[{"publication":"Nature Human Behaviour","issue":"10","doi":"10.1038/s41562-021-01114-8","publication_identifier":{"eissn":["2397-3374"]},"year":"2021","date_created":"2021-05-18T16:56:57Z","ddc":["000"],"has_accepted_license":"1","quality_controlled":"1","file":[{"date_created":"2023-11-07T08:27:23Z","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"14496","access_level":"open_access","checksum":"34f55e173f90dc1dab731063458ac780","relation":"main_file","file_size":5232761,"date_updated":"2023-11-07T08:27:23Z"}],"corr_author":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","description":"News on IST Homepage"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"pmid":1,"volume":5,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","first_name":"Laura","last_name":"Schmid"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"title":"A unified framework of direct and indirect reciprocity","abstract":[{"lang":"eng","text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability."}],"publication_status":"published","external_id":{"pmid":["33986519"],"isi":["000650304000002"]},"page":"1292–1302","article_processing_charge":"No","status":"public","day":"13","ec_funded":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"citation":{"ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. 2021;5(10):1292–1302. doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” <i>Nature Human Behaviour</i>, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:<a href=\"https://doi.org/10.1038/s41562-021-01114-8\">10.1038/s41562-021-01114-8</a>.","chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” <i>Nature Human Behaviour</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., &#38; Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-021-01114-8\">https://doi.org/10.1038/s41562-021-01114-8</a>"},"_id":"9402","scopus_import":"1","type":"journal_article","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","article_type":"original","oa_version":"Submitted Version","intvolume":"         5","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Springer Nature","date_updated":"2026-09-04T22:30:49Z","month":"05","language":[{"iso":"eng"}],"date_published":"2021-05-13T00:00:00Z","oa":1,"file_date_updated":"2023-11-07T08:27:23Z","isi":1},{"isi":1,"oa":1,"file_date_updated":"2021-02-11T12:28:29Z","month":"02","language":[{"iso":"eng"}],"date_published":"2021-02-01T00:00:00Z","publisher":"Embo Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2026-09-04T22:30:52Z","article_type":"original","oa_version":"Published Version","intvolume":"        40","type":"journal_article","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","_id":"9010","scopus_import":"1","citation":{"apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>.","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862."},"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"},{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"01","article_processing_charge":"Yes (via OA deal)","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"publication_status":"published","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös"},{"last_name":"Marconi","first_name":"Marco","full_name":"Marconi, Marco"},{"full_name":"Vega, Andrea","last_name":"Vega","first_name":"Andrea"},{"full_name":"O’Brien, Jose","first_name":"Jose","last_name":"O’Brien"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia"},{"full_name":"Antonielli, Livio","last_name":"Antonielli","first_name":"Livio"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","last_name":"Montesinos López"},{"last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela"},{"last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A.","last_name":"Gutiérrez"},{"full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","last_name":"Wabnik"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková"}],"volume":40,"acknowledged_ssus":[{"_id":"Bio"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}]},"pmid":1,"corr_author":"1","quality_controlled":"1","file":[{"creator":"dernst","success":1,"content_type":"application/pdf","file_name":"2021_Embo_Otvos.pdf","date_created":"2021-02-11T12:28:29Z","file_size":2358617,"date_updated":"2021-02-11T12:28:29Z","checksum":"dc55c900f3b061d6c2790b8813d759a3","relation":"main_file","access_level":"open_access","file_id":"9110"}],"has_accepted_license":"1","ddc":["580"],"year":"2021","date_created":"2021-01-17T23:01:12Z","article_number":"e106862","issue":"3","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"doi":"10.15252/embj.2020106862","publication":"EMBO Journal"},{"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"article_processing_charge":"Yes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","related_material":{"record":[{"id":"10303","relation":"dissertation_contains","status":"public"}]},"pmid":1,"volume":22,"author":[{"first_name":"Andrea","last_name":"Vega","full_name":"Vega, Andrea"},{"full_name":"Fredes, Isabel","first_name":"Isabel","last_name":"Fredes"},{"last_name":"O’Brien","first_name":"José","full_name":"O’Brien, José"},{"last_name":"Shen","first_name":"Zhouxin","full_name":"Shen, Zhouxin"},{"full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","first_name":"Krisztina","last_name":"Ötvös"},{"last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"},{"last_name":"Briggs","first_name":"Steven P.","full_name":"Briggs, Steven P."