M"},{"last_name":"Roblek","full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko"},{"full_name":"Sibilia, M","last_name":"Sibilia","first_name":"M"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"issue":"1","title":"Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila","acknowledged_ssus":[{"_id":"LifeSc"}],"scopus_import":"1","article_type":"original","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8557"},{"status":"public","id":"11193","relation":"dissertation_contains"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.18.301481","relation":"earlier_version"},{"url":"https://ista.ac.at/en/news/resisting-the-pressure/","relation":"press_release","description":"News on the ISTA Website"}]},"date_published":"2022-01-06T00:00:00Z","citation":{"mla":"Belyaeva, Vera, et al. “Fos Regulates Macrophage Infiltration against Surrounding Tissue Resistance by a Cortical Actin-Based Mechanism in Drosophila.” <i>PLoS Biology</i>, vol. 20, no. 1, Public Library of Science, 2022, p. e3001494, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001494\">10.1371/journal.pbio.3001494</a>.","chicago":"Belyaeva, Vera, Stephanie Wachner, Attila György, Shamsi Emtenani, Igor Gridchyn, Maria Akhmanova, M Linder, Marko Roblek, M Sibilia, and Daria E Siekhaus. “Fos Regulates Macrophage Infiltration against Surrounding Tissue Resistance by a Cortical Actin-Based Mechanism in Drosophila.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001494\">https://doi.org/10.1371/journal.pbio.3001494</a>.","ama":"Belyaeva V, Wachner S, György A, et al. Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. <i>PLoS Biology</i>. 2022;20(1):e3001494. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001494\">10.1371/journal.pbio.3001494</a>","ieee":"V. Belyaeva <i>et al.</i>, “Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila,” <i>PLoS Biology</i>, vol. 20, no. 1. Public Library of Science, p. e3001494, 2022.","short":"V. Belyaeva, S. Wachner, A. György, S. Emtenani, I. Gridchyn, M. Akhmanova, M. Linder, M. Roblek, M. Sibilia, D.E. Siekhaus, PLoS Biology 20 (2022) e3001494.","ista":"Belyaeva V, Wachner S, György A, Emtenani S, Gridchyn I, Akhmanova M, Linder M, Roblek M, Sibilia M, Siekhaus DE. 2022. Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. PLoS Biology. 20(1), e3001494.","apa":"Belyaeva, V., Wachner, S., György, A., Emtenani, S., Gridchyn, I., Akhmanova, M., … Siekhaus, D. E. (2022). Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001494\">https://doi.org/10.1371/journal.pbio.3001494</a>"},"page":"e3001494","date_updated":"2026-08-22T22:30:08Z","acknowledgement":"We thank the following for their contributions: Plasmids were supplied by the Drosophila Genomics Resource Center (NIH 2P40OD010949-10A1); fly stocks were provided by K. Brueckner, B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center, FlyBase for essential genomic information, and the BDGP in situ database for data. For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C. P. Heisenberg, P. Martin, M. Sixt, and Siekhaus group members for discussions and T. Hurd, A. Ratheesh, and P. Rangan for comments on the manuscript.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publication":"PLoS Biology","project":[{"grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","grant_number":"24800"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","call_identifier":"FP7"}],"type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident macrophages and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here, we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio, which are themselves required for invasion. Both the filamin and the tetraspanin enhance the cortical activity of Rho1 and the formin Diaphanous and thus the assembly of cortical actin, which is a critical function since expressing a dominant active form of Diaphanous can rescue the Dfos macrophage invasion defect. In vivo imaging shows that Dfos enhances the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the properties of the macrophage nucleus from affecting tissue entry. We thus identify strengthening the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues. "}],"_id":"10614","doi":"10.1371/journal.pbio.3001494","month":"01","language":[{"iso":"eng"}],"day":"06","volume":20,"file_date_updated":"2022-01-12T13:50:04Z"},{"publication":"Nature Neuroscience","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"}],"type":"journal_article","_id":"12244","abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.","lang":"eng"}],"doi":"10.1038/s41593-022-01167-6","oa_version":"Published Version","article_processing_charge":"No","page":"1379-1393","citation":{"short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393.","apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>","ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393.","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.","ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>.","chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>."