--- OA_place: publisher _id: '10293' abstract: - lang: eng text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 citation: ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293 apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293 chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293. ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021. ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293. short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-11-15T17:12:57Z date_published: 2021-11-17T00:00:00Z date_updated: 2026-04-08T07:11:20Z day: '17' ddc: - '519' - '576' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/at:ista:10293 ec_funded: 1 file: - access_level: closed checksum: 86a05b430756ca12ae8107b6e6f3c1e5 content_type: application/zip creator: lschmid date_created: 2021-11-18T12:41:46Z date_updated: 2022-12-20T23:30:08Z embargo_to: open_access file_id: '10305' file_name: submission_new.zip file_size: 29703124 relation: source_file - access_level: open_access checksum: d940af042e94660c6b6a7b4f0b184d47 content_type: application/pdf creator: lschmid date_created: 2021-11-18T12:59:15Z date_updated: 2022-12-20T23:30:08Z embargo: 2022-10-18 file_id: '10306' file_name: thesis_new_upload.pdf file_size: 8320985 relation: main_file file_date_updated: 2022-12-20T23:30:08Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '171' project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9997' relation: part_of_dissertation status: public - id: '9402' relation: part_of_dissertation status: public - id: '2' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Evolution of cooperation via (in)direct reciprocity under imperfect information type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- _id: '9997' 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. 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).' article_number: '17443' article_processing_charge: Yes article_type: original author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Pouya full_name: Shati, Pouya last_name: Shati - first_name: Christian full_name: Hilbe, Christian last_name: Hilbe - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1 apa: Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1 chicago: Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1. ieee: L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, 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. mla: Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1. short: L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021). corr_author: '1' date_created: 2021-09-11T16:22:02Z date_published: 2021-08-31T00:00:00Z date_updated: 2026-07-22T22:30:38Z day: '31' ddc: - '003' department: - _id: GradSch - _id: KrCh doi: 10.1038/s41598-021-96932-1 ec_funded: 1 external_id: isi: - '000692406400018' pmid: - '34465830' file: - access_level: open_access checksum: 19df8816cf958b272b85841565c73182 content_type: application/pdf creator: cchlebak date_created: 2021-09-13T10:31:21Z date_updated: 2021-09-13T10:31:21Z file_id: '10006' file_name: 2021_ScientificReports_Schmid.pdf file_size: 2424943 relation: main_file success: 1 file_date_updated: 2021-09-13T10:31:21Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' keyword: - Multidisciplinary language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication: Scientific Reports publication_identifier: eissn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10293' relation: dissertation_contains status: public scopus_import: '1' status: public title: The evolution of indirect reciprocity under action and assessment generosity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- OA_place: publisher _id: '10135' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hana full_name: Semerádová, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semerádová citation: ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135 apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135 chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135. ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021. ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135. short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-10-13T13:42:48Z date_published: 2021-10-13T00:00:00Z date_updated: 2026-04-08T07:12:06Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10135 file: - access_level: closed checksum: ce7108853e6cec6224f17cd6429b51fe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cziletti date_created: 2021-10-27T07:45:37Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10186' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx file_size: 28508629 relation: source_file - access_level: open_access checksum: 0d7afb846e8e31ec794de47bf44e12ef content_type: application/pdf creator: cziletti date_created: 2021-10-27T07:45:57Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-10-28 file_id: '10187' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf file_size: 10623525 relation: main_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis publication_identifier: isbn: - 978-3-99078-014-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- _id: '9402' 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. acknowledgement: 'This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' article_processing_charge: No article_type: original author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8 apa: Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8 chicago: Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8. ieee: L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021. 