},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"has_accepted_license":"1","quality_controlled":"1","file":[{"checksum":"750de03dc3b715c37090126c1548ba13","relation":"main_file","access_level":"open_access","date_updated":"2021-10-05T13:36:42Z","file_size":3144854,"file_id":"10090","creator":"cchlebak","success":1,"date_created":"2021-10-05T13:36:42Z","file_name":"2021_EmboR_Vega.pdf","content_type":"application/pdf"}],"publication":"EMBO Reports","issue":"9","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"doi":"10.15252/embr.202051813","article_number":"e51813","year":"2021","date_created":"2021-08-15T22:01:30Z","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"publisher":"Wiley","date_updated":"2026-09-04T22:30:52Z","language":[{"iso":"eng"}],"month":"09","date_published":"2021-09-06T00:00:00Z","oa":1,"file_date_updated":"2021-10-05T13:36:42Z","isi":1,"_id":"9913","scopus_import":"1","type":"journal_article","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","article_type":"original","oa_version":"Published Version","intvolume":"        22","citation":{"short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>."},"status":"public","day":"06","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"47","status":"public"},{"id":"9913","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"9010","status":"public"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia","first_name":"Rashed"}],"OA_place":"publisher","supervisor":[{"first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"degree_awarded":"PhD","title":"Role of hormones in nitrate regulated growth","article_processing_charge":"No","page":"139","publication_status":"published","abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:10303","date_created":"2021-11-18T11:20:59Z","year":"2021","has_accepted_license":"1","ddc":["580","581"],"corr_author":"1","file":[{"creator":"rabualia","content_type":"application/pdf","file_name":"AbualiaPhDthesisfinalv3.pdf","date_created":"2021-11-22T14:48:21Z","date_updated":"2022-12-20T23:30:06Z","file_size":28005730,"access_level":"open_access","relation":"main_file","checksum":"dea38b98aa4da1cea03dcd0f10862818","embargo":"2022-11-23","file_id":"10331"},{"date_created":"2021-11-22T14:48:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"AbualiaPhDthesisfinalv3.docx","creator":"rabualia","file_id":"10332","access_level":"closed","relation":"source_file","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","embargo_to":"open_access","date_updated":"2022-12-20T23:30:06Z","file_size":62841883}],"_id":"10303","oa_version":"Published Version","type":"dissertation","date_published":"2021-11-22T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2026-04-08T07:20:07Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-12-20T23:30:06Z","oa":1,"alternative_title":["ISTA Thesis"],"status":"public","day":"22","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. <i>Role of Hormones in Nitrate Regulated Growth</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10303\">10.15479/at:ista:10303</a>.","apa":"Abualia, R. (2021). <i>Role of hormones in nitrate regulated growth</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10303\">https://doi.org/10.15479/at:ista:10303</a>."}},{"article_type":"original","intvolume":"       118","oa_version":"Published Version","type":"journal_article","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","_id":"9887","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2021-12-15T08:59:40Z","month":"12","language":[{"iso":"eng"}],"date_published":"2021-12-14T00:00:00Z","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"date_updated":"2026-09-04T22:30:55Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"14","status":"public","citation":{"mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021."},"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"last_name":"Dahhan","first_name":"Dana A","full_name":"Dahhan, Dana A"},{"first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden"},{"last_name":"Costanzo","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","first_name":"Mónika"},{"full_name":"Wang, Jie","last_name":"Wang","first_name":"Jie"},{"first_name":"Juan L","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire","first_name":"Emmanuel"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"},{"full_name":"Bednarek, Sebastian Y","last_name":"Bednarek","first_name":"Sebastian Y"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":118,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}],"record":[{"id":"14988","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14510"}]},"pmid":1,"article_processing_charge":"No","abstract":[{"text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.","lang":"eng"}],"external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"publication_status":"published","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","year":"2021","date_created":"2021-08-11T14:11:43Z","article_number":"e2113046118","issue":"51","doi":"10.1073/pnas.2113046118","publication_identifier":{"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","quality_controlled":"1","file":[{"file_id":"10546","relation":"main_file","checksum":"8d01e72e22c4fb1584e72d8601947069","access_level":"open_access","date_updated":"2021-12-15T08:59:40Z","file_size":2757340,"date_created":"2021-12-15T08:59:40Z","file_name":"2021_PNAS_Johnson.pdf","content_type":"application/pdf","creator":"cchlebak","success":1}],"has_accepted_license":"1","ddc":["580"]},{"status":"public","day":"01","alternative_title":["ISTA Thesis"],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"project":[{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"citation":{"mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021."