},"date_updated":"2026-08-22T22:30:09Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","oa":1,"file_date_updated":"2023-01-30T08:06:56Z","month":"10","language":[{"iso":"eng"}],"volume":25,"day":"01","tmp":{"short":"CC BY (4.0)","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)"},"status":"public","file":[{"file_id":"12437","access_level":"open_access","date_updated":"2023-01-30T08:06:56Z","file_name":"2022_NatureNeuroscience_Colombo.pdf","content_type":"application/pdf","success":1,"date_created":"2023-01-30T08:06:56Z","relation":"main_file","file_size":23789835,"creator":"dernst","checksum":"28431146873096f52e0107b534f178c9"}],"department":[{"_id":"SaSi"}],"has_accepted_license":"1","corr_author":"1","publication_status":"published","external_id":{"pmid":["36180790"],"isi":["000862214700001"]},"issue":"10","title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"article_type":"original","scopus_import":"1","related_material":{"link":[{"url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/","relation":"press_release","description":"News on ISTA website"}],"record":[{"id":"12378","relation":"dissertation_contains","status":"public"}]},"date_published":"2022-10-01T00:00:00Z","ddc":["570"],"isi":1,"date_created":"2023-01-16T09:53:07Z","quality_controlled":"1","pmid":1,"ec_funded":1,"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"intvolume":"        25","keyword":["General Neuroscience"],"year":"2022","author":[{"orcid":"0000-0001-9434-8902","last_name":"Colombo","full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J","last_name":"Cubero","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867"},{"first_name":"Lida","full_name":"Kanari, Lida","last_name":"Kanari"},{"first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","last_name":"Schulz"},{"last_name":"Scolamiero","full_name":"Scolamiero, Martina","first_name":"Martina"},{"first_name":"Jens","full_name":"Agerberg, Jens","last_name":"Agerberg"},{"first_name":"Hansruedi","full_name":"Mathys, Hansruedi","last_name":"Mathys"},{"first_name":"Li-Huei","full_name":"Tsai, Li-Huei","last_name":"Tsai"},{"last_name":"Chachólski","full_name":"Chachólski, Wojciech","first_name":"Wojciech"},{"first_name":"Kathryn","full_name":"Hess, Kathryn","last_name":"Hess"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"publisher":"Springer Nature"},{"ddc":["570"],"date_created":"2022-04-20T08:59:07Z","publication_identifier":{"issn":["2663-337X"]},"year":"2022","author":[{"last_name":"Wachner","full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","acknowledged_ssus":[{"_id":"LifeSc"}],"related_material":{"record":[{"id":"10614","relation":"part_of_dissertation","status":"public"},{"id":"544","relation":"part_of_dissertation","status":"public"}]},"date_published":"2022-04-20T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"has_accepted_license":"1","corr_author":"1","publication_status":"published","tmp":{"short":"CC BY (4.0)","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)"},"alternative_title":["ISTA Thesis"],"status":"public","file":[{"relation":"main_file","checksum":"999ab16884c4522486136ebc5ae8dbff","creator":"cchlebak","file_size":8820951,"embargo":"2023-04-20","file_id":"11195","access_level":"open_access","date_updated":"2023-04-21T22:30:03Z","content_type":"application/pdf","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","date_created":"2022-04-20T09:03:57Z"},{"date_created":"2022-04-22T12:41:00Z","file_name":"Thesis_Stephanie_Wachner_20200414.zip","content_type":"application/x-zip-compressed","access_level":"closed","date_updated":"2023-04-21T22:30:03Z","file_id":"11329","embargo_to":"open_access","file_size":65864612,"creator":"cchlebak","checksum":"fd92b1e38d53bdf8b458213882d41383","relation":"source_file"}],"degree_awarded":"PhD","month":"04","language":[{"iso":"eng"}],"day":"20","file_date_updated":"2023-04-21T22:30:03Z","page":"170","citation":{"chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>.","mla":"Wachner, Stephanie. <i>Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>.","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","apa":"Wachner, S. (2022). <i>Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022."},"date_updated":"2026-04-07T14:24:19Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"supervisor":[{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"type":"dissertation","project":[{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","grant_number":"24800","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration"}],"doi":"10.15479/at:ista:11193","_id":"11193","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"article_processing_charge":"No","oa_version":"Published Version"},{"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"has_accepted_license":"1","publication_status":"published","corr_author":"1","tmp":{"short":"CC BY (4.0)","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)"},"alternative_title":["ISTA Thesis"],"status":"public","file":[{"checksum":"8cd3ddfe9b53381dcf086023d8d8893a","creator":"cchlebak","file_size":23890382,"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Gloria_Colombo_Thesis.docx","date_created":"2023-01-25T14:31:32Z","embargo_to":"open_access","file_id":"12379","date_updated":"2023-04-12T22:30:03Z","access_level":"closed"},{"date_created":"2023-01-25T14:31:36Z","content_type":"application/pdf","file_name":"Gloria_Colombo_Thesis.pdf","date_updated":"2023-04-12T22:30:03Z","access_level":"open_access","file_id":"12380","creator":"cchlebak","checksum":"8af4319c18b516e8758e9a6cb02b103b","file_size":13802421,"embargo":"2023-04-11","relation":"main_file"}],"ddc":["570"],"date_created":"2023-01-25T14:27:43Z","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"year":"2022","OA_place":"publisher","author":[{"full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"related_material":{"record":[{"id":"12244","relation":"part_of_dissertation","status":"public"}]},"date_published":"2022-11-11T00:00:00Z","page":"142","citation":{"ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022."},"date_updated":"2026-04-07T14:29:41Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert"}],"type":"dissertation","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia.","lang":"eng"}],"_id":"12378","doi":"10.15479/at:ista:12378","article_processing_charge":"No","oa_version":"Published Version","degree_awarded":"PhD","month":"11","language":[{"iso":"eng"}],"day":"11","file_date_updated":"2023-04-12T22:30:03Z"}]