[{"ec_funded":1,"date_created":"2021-09-11T16:22:02Z","intvolume":"        11","citation":{"ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","apa":"Schmid, L., Shati, P., Hilbe, C., &#38; Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>."},"ddc":["003"],"publisher":"Springer Nature","publication":"Scientific Reports","article_type":"original","publication_identifier":{"eissn":["2045-2322"]},"volume":11,"date_updated":"2026-07-21T22:30:39Z","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10293"}]},"oa_version":"Published Version","status":"public","keyword":["Multidisciplinary"],"pmid":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","scopus_import":"1","file_date_updated":"2021-09-13T10:31:21Z","issue":"1","abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"has_accepted_license":"1","_id":"9997","type":"journal_article","language":[{"iso":"eng"}],"external_id":{"pmid":["34465830"],"isi":["000692406400018"]},"isi":1,"article_number":"17443","month":"08","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","first_name":"Laura"},{"first_name":"Pouya","full_name":"Shati, Pouya","last_name":"Shati"},{"last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"}],"day":"31","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-08-31T00:00:00Z","corr_author":"1","article_processing_charge":"Yes","publication_status":"published","year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"title":"The evolution of indirect reciprocity under action and assessment generosity","file":[{"checksum":"19df8816cf958b272b85841565c73182","content_type":"application/pdf","date_created":"2021-09-13T10:31:21Z","relation":"main_file","file_size":2424943,"success":1,"creator":"cchlebak","date_updated":"2021-09-13T10:31:21Z","file_id":"10006","access_level":"open_access","file_name":"2021_ScientificReports_Schmid.pdf"}],"quality_controlled":"1","doi":"10.1038/s41598-021-96932-1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}]},{"file_date_updated":"2022-12-20T23:30:05Z","status":"public","language":[{"iso":"eng"}],"month":"10","abstract":[{"lang":"eng","text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects."}],"_id":"10135","OA_place":"publisher","has_accepted_license":"1","type":"dissertation","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-014-5"]},"date_created":"2021-10-13T13:42:48Z","citation":{"ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","apa":"Semerádová, H. (2021). <i>Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>."},"ddc":["570"],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"oa":1,"date_updated":"2026-04-08T07:12:06Z","related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"file":[{"file_size":28508629,"relation":"source_file","embargo_to":"open_access","date_created":"2021-10-27T07:45:37Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"ce7108853e6cec6224f17cd6429b51fe","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","access_level":"closed","file_id":"10186","date_updated":"2022-12-20T23:30:05Z","creator":"cziletti"},{"file_size":10623525,"date_created":"2021-10-27T07:45:57Z","relation":"main_file","checksum":"0d7afb846e8e31ec794de47bf44e12ef","content_type":"application/pdf","embargo":"2022-10-28","file_id":"10187","access_level":"open_access","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","date_updated":"2022-12-20T23:30:05Z","creator":"cziletti"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","supervisor":[{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"}],"degree_awarded":"PhD","project":[{"grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis"}],"doi":"10.15479/at:ista:10135","corr_author":"1","article_processing_charge":"No","author":[{"full_name":"Semerádová, Hana","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semerádová"}],"day":"13","date_published":"2021-10-13T00:00:00Z","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published"},{"author":[{"last_name":"Schmid","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Schmid, Laura"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Hilbe","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"day":"13","date_published":"2021-05-13T00:00:00Z","corr_author":"1","article_processing_charge":"No","publication_status":"published","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"title":"A unified framework of direct and indirect reciprocity","file":[{"checksum":"34f55e173f90dc1dab731063458ac780","content_type":"application/pdf","date_created":"2023-11-07T08:27:23Z","relation":"main_file","file_size":5232761,"success":1,"creator":"dernst","date_updated":"2023-11-07T08:27:23Z","file_id":"14496","access_level":"open_access","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf"}],"quality_controlled":"1","doi":"10.1038/s41562-021-01114-8","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","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"ec_funded":1,"page":"1292–1302","citation":{"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>.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","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.","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>","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>","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."