},"_id":"8934","type":"dissertation","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_updated":"2026-04-16T10:07:18Z","month":"01","language":[{"iso":"eng"}],"date_published":"2021-01-01T00:00:00Z","oa":1,"file_date_updated":"2021-12-23T23:30:04Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8934","year":"2021","date_created":"2020-12-10T12:17:07Z","ddc":["005"],"has_accepted_license":"1","file":[{"file_id":"8969","embargo":"2021-12-22","access_level":"open_access","relation":"main_file","checksum":"d1b9db3725aed34dadd81274aeb9426c","file_size":5251507,"date_updated":"2021-12-23T23:30:04Z","date_created":"2020-12-22T20:08:44Z","content_type":"application/pdf","file_name":"Thesis-pdfa.pdf","creator":"akafshda"},{"checksum":"1661df7b393e6866d2460eba3c905130","relation":"source_file","access_level":"closed","embargo_to":"open_access","file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","file_id":"8970","creator":"akafshda","date_created":"2020-12-22T20:08:50Z","content_type":"application/zip","file_name":"source.zip"}],"corr_author":"1","related_material":{"record":[{"id":"6490","relation":"part_of_dissertation","status":"public"},{"id":"6780","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7158","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"66"},{"relation":"part_of_dissertation","id":"6378","status":"public"},{"relation":"part_of_dissertation","id":"311","status":"public"},{"status":"public","id":"6175","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6340","status":"public"},{"relation":"part_of_dissertation","id":"7014","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6009"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8728"},{"id":"8089","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"6380","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"id":"639","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1386","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6918","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7810"},{"status":"public","relation":"part_of_dissertation","id":"949"}]},"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","title":"Parameterized and algebro-geometric advances in static program analysis","supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"publication_status":"published","page":"278","article_processing_charge":"No","license":"https://creativecommons.org/publicdomain/zero/1.0/"},{"oa_version":"Submitted Version","intvolume":"         1","article_type":"original","type":"journal_article","acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","scopus_import":"1","_id":"10816","isi":1,"file_date_updated":"2022-06-18T22:30:03Z","oa":1,"date_published":"2021-12-16T00:00:00Z","month":"12","language":[{"iso":"eng"}],"date_updated":"2026-07-28T12:15:17Z","publisher":"Springer Nature","department":[{"_id":"PeJo"}],"OA_type":"green","ec_funded":1,"status":"public","day":"16","citation":{"ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. 2021;1(12):830-842. doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” <i>Nature Computational Science</i>, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>."},"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Guzmán","first_name":"José","full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242"},{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"last_name":"Espinoza Martinez","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xiaomin","last_name":"Zhang","orcid":"0000-0003-0256-6529","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin"},{"first_name":"Benjamin","last_name":"Suter","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"OA_place":"repository","volume":1,"acknowledged_ssus":[{"_id":"SSU"}],"biorxivid":1,"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/spot-the-difference/"}],"record":[{"status":"public","id":"10110","relation":"software"}]},"article_processing_charge":"No","page":"830-842","external_id":{"isi":["000888567500015"],"biorxivid":["10.1101/647800"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","date_created":"2022-03-04T08:32:36Z","year":"2021","doi":"10.1038/s43588-021-00157-1","publication_identifier":{"issn":["2662-8457"]},"issue":"12","publication":"Nature Computational Science","corr_author":"1","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"Guzmanetal2021.pdf","date_created":"2022-06-02T12:51:07Z","creator":"patrickd","embargo":"2022-06-17","file_id":"11430","file_size":1699466,"date_updated":"2022-06-18T22:30:03Z","access_level":"open_access","checksum":"9fec5b667909ef52be96d502e4f8c2ae","relation":"main_file"},{"creator":"patrickd","date_created":"2022-06-02T12:53:47Z","content_type":"application/pdf","file_name":"Guzmanetal2021Suppl.pdf","relation":"supplementary_material","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","title":"Supplementary Material","access_level":"open_access","date_updated":"2022-06-18T22:30:03Z","file_size":3005651,"embargo":"2022-06-17","file_id":"11431"}],"has_accepted_license":"1","ddc":["610"]},{"citation":{"apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>.","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>.","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>"},"project":[{"name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"alternative_title":["ISTA Thesis"],"day":"02","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_published":"2021-09-02T00:00:00Z","language":[{"iso":"eng"}],"month":"09","date_updated":"2026-04-08T07:19:09Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-09-03T22:30:04Z","oa":1,"_id":"9962","oa_version":"Published