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. mla: Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8. short: L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302. corr_author: '1' date_created: 2021-05-18T16:56:57Z date_published: 2021-05-13T00:00:00Z date_updated: 2026-07-22T22:30:38Z day: '13' ddc: - '000' department: - _id: KrCh - _id: GradSch doi: 10.1038/s41562-021-01114-8 ec_funded: 1 external_id: isi: - '000650304000002' pmid: - '33986519' file: - access_level: open_access checksum: 34f55e173f90dc1dab731063458ac780 content_type: application/pdf creator: dernst date_created: 2023-11-07T08:27:23Z date_updated: 2023-11-07T08:27:23Z file_id: '14496' file_name: 2021_NatureHumanBehaviour_Schmid_accepted.pdf file_size: 5232761 relation: main_file success: 1 file_date_updated: 2023-11-07T08:27:23Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '10' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 1292–1302 pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Nature Human Behaviour publication_identifier: eissn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/the-emergence-of-cooperation/ record: - id: '10293' relation: dissertation_contains status: public scopus_import: '1' status: public title: A unified framework of direct and indirect reciprocity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2021' ... --- _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. acknowledgement: This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC). article_number: e51813 article_processing_charge: Yes article_type: original author: - first_name: Andrea full_name: Vega, Andrea last_name: Vega - first_name: Isabel full_name: Fredes, Isabel last_name: Fredes - first_name: José full_name: O’Brien, José last_name: O’Brien - first_name: Zhouxin full_name: Shen, Zhouxin last_name: Shen - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Steven P. full_name: Briggs, Steven P. last_name: Briggs - first_name: Rodrigo A. full_name: Gutiérrez, Rodrigo A. last_name: Gutiérrez citation: ama: Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813 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. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813 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.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813. ieee: A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021. ista: Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813. mla: Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813. 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 date_published: 2021-09-06T00:00:00Z date_updated: 2026-07-22T22:30:40Z day: '06' ddc: - '580' department: - _id: EvBe - _id: GradSch doi: 10.15252/embr.202051813 external_id: isi: - '000681754200001' pmid: - '34357701 ' file: - access_level: open_access checksum: 750de03dc3b715c37090126c1548ba13 content_type: application/pdf creator: cchlebak date_created: 2021-10-05T13:36:42Z date_updated: 2021-10-05T13:36:42Z file_id: '10090' file_name: 2021_EmboR_Vega.pdf file_size: 3144854 relation: main_file success: 1 file_date_updated: 2021-10-05T13:36:42Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '10303' relation: dissertation_contains status: public scopus_import: '1' status: public title: Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2021' ... --- OA_place: publisher _id: '10303' 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. ' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 citation: ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303 apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303 chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303. ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021. ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303. short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-11-18T11:20:59Z date_published: 2021-11-22T00:00:00Z date_updated: 2026-04-08T07:20:07Z day: '22' ddc: - '580' - '581' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10303 file: - access_level: open_access checksum: dea38b98aa4da1cea03dcd0f10862818 content_type: application/pdf creator: rabualia date_created: 2021-11-22T14:48:21Z date_updated: 2022-12-20T23:30:06Z embargo: 2022-11-23 file_id: '10331' file_name: AbualiaPhDthesisfinalv3.pdf file_size: 28005730 relation: main_file - access_level: closed checksum: 4cd62da5ec5ba4c32e61f0f6d9e61920 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rabualia date_created: 2021-11-22T14:48:34Z date_updated: 2022-12-20T23:30:06Z embargo_to: open_access file_id: '10332' file_name: AbualiaPhDthesisfinalv3.docx file_size: 62841883 relation: source_file file_date_updated: 2022-12-20T23:30:06Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '139' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '47' relation: part_of_dissertation status: public - id: '9913' relation: part_of_dissertation status: public - id: '9010' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Role of hormones in nitrate regulated growth tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9397' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev citation: ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397 apa: Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397 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. https://doi.org/10.15479/at:ista:9397. 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. 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. mla: Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397. 