},"ddc":["000"],"intvolume":"         5","date_created":"2021-05-18T16:56:57Z","publication":"Nature Human Behaviour","publisher":"Springer Nature","article_type":"original","publication_identifier":{"eissn":["2397-3374"]},"volume":5,"oa":1,"date_updated":"2026-07-21T22:30:39Z","related_material":{"record":[{"id":"10293","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","relation":"press_release","description":"News on IST Homepage"}]},"oa_version":"Submitted Version","pmid":1,"status":"public","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.","scopus_import":"1","file_date_updated":"2023-11-07T08:27:23Z","issue":"10","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."}],"has_accepted_license":"1","_id":"9402","type":"journal_article","language":[{"iso":"eng"}],"external_id":{"isi":["000650304000002"],"pmid":["33986519"]},"isi":1,"month":"05"},{"publisher":"Wiley","publication":"EMBO Reports","citation":{"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>.","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>","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.","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>.","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)."},"date_created":"2021-08-15T22:01:30Z","ddc":["580"],"intvolume":"        22","article_type":"original","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"volume":22,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}]},"oa":1,"date_updated":"2026-07-21T22:30:42Z","oa_version":"Published Version","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).","status":"public","pmid":1,"scopus_import":"1","file_date_updated":"2021-10-05T13:36:42Z","issue":"9","has_accepted_license":"1","_id":"9913","abstract":[{"lang":"eng","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."}],"type":"journal_article","article_number":"e51813","external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"isi":1,"language":[{"iso":"eng"}],"month":"09","day":"06","author":[{"last_name":"Vega","first_name":"Andrea","full_name":"Vega, Andrea"},{"last_name":"Fredes","first_name":"Isabel","full_name":"Fredes, Isabel"},{"full_name":"O’Brien, José","first_name":"José","last_name":"O’Brien"},{"full_name":"Shen, Zhouxin","first_name":"Zhouxin","last_name":"Shen"},{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","last_name":"Ötvös","full_name":"Ötvös, Krisztina","first_name":"Krisztina"},{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","full_name":"Abualia, Rashed","first_name":"Rashed"},{"first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Briggs","full_name":"Briggs, Steven P.","first_name":"Steven P."},{"full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A.","last_name":"Gutiérrez"}],"date_published":"2021-09-06T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","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","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"Yes","publication_status":"published","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","file":[{"file_id":"10090","access_level":"open_access","file_name":"2021_EmboR_Vega.pdf","date_updated":"2021-10-05T13:36:42Z","creator":"cchlebak","success":1,"file_size":3144854,"date_created":"2021-10-05T13:36:42Z","relation":"main_file","checksum":"750de03dc3b715c37090126c1548ba13","content_type":"application/pdf"}],"doi":"10.15252/embr.202051813","quality_controlled":"1"},{"doi":"10.15479/at:ista:10303","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file":[{"file_size":28005730,"date_created":"2021-11-22T14:48:21Z","relation":"main_file","checksum":"dea38b98aa4da1cea03dcd0f10862818","content_type":"application/pdf","embargo":"2022-11-23","file_id":"10331","access_level":"open_access","file_name":"AbualiaPhDthesisfinalv3.pdf","date_updated":"2022-12-20T23:30:06Z","creator":"rabualia"},{"date_updated":"2022-12-20T23:30:06Z","creator":"rabualia","access_level":"closed","file_id":"10332","file_name":"AbualiaPhDthesisfinalv3.docx","date_created":"2021-11-22T14:48:34Z","embargo_to":"open_access","relation":"source_file","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":62841883}],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva"}],"title":"Role of hormones in nitrate regulated growth","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2021","publication_status":"published","article_processing_charge":"No","corr_author":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-11-22T00:00:00Z","day":"22","author":[{"first_name":"Rashed","full_name":"Abualia, Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"}],"month":"11","language":[{"iso":"eng"}],"type":"dissertation","OA_place":"publisher","_id":"10303","has_accepted_license":"1","abstract":[{"lang":"eng","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. "}],"file_date_updated":"2022-12-20T23:30:06Z","status":"public","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"47"},{"relation":"part_of_dissertation","status":"public","id":"9913"},{"id":"9010","relation":"part_of_dissertation","status":"public"}]},"oa":1,"date_updated":"2026-04-08T07:20:07Z","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","ddc":["580","581"],"citation":{"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.","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>.","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>","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","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>."