Version","type":"dissertation","has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"file_id":"9971","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","relation":"source_file","access_level":"closed","date_updated":"2022-09-03T22:30:04Z","file_size":10629190,"embargo_to":"open_access","date_created":"2021-08-30T09:17:39Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Hansen.docx","creator":"ahansen"},{"creator":"ahansen","date_created":"2021-08-30T09:29:44Z","content_type":"application/pdf","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","checksum":"204fa40321a1c6289b68c473634c4bf3","relation":"main_file","file_size":13457469,"date_updated":"2022-09-03T22:30:04Z","file_id":"9972","embargo":"2022-09-02"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:9962","date_created":"2021-08-29T12:36:50Z","year":"2021","supervisor":[{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","degree_awarded":"PhD","article_processing_charge":"No","page":"182","publication_status":"published","abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"related_material":{"record":[{"status":"public","id":"8569","relation":"part_of_dissertation"},{"id":"960","relation":"part_of_dissertation","status":"public"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher"},{"related_material":{"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/spot-the-difference/","relation":"press_release"}],"record":[{"relation":"used_for_analysis_in","id":"10816","status":"public"}]},"_id":"10110","type":"software","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Guzmán","first_name":"José","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"last_name":"Espinoza Martinez","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082"},{"first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0256-6529","full_name":"Zhang, Xiaomin"},{"last_name":"Suter","first_name":"Benjamin","full_name":"Suter, Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas"}],"date_updated":"2026-09-04T22:31:05Z","publisher":"IST Austria","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"date_published":"2021-12-16T00:00:00Z","month":"12","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","file_date_updated":"2021-10-08T08:46:04Z","oa":1,"abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"license":"https://opensource.org/licenses/GPL-3.0","day":"16","status":"public","doi":"10.15479/AT:ISTA:10110","tmp":{"short":"GPL 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","name":"GNU General Public License 3.0"},"date_created":"2021-10-08T06:44:22Z","year":"2021","ddc":["005"],"has_accepted_license":"1","file":[{"file_id":"10114","file_size":332990101,"date_updated":"2021-10-08T08:46:04Z","access_level":"open_access","relation":"main_file","checksum":"f92f8931cad0aa7e411c1715337bf408","content_type":"application/x-zip-compressed","file_name":"patternseparation-main (1).zip","date_created":"2021-10-08T08:46:04Z","success":1,"creator":"cchlebak"}],"citation":{"ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>."}},{"intvolume":"        10","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","scopus_import":"1","_id":"9437","isi":1,"file_date_updated":"2021-05-31T09:43:09Z","oa":1,"date_published":"2021-04-29T00:00:00Z","month":"04","language":[{"iso":"eng"}],"date_updated":"2026-09-04T22:31:06Z","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"},{"_id":"PeJo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"status":"public","day":"29","citation":{"ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal C, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>","ieee":"P. Bhandari <i>et al.</i>, “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>, vol. 10, e68274, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/ELIFE.68274\">10.7554/ELIFE.68274</a>.","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.68274\">https://doi.org/10.7554/ELIFE.68274</a>"},"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"last_name":"Vandael","first_name":"David H","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fernández-Fernández, Diego","last_name":"Fernández-Fernández","first_name":"Diego"},{"last_name":"Fritzius","first_name":"Thorsten","full_name":"Fritzius, Thorsten"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David"},{"last_name":"Önal","first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C"},{"last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"last_name":"Kulik","first_name":"Akos","full_name":"Kulik, Akos"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"last_name":"Koppensteiner","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":10,"pmid":1,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}],"record":[{"relation":"dissertation_contains","id":"19271","status":"public"},{"relation":"dissertation_contains","id":"9562","status":"public"}]},"article_processing_charge":"No","external_id":{"pmid":["33913808"],"isi":["000651761700001"]},"publication_status":"published","abstract":[{"text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.","lang":"eng"}],"title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","date_created":"2021-05-30T22:01:23Z","year":"2021","article_number":"e68274","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/ELIFE.68274","publication":"eLife","quality_controlled":"1","file":[{"creator":"cziletti","success":1,"content_type":"application/pdf","file_name":"2021_eLife_Bhandari.pdf","date_created":"2021-05-31T09:43:09Z","file_size":8174719,"date_updated":"2021-05-31T09:43:09Z","checksum":"6ebcb79999f889766f7cd79ee134ad28","relation":"main_file","access_level":"open_access","file_id":"9440"}],"has_accepted_license":"1","ddc":["570"]},{"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:9562","year":"2021","date_created":"2021-06-17T14:10:47Z","has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"date_created":"2021-06-17T14:03:14Z","content_type":"application/pdf","file_name":"Thesis.pdf","creator":"dkleindienst","file_id":"9563","embargo":"2022-07-01","relation":"main_file","checksum":"659df5518db495f679cb1df9e9bd1d94","access_level":"open_access","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