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. corr_author: '1' date_created: 2021-05-17T12:31:30Z date_published: 2021-05-18T00:00:00Z date_updated: 2026-04-08T07:12:51Z day: '18' ddc: - '571' degree_awarded: PhD department: - _id: CaHe - _id: GradSch doi: 10.15479/at:ista:9397 file: - access_level: closed checksum: 7f98532f5324a0b2f3fa8de2967baa19 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: khuljev date_created: 2021-05-17T12:29:12Z date_updated: 2022-05-21T22:30:04Z embargo_to: open_access file_id: '9398' file_name: KHuljev_Thesis_corrections.docx file_size: 47799741 relation: source_file - access_level: open_access checksum: bf512f8a1e572a543778fc4b227c01ba content_type: application/pdf creator: khuljev date_created: 2021-05-18T14:50:28Z date_updated: 2022-05-21T22:30:04Z embargo: 2022-05-20 file_id: '9401' file_name: new_KHuljev_Thesis_corrections.pdf file_size: 16542131 relation: main_file file_date_updated: 2022-05-21T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '101' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '8934' abstract: - lang: eng 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." 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).' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934 apa: Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934 chicago: Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934. ieee: A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021. ista: Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. mla: Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934. short: A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2020-12-10T12:17:07Z date_published: 2021-01-01T00:00:00Z date_updated: 2026-04-16T10:07:18Z day: '01' ddc: - '005' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/AT:ISTA:8934 file: - access_level: open_access checksum: d1b9db3725aed34dadd81274aeb9426c content_type: application/pdf creator: akafshda date_created: 2020-12-22T20:08:44Z date_updated: 2021-12-23T23:30:04Z embargo: 2021-12-22 file_id: '8969' file_name: Thesis-pdfa.pdf file_size: 5251507 relation: main_file - access_level: closed checksum: 1661df7b393e6866d2460eba3c905130 content_type: application/zip creator: akafshda date_created: 2020-12-22T20:08:50Z date_updated: 2021-03-04T23:30:04Z embargo_to: open_access file_id: '8970' file_name: source.zip file_size: 10636756 relation: source_file file_date_updated: 2021-12-23T23:30:04Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/publicdomain/zero/1.0/ month: '01' oa: 1 oa_version: Published Version page: '278' 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 publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6490' relation: part_of_dissertation status: public - id: '6780' relation: part_of_dissertation status: public - id: '7158' relation: part_of_dissertation status: public - id: '66' relation: part_of_dissertation status: public - id: '6378' relation: part_of_dissertation status: public - id: '311' relation: part_of_dissertation status: public - id: '6175' relation: part_of_dissertation status: public - id: '6340' relation: part_of_dissertation status: public - id: '7014' relation: part_of_dissertation status: public - id: '6009' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '8728' relation: part_of_dissertation status: public - id: '8089' relation: part_of_dissertation status: public - id: '6380' relation: part_of_dissertation status: public - id: '5977' relation: part_of_dissertation status: public - id: '6056' relation: part_of_dissertation status: public - id: '639' relation: part_of_dissertation status: public - id: '1386' relation: part_of_dissertation status: public - id: '6918' relation: part_of_dissertation status: public - id: '7810' relation: part_of_dissertation status: public - id: '949' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Parameterized and algebro-geometric advances in static program analysis tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9728' 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." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nishchal full_name: Agrawal, Nishchal id: 469E6004-F248-11E8-B48F-1D18A9856A87 last_name: Agrawal citation: ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728 apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728 chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728. ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021. ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728. short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-07-27T13:40:30Z date_published: 2021-07-29T00:00:00Z date_updated: 2026-04-16T08:43:20Z day: '29' ddc: - '532' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:9728 file: - access_level: closed checksum: 77436be3563a90435024307b1b5ee7e8 content_type: application/x-zip-compressed creator: nagrawal date_created: 2021-07-28T13:32:02Z date_updated: 2022-07-29T22:30:05Z embargo_to: open_access file_id: '9744' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip file_size: 22859658 relation: source_file - access_level: open_access checksum: 72a891d7daba85445c29b868c22575ed content_type: application/pdf creator: nagrawal date_created: 2021-07-28T13:32:05Z date_updated: 2022-07-29T22:30:05Z embargo: 2022-07-28 file_id: '9745' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf file_size: 18658048 relation: main_file file_date_updated: 2022-07-29T22:30:05Z has_accepted_license: '1' keyword: - Drag Reduction - Transition to Turbulence - Multiphase Flows - particle Laden Flows - Complex Flows - Experiments - Fluid Dynamics language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '118' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6189' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Transition to turbulence and drag reduction in particle-laden pipe flows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9992' 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. " acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 