},"date_created":"2021-11-18T11:20:59Z","page":"139"},{"degree_awarded":"PhD","doi":"10.15479/at:ista:9397","file":[{"date_created":"2021-05-17T12:29:12Z","embargo_to":"open_access","relation":"source_file","checksum":"7f98532f5324a0b2f3fa8de2967baa19","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":47799741,"date_updated":"2022-05-21T22:30:04Z","creator":"khuljev","file_id":"9398","access_level":"closed","file_name":"KHuljev_Thesis_corrections.docx"},{"creator":"khuljev","date_updated":"2022-05-21T22:30:04Z","access_level":"open_access","file_id":"9401","file_name":"new_KHuljev_Thesis_corrections.pdf","embargo":"2022-05-20","checksum":"bf512f8a1e572a543778fc4b227c01ba","content_type":"application/pdf","date_created":"2021-05-18T14:50:28Z","relation":"main_file","file_size":16542131}],"department":[{"_id":"CaHe"},{"_id":"GradSch"}],"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","corr_author":"1","article_processing_charge":"No","author":[{"first_name":"Karla","full_name":"Huljev, Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"day":"18","date_published":"2021-05-18T00:00:00Z","language":[{"iso":"eng"}],"month":"05","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"_id":"9397","OA_place":"publisher","has_accepted_license":"1","type":"dissertation","file_date_updated":"2022-05-21T22:30:04Z","status":"public","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"oa":1,"date_updated":"2026-04-08T07:12:51Z","publication_identifier":{"issn":["2663-337X"]},"page":"101","date_created":"2021-05-17T12:31:30Z","citation":{"ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>."},"ddc":["571"],"publisher":"Institute of Science and Technology Austria"},{"license":"https://creativecommons.org/publicdomain/zero/1.0/","article_processing_charge":"No","corr_author":"1","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"date_published":"2021-01-01T00:00:00Z","day":"01","author":[{"first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2021","publication_status":"published","file":[{"embargo":"2021-12-22","file_name":"Thesis-pdfa.pdf","file_id":"8969","access_level":"open_access","date_updated":"2021-12-23T23:30:04Z","creator":"akafshda","file_size":5251507,"relation":"main_file","date_created":"2020-12-22T20:08:44Z","content_type":"application/pdf","checksum":"d1b9db3725aed34dadd81274aeb9426c"},{"checksum":"1661df7b393e6866d2460eba3c905130","content_type":"application/zip","date_created":"2020-12-22T20:08:50Z","relation":"source_file","embargo_to":"open_access","file_size":10636756,"creator":"akafshda","date_updated":"2021-03-04T23:30:04Z","access_level":"closed","file_id":"8970","file_name":"source.zip"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"title":"Parameterized and algebro-geometric advances in static program analysis","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8934","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","ddc":["005"],"citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","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>.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","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>","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>","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>.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria."},"date_created":"2020-12-10T12:17:07Z","page":"278","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","related_material":{"record":[{"id":"6490","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6780"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"id":"66","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6378"},{"id":"311","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6175"},{"id":"6340","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7014"},{"relation":"part_of_dissertation","status":"public","id":"6009"},{"status":"public","relation":"part_of_dissertation","id":"1437"},{"status":"public","relation":"part_of_dissertation","id":"8728"},{"id":"8089","status":"public","relation":"part_of_dissertation"},{"id":"6380","relation":"part_of_dissertation","status":"public"},{"id":"5977","status":"public","relation":"part_of_dissertation"},{"id":"6056","status":"public","relation":"part_of_dissertation"},{"id":"639","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1386"},{"id":"6918","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7810"},{"status":"public","relation":"part_of_dissertation","id":"949"}]},"date_updated":"2026-04-16T10:07:18Z","oa":1,"file_date_updated":"2021-12-23T23:30:04Z","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).","status":"public","month":"01","language":[{"iso":"eng"}],"type":"dissertation","OA_place":"publisher","_id":"8934","has_accepted_license":"1","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"}]},{"page":"118","citation":{"short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria."},"date_created":"2021-07-27T13:40:30Z","ddc":["532"],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-16T08:43:20Z","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6189"}]},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"status":"public","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"file_date_updated":"2022-07-29T22:30:05Z","abstract":[{"lang":"eng","text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work."