z"},{"creator":"dkleindienst","file_name":"Thesis_source.zip","content_type":"application/zip","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z","file_size":369804895,"embargo_to":"open_access","access_level":"closed","checksum":"3bcf63a2b19e5b6663be051bea332748","relation":"source_file","file_id":"9564"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"related_material":{"record":[{"id":"9437","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"612","status":"public"},{"relation":"part_of_dissertation","id":"8532","status":"public"},{"status":"public","id":"9756","relation":"part_of_dissertation"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Kleindienst","first_name":"David","full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi"}],"page":"124","article_processing_charge":"No","abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"status":"public","day":"01","citation":{"ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>."},"_id":"9562","oa_version":"Published Version","type":"dissertation","month":"06","language":[{"iso":"eng"}],"date_published":"2021-06-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"date_updated":"2026-07-06T13:11:44Z","oa":1,"file_date_updated":"2022-07-02T22:30:04Z"},{"file_date_updated":"2021-08-06T06:44:31Z","oa":1,"isi":1,"date_updated":"2026-09-04T22:31:08Z","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"arxiv":1,"date_published":"2021-07-01T00:00:00Z","month":"07","language":[{"iso":"eng"}],"type":"journal_article","acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","intvolume":"         5","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"9760","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"citation":{"chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>.","apa":"Sack, S., &#38; Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>.","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” <i>Quantum</i>, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021.","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. 2021;5. doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"01","status":"public","publication_status":"published","external_id":{"arxiv":["2101.05742"],"isi":["000669830600001"]},"abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.","lang":"eng"}],"article_processing_charge":"Yes","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","volume":5,"author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan","last_name":"Sack"},{"last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"14622","relation":"dissertation_contains","status":"public"}]},"file":[{"creator":"cchlebak","date_created":"2021-08-06T06:44:31Z","content_type":"application/pdf","file_name":"2021_Quantum_Sack.pdf","relation":"main_file","checksum":"9706c2bb8e748e9b5b138381995a7f6f","access_level":"open_access","file_size":2312482,"date_updated":"2021-08-06T06:44:31Z","file_id":"9774"}],"quality_controlled":"1","corr_author":"1","ddc":["530"],"has_accepted_license":"1","article_number":"491","date_created":"2021-08-01T22:01:21Z","year":"2021","publication":"Quantum","publication_identifier":{"eissn":["2521-327X"]},"doi":"10.22331/Q-2021-07-01-491"},{"title":"Experimental observation of the origin and structure of elastoinertial turbulence","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"article_processing_charge":"No","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"external_id":{"arxiv":["2103.00023"],"pmid":[" 34732570"],"isi":["000720926900019"]},"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19906"}]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","first_name":"George H","last_name":"Choueiri"},{"first_name":"Jose M","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M"},{"full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","first_name":"Atul","last_name":"Varshney"},{"first_name":"Sarath","last_name":"Sankar","full_name":"Sankar, Sarath"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn"}],"volume":118,"main_file_link":[{"url":"https://arxiv.org/abs/2103.00023","open_access":"1"}],"corr_author":"1","quality_controlled":"1","issue":"45","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2102350118","publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2021","date_created":"2021-11-17T13:24:24Z","article_number":"e2102350118","month":"11","language":[{"iso":"eng"}],"date_published":"2021-11-03T00:00:00Z","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","arxiv":1,"date_updated":"2026-09-04T22:31:09Z","isi":1,"oa":1,"_id":"10299","scopus_import":"1","article_type":"original","oa_version":"Preprint","intvolume":"       118","type":"journal_article","acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","citation":{"ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45. National Academy of Sciences, 2021.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(45). doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. 118(45), e2102350118.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., &#38; Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>.","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>."