}],"OA_place":"publisher","_id":"9728","has_accepted_license":"1","type":"dissertation","language":[{"iso":"eng"}],"month":"07","author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","last_name":"Agrawal","full_name":"Agrawal, Nishchal","first_name":"Nishchal"}],"day":"29","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-07-29T00:00:00Z","corr_author":"1","article_processing_charge":"No","publication_status":"published","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","supervisor":[{"full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"file":[{"file_size":22859658,"relation":"source_file","embargo_to":"open_access","date_created":"2021-07-28T13:32:02Z","content_type":"application/x-zip-compressed","checksum":"77436be3563a90435024307b1b5ee7e8","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","access_level":"closed","file_id":"9744","date_updated":"2022-07-29T22:30:05Z","creator":"nagrawal"},{"file_size":18658048,"relation":"main_file","date_created":"2021-07-28T13:32:05Z","content_type":"application/pdf","checksum":"72a891d7daba85445c29b868c22575ed","embargo":"2022-07-28","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","access_level":"open_access","file_id":"9745","date_updated":"2022-07-29T22:30:05Z","creator":"nagrawal"}],"doi":"10.15479/at:ista:9728","acknowledged_ssus":[{"_id":"M-Shop"}],"degree_awarded":"PhD"},{"publication_status":"published","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","last_name":"Hörmayer"}],"day":"13","date_published":"2021-09-13T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","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","short":"CC BY-NC-ND (4.0)"},"corr_author":"1","article_processing_charge":"No","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"project":[{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"doi":"10.15479/at:ista:9992","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"Wound healing in the Arabidopsis root meristem","supervisor":[{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"lhoermaye","date_updated":"2021-09-15T22:30:26Z","file_name":"Thesis_vupload.docx","file_id":"9993","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"c763064adaa720e16066c1a4f9682bbb","embargo_to":"open_access","relation":"source_file","date_created":"2021-09-09T07:29:48Z","file_size":25179004},{"checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","content_type":"application/pdf","date_created":"2021-09-09T14:25:08Z","relation":"main_file","file_size":6246900,"creator":"lhoermaye","date_updated":"2021-09-15T22:30:26Z","file_id":"9996","access_level":"open_access","file_name":"Thesis_vfinal_pdfa.pdf","embargo":"2021-09-09"}],"oa":1,"date_updated":"2026-04-08T07:11:47Z","related_material":{"record":[{"id":"6943","status":"public","relation":"part_of_dissertation"},{"id":"8002","relation":"part_of_dissertation","status":"public"},{"id":"6351","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"ec_funded":1,"page":"168","citation":{"mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021."},"date_created":"2021-09-09T07:37:20Z","ddc":["575"],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"_id":"9992","OA_place":"publisher","has_accepted_license":"1","type":"dissertation","language":[{"iso":"eng"}],"month":"09","status":"public","file_date_updated":"2021-09-15T22:30:26Z"},{"doi":"10.15479/at:ista:9962","project":[{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of radial neuronal migration"}],"degree_awarded":"PhD","file":[{"checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2021-08-30T09:17:39Z","relation":"source_file","embargo_to":"open_access","file_size":10629190,"creator":"ahansen","date_updated":"2022-09-03T22:30:04Z","file_id":"9971","access_level":"closed","file_name":"Thesis_Hansen.docx"},{"date_updated":"2022-09-03T22:30:04Z","creator":"ahansen","embargo":"2022-09-02","file_name":"Thesis_Hansen_PDFA-1a.pdf","file_id":"9972","access_level":"open_access","relation":"main_file","date_created":"2021-08-30T09:29:44Z","content_type":"application/pdf","checksum":"204fa40321a1c6289b68c473634c4bf3","file_size":13457469}],"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","supervisor":[{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2021","publication_status":"published","corr_author":"1","article_processing_charge":"No","date_published":"2021-09-02T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H"}],"day":"02","month":"09","language":[{"iso":"eng"}],"type":"dissertation","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."}],"_id":"9962","OA_place":"publisher","has_accepted_license":"1","file_date_updated":"2022-09-03T22:30:04Z","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"status":"public","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","oa":1,"date_updated":"2026-04-08T07:19:09Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8569"},{"id":"960","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"citation":{"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.","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>.","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>","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.