},"project":[{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow in complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188"}],"status":"public","day":"03"},{"volume":279,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","last_name":"Bao","first_name":"Zhigang"},{"first_name":"László","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli"}],"publication_status":"published","external_id":{"arxiv":["1708.01597"],"isi":["000559623200009"]},"abstract":[{"lang":"eng","text":"We consider the sum of two large Hermitian matrices A and B with a Haar unitary conjugation bringing them into a general relative position. We prove that the eigenvalue density on the scale slightly above the local eigenvalue spacing is asymptotically given by the free additive convolution of the laws of A and B as the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues and optimal rate of convergence in Voiculescu's theorem. Our previous works [4], [5] established these results in the bulk spectrum, the current paper completely settles the problem at the spectral edges provided they have the typical square-root behavior. The key element of our proof is to compensate the deterioration of the stability of the subordination equations by sharp error estimates that properly account for the local density near the edge. Our results also hold if the Haar unitary matrix is replaced by the Haar orthogonal matrix."}],"article_processing_charge":"No","keyword":["Analysis"],"title":"Spectral rigidity for addition of random matrices at the regular edge","article_number":"108639","date_created":"2022-03-18T10:18:59Z","year":"2020","publication":"Journal of Functional Analysis","publication_identifier":{"issn":["0022-1236"]},"doi":"10.1016/j.jfa.2020.108639","issue":"7","quality_controlled":"1","corr_author":"1","main_file_link":[{"url":"https://arxiv.org/abs/1708.01597","open_access":"1"}],"type":"journal_article","acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804.","intvolume":"       279","oa_version":"Preprint","article_type":"original","scopus_import":"1","_id":"10862","oa":1,"isi":1,"date_updated":"2025-04-15T08:05:01Z","department":[{"_id":"LaEr"}],"arxiv":1,"publisher":"Elsevier","date_published":"2020-10-15T00:00:00Z","month":"10","language":[{"iso":"eng"}],"ec_funded":1,"day":"15","status":"public","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"citation":{"mla":"Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” <i>Journal of Functional Analysis</i>, vol. 279, no. 7, 108639, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">10.1016/j.jfa.2020.108639</a>.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2020). Spectral rigidity for addition of random matrices at the regular edge. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">https://doi.org/10.1016/j.jfa.2020.108639</a>","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” <i>Journal of Functional Analysis</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">https://doi.org/10.1016/j.jfa.2020.108639</a>.","ista":"Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639.","ama":"Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices at the regular edge. <i>Journal of Functional Analysis</i>. 2020;279(7). doi:<a href=\"https://doi.org/10.1016/j.jfa.2020.108639\">10.1016/j.jfa.2020.108639</a>","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random matrices at the regular edge,” <i>Journal of Functional Analysis</i>, vol. 279, no. 7. Elsevier, 2020.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020)."}},{"_id":"10865","scopus_import":"1","type":"book_chapter","acknowledgement":"We would like to thank the anonymous reviewers of PKC 2019 for their useful comments and suggestions. We thank Omer Paneth for pointing out to us the connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first author would like to acknowledge Pandu Rangan for his involvement during the initial discussion phase of the project.","oa_version":"Preprint","intvolume":"     12110","publisher":"Springer Nature","date_updated":"2026-04-16T10:21:31Z","language":[{"iso":"eng"}],"month":"04","date_published":"2020-04-29T00:00:00Z","oa":1,"isi":1,"status":"public","day":"29","series_title":"LNCS","place":"Cham","citation":{"mla":"Chakraborty, Suvradip, et al. “Witness Maps and Applications.” <i>Public-Key Cryptography</i>, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp. 220–46, doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_8\">10.1007/978-3-030-45374-9_8</a>.","apa":"Chakraborty, S., Prabhakaran, M., &#38; Wichs, D. (2020). Witness maps and applications. In A. Kiayias (Ed.), <i>Public-Key Cryptography</i> (Vol. 12110, pp. 220–246). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_8\">https://doi.org/10.1007/978-3-030-45374-9_8</a>","chicago":"Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps and Applications.” In <i>Public-Key Cryptography</i>, edited by A Kiayias, 12110:220–46. LNCS. Cham: Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_8\">https://doi.org/10.1007/978-3-030-45374-9_8</a>.","ama":"Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In: Kiayias A, ed. <i>Public-Key Cryptography</i>. Vol 12110. LNCS. Cham: Springer Nature; 2020:220-246. doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_8\">10.1007/978-3-030-45374-9_8</a>","ista":"Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246.","short":"S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246.","ieee":"S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,” in <i>Public-Key Cryptography</i>, vol. 12110, A. Kiayias, Ed. Cham: Springer Nature, 2020, pp. 220–246."},"volume":12110,"editor":[{"full_name":"Kiayias, A","last_name":"Kiayias","first_name":"A"}],"author":[{"last_name":"Chakraborty","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","full_name":"Chakraborty, Suvradip"},{"first_name":"Manoj","last_name":"Prabhakaran","full_name":"Prabhakaran, Manoj"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Witness maps and applications","abstract":[{"lang":"eng","text":"We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an   NP  statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM.\r\nOur main construction is a DMWM for all   NP  relations, assuming sub-exponentially secure indistinguishability obfuscation (  iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on   iO  and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure   iO  and sub-exponentially secure OWF.