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","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>.","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>"},"date_created":"2021-08-29T12:36:50Z","publisher":"Institute of Science and Technology Austria","page":"182"},{"month":"07","language":[{"iso":"eng"}],"type":"dissertation","_id":"9623","has_accepted_license":"1","OA_place":"publisher","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"file_date_updated":"2022-07-02T22:30:06Z","status":"public","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9006"},{"id":"9750","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2026-07-06T12:45:39Z","oa":1,"publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","date_created":"2021-07-01T14:50:17Z","citation":{"ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021."},"ddc":["570"],"page":"111","doi":"10.15479/at:ista:9623","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","file":[{"file_name":"PhDThesis_SCM.docx","file_id":"9624","access_level":"closed","date_updated":"2022-07-02T22:30:06Z","creator":"scaballe","file_size":131946790,"relation":"source_file","embargo_to":"open_access","date_created":"2021-07-01T14:48:54Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"e039225a47ef32666d59bf35ddd30ecf"},{"embargo":"2022-07-01","file_id":"9625","access_level":"open_access","file_name":"PhDThesis_SCM.pdf","date_updated":"2022-07-02T22:30:06Z","creator":"scaballe","file_size":17094958,"date_created":"2021-07-01T14:46:25Z","relation":"main_file","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","content_type":"application/pdf"}],"supervisor":[{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2021","publication_status":"published","article_processing_charge":"No","corr_author":"1","date_published":"2021-07-01T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","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","short":"CC BY-NC-ND (4.0)"},"author":[{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia"}]},{"file_date_updated":"2022-12-20T23:30:05Z","status":"public","language":[{"iso":"eng"}],"month":"11","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"has_accepted_license":"1","_id":"10307","OA_place":"publisher","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"page":"73","citation":{"ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>.","apa":"Tomasek, K. (2021). <i>Pathogenic Escherichia coli hijack the host immune response</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10307\">https://doi.org/10.15479/at:ista:10307</a>","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","mla":"Tomasek, Kathrin. <i>Pathogenic Escherichia Coli Hijack the Host Immune Response</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10307\">10.15479/at:ista:10307</a>.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021."},"ddc":["570"],"date_created":"2021-11-18T15:05:06Z","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"oa":1,"date_updated":"2026-07-06T12:48:19Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"file":[{"relation":"main_file","date_created":"2021-11-18T15:07:31Z","content_type":"application/pdf","checksum":"b39c9e0ef18d0484d537a67551effd02","file_size":13266088,"date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","embargo":"2022-11-18","file_name":"ThesisTomasekKathrin.pdf","file_id":"10308","access_level":"open_access"},{"file_size":7539509,"date_created":"2021-11-18T15:07:46Z","embargo_to":"open_access","relation":"source_file","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"10309","file_name":"ThesisTomasekKathrin.docx","date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek"}],"department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"title":"Pathogenic Escherichia coli hijack the host immune response","supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Michael K","full_name":"Sixt, Michael K"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:10307","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"corr_author":"1","article_processing_charge":"No","author":[{"last_name":"Tomasek","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","full_name":"Tomasek, Kathrin"}],"day":"18","date_published":"2021-11-18T00:00:00Z","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published"},{"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"doi":"10.1101/2021.09.28.460602","type":"preprint","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"_id":"10077","month":"09","language":[{"iso":"eng"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","status":"public","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"oa":1,"date_updated":"2026-07-21T22:31:03Z","related_material":{"record":[{"id":"11932","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"later_version","id":"14656"}]},"publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","year":"2021","date_created":"2021-10-04T06:23:34Z","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. .","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>."