\r\nAs an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of   1−o(1) ."}],"external_id":{"isi":["001299210200008"]},"publication_status":"published","page":"220-246","article_processing_charge":"No","publication":"Public-Key Cryptography","doi":"10.1007/978-3-030-45374-9_8","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030453732"],"eisbn":["9783030453749"],"issn":["0302-9743"]},"year":"2020","date_created":"2022-03-18T11:35:51Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/090"}],"quality_controlled":"1","corr_author":"1"},{"title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"abstract":[{"text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management.","lang":"eng"}],"external_id":{"isi":["000548893200082"],"arxiv":["2004.14599"],"pmid":["32530634"]},"publication_status":"published","page":"5323-5329","article_processing_charge":"No","pmid":1,"volume":20,"author":[{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"full_name":"Capote-Robayna, Nathaniel","last_name":"Capote-Robayna","first_name":"Nathaniel"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/2004.14599","open_access":"1"}],"quality_controlled":"1","publication":"Nano Letters","issue":"7","doi":"10.1021/acs.nanolett.0c01673","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"year":"2020","date_created":"2022-03-18T11:37:38Z","publisher":"American Chemical Society","arxiv":1,"department":[{"_id":"NanoFab"}],"date_updated":"2023-09-05T12:05:58Z","month":"07","language":[{"iso":"eng"}],"date_published":"2020-07-01T00:00:00Z","oa":1,"isi":1,"_id":"10866","scopus_import":"1","acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA.","type":"journal_article","article_type":"original","oa_version":"Preprint","intvolume":"        20","citation":{"mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>.","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>","chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. 2020;20(7):5323-5329. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>","ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","ieee":"J. Duan <i>et al.</i>, “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.","short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329."},"status":"public","day":"01"},{"article_type":"original","intvolume":"      2020","oa_version":"Preprint","acknowledgement":" Supported by the Russian Foundation for Basic Research grant 18-01-00036.","type":"journal_article","_id":"10867","scopus_import":"1","isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"02","date_published":"2020-02-01T00:00:00Z","publisher":"Oxford University Press","department":[{"_id":"HeEd"}],"arxiv":1,"date_updated":"2023-08-24T14:19:55Z","status":"public","day":"01","citation":{"ieee":"A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,” <i>International Mathematics Research Notices</i>, vol. 2020, no. 3. Oxford University Press, pp. 669–697, 2020.","short":"A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020) 669–697.","ama":"Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. <i>International Mathematics Research Notices</i>. 2020;2020(3):669-697. doi:<a href=\"https://doi.org/10.1093/imrn/rny037\">10.1093/imrn/rny037</a>","ista":"Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020(3), 669–697.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/imrn/rny037\">https://doi.org/10.1093/imrn/rny037</a>.","apa":"Akopyan, A., &#38; Karasev, R. (2020). Waist of balls in hyperbolic and spherical spaces. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rny037\">https://doi.org/10.1093/imrn/rny037</a>","mla":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” <i>International Mathematics Research Notices</i>, vol. 2020, no. 3, Oxford University Press, 2020, pp. 669–97, doi:<a href=\"https://doi.org/10.1093/imrn/rny037\">10.1093/imrn/rny037</a>."},"author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":2020,"page":"669-697","article_processing_charge":"No","abstract":[{"text":"In this paper we find a tight estimate for Gromov’s waist of the balls in spaces of constant curvature, deduce the estimates for the balls in Riemannian manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar result for normed spaces.","lang":"eng"}],"external_id":{"isi":["000522852700002"],"arxiv":["1702.07513"]},"publication_status":"published","title":"Waist of balls in hyperbolic and spherical spaces","keyword":["General Mathematics"],"year":"2020","date_created":"2022-03-18T11:39:30Z","issue":"3","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"doi":"10.1093/imrn/rny037","publication":"International Mathematics Research Notices","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.07513","open_access":"1"}]},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.05.031"}],"year":"2020","date_created":"2022-04-07T07:43:36Z","publication":"Neuron","issue":"6","doi":"10.1016/j.neuron.2020.05.031","publication_identifier":{"issn":["0896-6273"]},"abstract":[{"lang":"eng","text":"In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging."}],"publication_status":"published","external_id":{"pmid":["32553207"]},"page":"899-911","article_processing_charge":"No","title":"Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging","keyword":["General Neuroscience"],"volume":106,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ukrae H.","last_name":"Cho","full_name":"Cho, Ukrae H."},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER"}],"pmid":1,"citation":{"chicago":"Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">https://doi.org/10.1016/j.neuron.2020.05.031</a>.","apa":"Cho, U. H., &#38; Hetzer, M. (2020). Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">https://doi.org/10.1016/j.neuron.2020.05.031</a>","mla":"Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” <i>Neuron</i>, vol. 106, no. 6, Elsevier, 2020, pp. 899–911, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">10.1016/j.neuron.2020.05.031</a>.","ieee":"U. H. Cho and M. Hetzer, “Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging,” <i>Neuron</i>, vol. 106, no. 6. Elsevier, pp. 899–911, 2020.","short":"U.H. Cho, M. Hetzer, Neuron 106 (2020) 899–911.","ama":"Cho UH, Hetzer M. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. <i>Neuron</i>. 2020;106(6):899-911. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.05.031\">10.1016/j.neuron.2020.05.031</a>","ista":"Cho UH, Hetzer M. 2020. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. 106(6), 899–911."},"day":"17","status":"public","oa":1,"publisher":"Elsevier","date_updated":"2024-10-14T11:15:26Z","month":"06","language":[{"iso":"eng"}],"date_published":"2020-06-17T00:00:00Z","type":"journal_article","article_type":"review","intvolume":"       106","oa_version":"Published Version","_id":"11054","scopus_import":"1"},{"file_date_updated":"2022-04-08T06:53:10Z","oa":1,"date_updated":"2024-10-14T11:17:02Z","publisher":"eLife Sciences Publications","date_published":"2020-09-08T00:00:00Z","language":[{"iso":"eng"}],"month":"09","type":"journal_article","oa_version":"Published Version","intvolume":"         9","article_type":"original","scopus_import":"1","_id":"11055","citation":{"ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).","ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.","apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., &#38; Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>","chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>.","mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>, vol. 9, e54383, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"08","status":"public","external_id":{"pmid":["32896271"]},"publication_status":"published","abstract":[{"text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro.","lang":"eng"}],"article_processing_charge":"No","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","volume":9,"author":[{"full_name":"Bersini, Simone","first_name":"Simone","last_name":"Bersini"},{"last_name":"Schulte","first_name":"Roberta","full_name":"Schulte, Roberta"},{"last_name":"Huang","first_name":"Ling","full_name":"Huang, Ling"},{"last_name":"Tsai","first_name":"Hannah","full_name":"Tsai, Hannah"},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","pmid":1,"file":[{"creator":"dernst","success":1,"date_created":"2022-04-08T06:53:10Z","content_type":"application/pdf","file_name":"2020_eLife_Bersini.pdf","checksum":"f8b3821349a194050be02570d8fe7d4b","relation":"main_file","access_level":"open_access","file_size":4399825,"date_updated":"2022-04-08T06:53:10Z","file_id":"11132"}],"quality_controlled":"1","ddc":["570"],"has_accepted_license":"1","article_number":"e54383","date_created":"2022-04-07T07:43:48Z","year":"2020","publication":"eLife","doi":"10.7554/elife.54383","publication_identifier":{"issn":["2050-084X"]}},{"file":[{"date_created":"2022-04-08T07:06:05Z","file_name":"2020_AdvancedBiosystems_Bersini.pdf","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"11134","access_level":"open_access","relation":"main_file","checksum":"5584d9a1609812dc75c02ce1e35d2ec0","date_updated":"2022-04-08T07:06:05Z","file_size":2490829}],"quality_controlled":"1","ddc":["570"],"has_accepted_license":"1","article_number":"2000044","year":"2020","date_created":"2022-04-07T07:43:57Z","publication":"Advanced Biosystems","issue":"5","publication_identifier":{"issn":["2366-7478","2366-7478"]},"doi":"10.1002/adbi.202000044","abstract":[{"text":"Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established.","lang":"eng"}],"external_id":{"pmid":["32402127"]},"publication_status":"published","article_processing_charge":"No","title":"Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease","keyword":["General Biochemistry","Genetics and Molecular Biology","Biomedical Engineering","Biomaterials"],"volume":4,"extern":"1","author":[{"full_name":"Bersini, Simone","last_name":"Bersini","first_name":"Simone"},{"full_name":"Arrojo e Drigo, Rafael","last_name":"Arrojo e Drigo","first_name":"Rafael"},{"full_name":"Huang, Ling","first_name":"Ling","last_name":"Huang"},{"first_name":"Maxim N.","last_name":"Shokhirev","full_name":"Shokhirev, Maxim N."},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"citation":{"apa":"Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., &#38; Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. Wiley. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>","chicago":"Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>.","mla":"Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>, vol. 4, no. 5, 2000044, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>.","short":"S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020).","ieee":"S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” <i>Advanced Biosystems</i>, vol. 4, no. 5. Wiley, 2020.","ista":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.","ama":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. 2020;4(5). doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>"},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","day":"01","oa":1,"file_date_updated":"2022-04-08T07:06:05Z","publisher":"Wiley","date_updated":"2024-10-14T11:18:07Z","month":"05","language":[{"iso":"eng"}],"date_published":"2020-05-01T00:00:00Z","type":"journal_article","article_type":"original","intvolume":"         4","oa_version":"Published Version","_id":"11056","scopus_import":"1"}]