},"tmp":{"image":"/images/cc_by_nc_nd.png","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","short":"CC BY-NC-ND (4.0)"},"date_published":"2021-09-29T00:00:00Z","publication":"bioRxiv","das_tickbox":"1","ec_funded":1,"author":[{"full_name":"Nardin, Michele","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"first_name":"Cristina","full_name":"Savin, Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87"}],"day":"29","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"article_processing_charge":"No"},{"doi":"10.15479/at:ista:9562","acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"RySh"}],"supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","file":[{"file_size":77299142,"content_type":"application/pdf","checksum":"659df5518db495f679cb1df9e9bd1d94","relation":"main_file","date_created":"2021-06-17T14:03:14Z","file_name":"Thesis.pdf","file_id":"9563","access_level":"open_access","embargo":"2022-07-01","creator":"dkleindienst","date_updated":"2022-07-02T22:30:04Z"},{"creator":"dkleindienst","date_updated":"2022-07-02T22:30:04Z","access_level":"closed","file_id":"9564","file_name":"Thesis_source.zip","checksum":"3bcf63a2b19e5b6663be051bea332748","content_type":"application/zip","date_created":"2021-06-17T14:04:30Z","embargo_to":"open_access","relation":"source_file","file_size":369804895}],"publication_status":"published","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","author":[{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David"}],"date_published":"2021-06-01T00:00:00Z","article_processing_charge":"No","corr_author":"1","_id":"9562","has_accepted_license":"1","OA_place":"publisher","abstract":[{"lang":"eng","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."}],"type":"dissertation","language":[{"iso":"eng"}],"month":"06","status":"public","file_date_updated":"2022-07-02T22:30:04Z","related_material":{"record":[{"id":"9437","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"612"},{"id":"8532","relation":"part_of_dissertation","status":"public"},{"id":"9756","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2026-07-06T13:11:44Z","oa":1,"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"page":"124","publisher":"Institute of Science and Technology Austria","date_created":"2021-06-17T14:10:47Z","ddc":["570"],"citation":{"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>","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.","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.","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>.","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>","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.","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>."},"publication_identifier":{"issn":["2663-337X"]}},{"conference":{"end_date":"2020-05-01","location":"Virtual ; Addis Ababa, Ethiopia","start_date":"2020-04-26","name":"ICLR: International Conference on Learning Representations"},"scopus_import":"1","file_date_updated":"2022-01-26T07:35:17Z","status":"public","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award).\r\n","month":"03","language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity."}],"_id":"10672","has_accepted_license":"1","main_file_link":[{"url":"https://openreview.net/forum?id=Bke61krFvS","open_access":"1"}],"date_created":"2022-01-25T15:50:00Z","ddc":["000"],"citation":{"mla":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” <i>8th International Conference on Learning Representations</i>, ICLR, 2020.","short":"M. Lechner, in:, 8th International Conference on Learning Representations, ICLR, 2020.","chicago":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” In <i>8th International Conference on Learning Representations</i>. ICLR, 2020.","apa":"Lechner, M. (2020). Learning representations for binary-classification without backpropagation. In <i>8th International Conference on Learning Representations</i>. Virtual ; Addis Ababa, Ethiopia: ICLR.","ista":"Lechner M. 2020. Learning representations for binary-classification without backpropagation. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"M. Lechner, “Learning representations for binary-classification without backpropagation,” in <i>8th International Conference on Learning Representations</i>, Virtual ; Addis Ababa, Ethiopia, 2020.","ama":"Lechner M. Learning representations for binary-classification without backpropagation. In: <i>8th International Conference on Learning Representations</i>. ICLR; 2020."},"publisher":"ICLR","publication":"8th International Conference on Learning Representations","oa_version":"Published Version","oa":1,"date_updated":"2025-04-15T06:25:56Z","file":[{"file_size":249431,"success":1,"checksum":"ea13d42dd4541ddb239b6a75821fd6c9","content_type":"application/pdf","date_created":"2022-01-26T07:35:17Z","relation":"main_file","access_level":"open_access","file_id":"10677","file_name":"iclr_2020.pdf","creator":"mlechner","date_updated":"2022-01-26T07:35:17Z"}],"title":"Learning representations for binary-classification without backpropagation","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"quality_controlled":"1","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","corr_author":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png"},"date_published":"2020-03-11T00:00:00Z","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias"}],"day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","publication_status":"published"},{"file":[{"file_name":"2020_PMLR_Hasani.pdf","access_level":"open_access","file_id":"10691","creator":"cchlebak","date_updated":"2022-01-26T11:08:51Z","file_size":2329798,"success":1,"content_type":"application/pdf","checksum":"c9a4a29161777fc1a89ef451c040e3b1","relation":"main_file","date_created":"2022-01-26T11:08:51Z"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"title":"A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"article_processing_charge":"No","author":[{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png"},"date_published":"2020-01-01T00:00:00Z","year":"2020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","file_date_updated":"2022-01-26T11:08:51Z","scopus_import":"1","conference":{"name":"ML: Machine Learning","start_date":"2020-07-12","end_date":"2020-07-18","location":"Virtual"},"status":"public","acknowledgement":"RH and RG are partially supported by Horizon-2020 ECSEL Project grant No. 783163 (iDev40), Productive 4.0, and ATBMBFW CPS-IoT Ecosystem. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award). AA is supported by the National Science Foundation (NSF) Graduate Research Fellowship\r\nProgram. RH and DR are partially supported by The Boeing Company and JP Morgan Chase. This research work is\r\npartially drawn from the PhD dissertation of RH.\r\n","language":[{"iso":"eng"}],"series_title":"PMLR","abstract":[{"lang":"eng","text":"We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level."}],"has_accepted_license":"1","_id":"10673","type":"conference","main_file_link":[{"url":"http://proceedings.mlr.press/v119/hasani20a.html","open_access":"1"}],"publication_identifier":{"issn":["2640-3498"]},"page":"4082-4093","citation":{"mla":"Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, 2020, pp. 4082–93.","short":"R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–4093.","apa":"Hasani, R., Lechner, M., Amini, A., Rus, D., &#38; Grosu, R. (2020). A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (pp. 4082–4093). Virtual.","chicago":"Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu Grosu. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 4082–93. PMLR, 2020.","ista":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2020. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. Proceedings of the 37th International Conference on Machine Learning. ML: Machine LearningPMLR, PMLR, , 4082–4093.","ama":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. PMLR. ; 2020:4082-4093.","ieee":"R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Virtual, 2020, pp. 4082–4093."},"date_created":"2022-01-25T15:50:34Z","ddc":["000"],"publication":"Proceedings of the 37th International Conference on Machine Learning","oa_version":"Published Version","alternative_title":["PMLR"],"date_updated":"2025-04-15T06:25:56Z","oa":1},{"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1709.05202"}],"volume":252,"publication_identifier":{"eissn":["1730-6337"],"issn":["0039-3223"]},"page":"251-297","intvolume":"       252","citation":{"short":"S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297.","mla":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” <i>Studia Mathematica</i>, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:<a href=\"https://doi.org/10.4064/sm180411-11-2\">10.4064/sm180411-11-2</a>.","ama":"Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. <i>Studia Mathematica</i>. 2020;252(3):251-297. doi:<a href=\"https://doi.org/10.4064/sm180411-11-2\">10.4064/sm180411-11-2</a>","ieee":"S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” <i>Studia Mathematica</i>, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020.","chicago":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” <i>Studia Mathematica</i>. Instytut Matematyczny, 2020. <a href=\"https://doi.org/10.4064/sm180411-11-2\">https://doi.org/10.4064/sm180411-11-2</a>.","apa":"Hensel, S., &#38; Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. <i>Studia Mathematica</i>. Instytut Matematyczny. <a href=\"https://doi.org/10.4064/sm180411-11-2\">https://doi.org/10.4064/sm180411-11-2</a>","ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297."},"date_created":"2021-02-25T08:55:03Z","publication":"Studia Mathematica","publisher":"Instytut Matematyczny","oa_version":"Preprint","date_updated":"2025-06-24T12:07:06Z","oa":1,"scopus_import":"1","issue":"3","keyword":["General Mathematics"],"status":"public","external_id":{"isi":["000558100500002"],"arxiv":["1709.05202"]},"isi":1,"language":[{"iso":"eng"}],"month":"03","abstract":[{"lang":"eng","text":"In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \\textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces."}],"_id":"9196","type":"journal_article","arxiv":1,"article_processing_charge":"No","author":[{"last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","full_name":"Hensel, Sebastian"},{"last_name":"Rosati","first_name":"Tommaso","full_name":"Rosati, Tommaso"}],"day":"01","date_published":"2020-03-01T00:00:00Z","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","department":[{"_id":"JuFi"},{"_id":"GradSch"}],"title":"Modelled distributions of Triebel–Lizorkin type","quality_controlled":"1","doi":"10.4064/sm180411-11-2"},{"language":[{"iso":"eng"}],"month":"01","_id":"7196","OA_place":"publisher","has_accepted_license":"1","abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"type":"dissertation","file_date_updated":"2020-07-14T12:47:52Z","status":"public","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"5751"},{"status":"public","relation":"dissertation_contains","id":"7210"},{"relation":"dissertation_contains","status":"public","id":"7212"}]},"date_updated":"2026-04-16T08:32:37Z","oa":1,"publication_identifier":{"eissn":["2663-337X"]},"page":"144","publisher":"Institute of Science and Technology Austria","ddc":["519"],"date_created":"2019-12-20T12:26:36Z","citation":{"mla":"Tkadlec, Josef. <i>A Role of Graphs in Evolutionary Processes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>.","apa":"Tkadlec, J. (2020). <i>A role of graphs in evolutionary processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020."},"doi":"10.15479/AT:ISTA:7196","degree_awarded":"PhD","file":[{"file_name":"thesis.zip","file_id":"7255","access_level":"closed","creator":"jtkadlec","date_updated":"2020-07-14T12:47:52Z","file_size":21100497,"content_type":"application/zip","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","relation":"source_file","date_created":"2020-01-12T11:49:49Z"},{"file_size":11670983,"relation":"main_file","date_created":"2020-01-28T07:32:42Z","content_type":"application/pdf","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","file_name":"2020_Tkadlec_Thesis.pdf","file_id":"7367","access_level":"open_access","date_updated":"2020-07-14T12:47:52Z","creator":"dernst"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"supervisor":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"title":"A role of graphs in evolutionary processes","year":"2020","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","article_processing_charge":"No","corr_author":"1","day":"12","author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","full_name":"Tkadlec, Josef","first_name":"Josef"}],"date_published":"2020-01-12T00:00:00Z"},{"file":[{"date_created":"2020-02-06T14:43:54Z","relation":"main_file","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","content_type":"application/pdf","file_size":76195184,"date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe","access_level":"open_access","file_id":"7461","file_name":"thesis_ist-final_noack.pdf"},{"date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe","access_level":"closed","file_id":"7462","file_name":"latex-files.zip","description":"latex source files, figures","date_created":"2020-02-06T14:52:45Z","relation":"source_file","checksum":"7a52383c812b0be64d3826546509e5a4","content_type":"application/x-zip-compressed","file_size":122103715}],"department":[{"_id":"HeEd"},{"_id":"GradSch"}],"title":"The hole system of triangulated shapes","supervisor":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7460","corr_author":"1","article_processing_charge":"No","author":[{"last_name":"Ölsböck","orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","full_name":"Ölsböck, Katharina"}],"day":"10","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"date_published":"2020-02-10T00:00:00Z","year":"2020","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","file_date_updated":"2020-07-14T12:47:58Z","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"status":"public","language":[{"iso":"eng"}],"month":"02","abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"OA_place":"publisher","_id":"7460","has_accepted_license":"1","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"page":"155","date_created":"2020-02-06T14:56:53Z","ddc":["514"],"citation":{"ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>.","apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>."},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-08T07:23:21Z","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6608"}]}},{"month":"02","language":[{"iso":"eng"}],"type":"dissertation","abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}],"_id":"7514","has_accepted_license":"1","OA_place":"publisher","file_date_updated":"2020-07-14T12:47:59Z","status":"public","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","date_updated":"2026-04-08T07:25:40Z","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7524"}]},"publication_identifier":{"issn":["2663-337X"]},"citation":{"ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","apa":"Mayer, S. (2020). <i>The free energy of a dilute two-dimensional Bose gas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","mla":"Mayer, Simon. <i>The Free Energy of a Dilute Two-Dimensional Bose Gas</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>."},"date_created":"2020-02-24T09:17:27Z","ddc":["510"],"publisher":"Institute of Science and Technology Austria","page":"148","ec_funded":1,"degree_awarded":"PhD","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"doi":"10.15479/AT:ISTA:7514","file":[{"file_id":"7515","access_level":"open_access","file_name":"thesis.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":1563429,"checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","content_type":"application/pdf","date_created":"2020-02-24T09:15:06Z","relation":"main_file"},{"file_size":2028038,"date_created":"2020-02-24T09:15:16Z","relation":"source_file","checksum":"ad7425867b52d7d9e72296e87bc9cb67","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"7516","file_name":"thesis_source.zip","date_updated":"2020-07-14T12:47:59Z","creator":"dernst"}],"title":"The free energy of a dilute two-dimensional Bose gas","supervisor":[{"first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"RoSe"},{"_id":"GradSch"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2020","publication_status":"published","corr_author":"1","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2020-02-24T00:00:00Z","author":[{"first_name":"Simon","full_name":"Mayer, Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"}],"day":"24"}]