citation: ama: Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992 apa: Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992 chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992. ieee: 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. mla: Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992. short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-09-09T07:37:20Z date_published: 2021-09-13T00:00:00Z date_updated: 2026-04-08T07:11:47Z day: '13' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:9992 ec_funded: 1 file: - access_level: closed checksum: c763064adaa720e16066c1a4f9682bbb content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lhoermaye date_created: 2021-09-09T07:29:48Z date_updated: 2021-09-15T22:30:26Z embargo_to: open_access file_id: '9993' file_name: Thesis_vupload.docx file_size: 25179004 relation: source_file - access_level: open_access checksum: 53911b06e93d7cdbbf4c7f4c162fa70f content_type: application/pdf creator: lhoermaye date_created: 2021-09-09T14:25:08Z date_updated: 2021-09-15T22:30:26Z embargo: 2021-09-09 file_id: '9996' file_name: Thesis_vfinal_pdfa.pdf file_size: 6246900 relation: main_file file_date_updated: 2021-09-15T22:30:26Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '168' project: - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6943' relation: part_of_dissertation status: public - id: '8002' relation: part_of_dissertation status: public - id: '6351' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Wound healing in the Arabidopsis root meristem tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9962' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen citation: ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962 apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962 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. https://doi.org/10.15479/at:ista:9962. 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. mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962. 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. corr_author: '1' date_created: 2021-08-29T12:36:50Z date_published: 2021-09-02T00:00:00Z date_updated: 2026-04-08T07:19:09Z day: '02' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/at:ista:9962 file: - access_level: closed checksum: 66b56f5b988b233dc66a4f4b4fb2cdfe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ahansen date_created: 2021-08-30T09:17:39Z date_updated: 2022-09-03T22:30:04Z embargo_to: open_access file_id: '9971' file_name: Thesis_Hansen.docx file_size: 10629190 relation: source_file - access_level: open_access checksum: 204fa40321a1c6289b68c473634c4bf3 content_type: application/pdf creator: ahansen date_created: 2021-08-30T09:29:44Z date_updated: 2022-09-03T22:30:04Z embargo: 2022-09-02 file_id: '9972' file_name: Thesis_Hansen_PDFA-1a.pdf file_size: 13457469 relation: main_file file_date_updated: 2022-09-03T22:30:04Z has_accepted_license: '1' keyword: - Neuronal migration - Non-cell-autonomous - Cell-autonomous - Neurodevelopmental disease language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '182' project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular mechanisms of radial neuronal migration publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8569' relation: part_of_dissertation status: public - id: '960' relation: part_of_dissertation status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9623' abstract: - lang: eng 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" acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 citation: ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623 apa: 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. https://doi.org/10.15479/at:ista:9623 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. https://doi.org/10.15479/at:ista:9623. 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. 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. mla: 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, doi:10.15479/at:ista:9623. 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. corr_author: '1' date_created: 2021-07-01T14:50:17Z date_published: 2021-07-01T00:00:00Z date_updated: 2026-07-06T12:45:39Z ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:9623 file: - access_level: closed checksum: e039225a47ef32666d59bf35ddd30ecf content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: scaballe date_created: 2021-07-01T14:48:54Z date_updated: 2022-07-02T22:30:06Z embargo_to: open_access file_id: '9624' file_name: PhDThesis_SCM.docx file_size: 131946790 relation: source_file - access_level: open_access checksum: dd4d78962ea94ad95e97ca7d9af08f4b content_type: application/pdf creator: scaballe date_created: 2021-07-01T14:46:25Z date_updated: 2022-07-02T22:30:06Z embargo: 2022-07-01 file_id: '9625' file_name: PhDThesis_SCM.pdf file_size: 17094958 relation: main_file file_date_updated: 2022-07-02T22:30:06Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '111' publication_identifier: isbn: - 978-3-99078-012-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9006' relation: part_of_dissertation status: public - id: '9750' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10307' 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. acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: PreCl - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X citation: ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307 apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307 chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307. ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021. ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307. short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-11-18T15:05:06Z date_published: 2021-11-18T00:00:00Z date_updated: 2026-07-06T12:48:19Z day: '18' ddc: - '570' degree_awarded: PhD department: - _id: MiSi - _id: CaGu - _id: GradSch doi: 10.15479/at:ista:10307 file: - access_level: open_access checksum: b39c9e0ef18d0484d537a67551effd02 content_type: application/pdf creator: ktomasek date_created: 2021-11-18T15:07:31Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-11-18 file_id: '10308' file_name: ThesisTomasekKathrin.pdf file_size: 13266088 relation: main_file - access_level: closed checksum: c0c440ee9e5ef1102a518a4f9f023e7c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ktomasek date_created: 2021-11-18T15:07:46Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10309' file_name: ThesisTomasekKathrin.docx file_size: 7539509 relation: source_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '73' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10316' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Pathogenic Escherichia coli hijack the host immune response type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- _id: '10077' 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. 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. article_processing_charge: No author: - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin citation: ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602 apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. https://doi.org/10.1101/2021.09.28.460602 chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, n.d. https://doi.org/10.1101/2021.09.28.460602. ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. . ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602. mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, doi:10.1101/2021.09.28.460602. short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.). das_tickbox: '1' date_created: 2021-10-04T06:23:34Z date_published: 2021-09-29T00:00:00Z date_updated: 2026-07-22T22:31:03Z day: '29' department: - _id: GradSch - _id: JoCs - _id: GaTk doi: 10.1101/2021.09.28.460602 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2021.09.28.460602 month: '09' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism publication: bioRxiv publication_status: draft related_material: record: - id: '11932' relation: dissertation_contains status: public - id: '14656' relation: later_version status: public status: public title: The structure of hippocampal CA1 interactions optimizes spatial coding across experience tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- OA_place: publisher _id: '9562' 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. acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst 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:10.15479/at:ista:9562' apa: '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. https://doi.org/10.15479/at:ista:9562' 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. https://doi.org/10.15479/at:ista:9562.' 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.' mla: '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, doi:10.15479/at:ista:9562.' 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.' corr_author: '1' date_created: 2021-06-17T14:10:47Z date_published: 2021-06-01T00:00:00Z date_updated: 2026-07-06T13:11:44Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:9562 file: - access_level: open_access checksum: 659df5518db495f679cb1df9e9bd1d94 content_type: application/pdf creator: dkleindienst date_created: 2021-06-17T14:03:14Z date_updated: 2022-07-02T22:30:04Z embargo: 2022-07-01 file_id: '9563' file_name: Thesis.pdf file_size: 77299142 relation: main_file - access_level: closed checksum: 3bcf63a2b19e5b6663be051bea332748 content_type: application/zip creator: dkleindienst date_created: 2021-06-17T14:04:30Z date_updated: 2022-07-02T22:30:04Z embargo_to: open_access file_id: '9564' file_name: Thesis_source.zip file_size: 369804895 relation: source_file file_date_updated: 2022-07-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '124' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9437' relation: part_of_dissertation status: public - id: '612' relation: part_of_dissertation status: public - id: '8532' relation: part_of_dissertation status: public - id: '9756' relation: part_of_dissertation status: public status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- _id: '10672' 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. acknowledgement: "This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award).\r\n" article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner citation: ama: 'Lechner M. Learning representations for binary-classification without backpropagation. In: 8th International Conference on Learning Representations. ICLR; 2020.' apa: 'Lechner, M. (2020). Learning representations for binary-classification without backpropagation. In 8th International Conference on Learning Representations. Virtual ; Addis Ababa, Ethiopia: ICLR.' chicago: Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” In 8th International Conference on Learning Representations. ICLR, 2020. ieee: M. Lechner, “Learning representations for binary-classification without backpropagation,” in 8th International Conference on Learning Representations, Virtual ; Addis Ababa, Ethiopia, 2020. ista: 'Lechner M. 2020. Learning representations for binary-classification without backpropagation. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” 8th International Conference on Learning Representations, ICLR, 2020. short: M. Lechner, in:, 8th International Conference on Learning Representations, ICLR, 2020. conference: end_date: 2020-05-01 location: Virtual ; Addis Ababa, Ethiopia name: 'ICLR: International Conference on Learning Representations' start_date: 2020-04-26 corr_author: '1' date_created: 2022-01-25T15:50:00Z date_published: 2020-03-11T00:00:00Z date_updated: 2025-04-15T06:25:56Z day: '11' ddc: - '000' department: - _id: GradSch - _id: ToHe file: - access_level: open_access checksum: ea13d42dd4541ddb239b6a75821fd6c9 content_type: application/pdf creator: mlechner date_created: 2022-01-26T07:35:17Z date_updated: 2022-01-26T07:35:17Z file_id: '10677' file_name: iclr_2020.pdf file_size: 249431 relation: main_file success: 1 file_date_updated: 2022-01-26T07:35:17Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ main_file_link: - open_access: '1' url: https://openreview.net/forum?id=Bke61krFvS month: '03' oa: 1 oa_version: Published Version project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication: 8th International Conference on Learning Representations publication_status: published publisher: ICLR quality_controlled: '1' scopus_import: '1' status: public title: Learning representations for binary-classification without backpropagation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '10673' 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. 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" alternative_title: - PMLR article_processing_charge: No author: - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In: Proceedings of the 37th International Conference on Machine Learning. PMLR. ; 2020:4082-4093.' apa: 'Hasani, R., Lechner, M., Amini, A., Rus, D., & Grosu, R. (2020). A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In Proceedings of the 37th International Conference on Machine Learning (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 Proceedings of the 37th International Conference on Machine Learning, 4082–93. PMLR, 2020.' ieee: 'R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, pp. 4082–4093.' 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.' mla: 'Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” Proceedings of the 37th International Conference on Machine Learning, 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. conference: end_date: 2020-07-18 location: Virtual name: 'ML: Machine Learning' start_date: 2020-07-12 date_created: 2022-01-25T15:50:34Z date_published: 2020-01-01T00:00:00Z date_updated: 2025-04-15T06:25:56Z ddc: - '000' department: - _id: GradSch - _id: ToHe file: - access_level: open_access checksum: c9a4a29161777fc1a89ef451c040e3b1 content_type: application/pdf creator: cchlebak date_created: 2022-01-26T11:08:51Z date_updated: 2022-01-26T11:08:51Z file_id: '10691' file_name: 2020_PMLR_Hasani.pdf file_size: 2329798 relation: main_file success: 1 file_date_updated: 2022-01-26T11:08:51Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://proceedings.mlr.press/v119/hasani20a.html oa: 1 oa_version: Published Version page: 4082-4093 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication: Proceedings of the 37th International Conference on Machine Learning publication_identifier: issn: - 2640-3498 publication_status: published quality_controlled: '1' scopus_import: '1' series_title: PMLR status: public title: 'A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '9196' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tommaso full_name: Rosati, Tommaso last_name: Rosati citation: ama: Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2 apa: Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2 chicago: Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2. ieee: S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020. ista: Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297. mla: Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2. short: S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297. date_created: 2021-02-25T08:55:03Z date_published: 2020-03-01T00:00:00Z date_updated: 2025-06-24T12:07:06Z day: '01' department: - _id: JuFi - _id: GradSch doi: 10.4064/sm180411-11-2 external_id: arxiv: - '1709.05202' isi: - '000558100500002' intvolume: ' 252' isi: 1 issue: '3' keyword: - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1709.05202 month: '03' oa: 1 oa_version: Preprint page: 251-297 publication: Studia Mathematica publication_identifier: eissn: - 1730-6337 issn: - 0039-3223 publication_status: published publisher: Instytut Matematyczny quality_controlled: '1' scopus_import: '1' status: public title: Modelled distributions of Triebel–Lizorkin type type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 252 year: '2020' ... --- OA_place: publisher _id: '7196' abstract: - lang: eng 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.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196 apa: Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196 chicago: Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196. ieee: J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020. ista: Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria. mla: Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196. short: J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2019-12-20T12:26:36Z date_published: 2020-01-12T00:00:00Z date_updated: 2026-04-16T08:32:37Z day: '12' ddc: - '519' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/AT:ISTA:7196 file: - access_level: closed checksum: 451f8e64b0eb26bf297644ac72bfcbe9 content_type: application/zip creator: jtkadlec date_created: 2020-01-12T11:49:49Z date_updated: 2020-07-14T12:47:52Z file_id: '7255' file_name: thesis.zip file_size: 21100497 relation: source_file - access_level: open_access checksum: d8c44cbc4f939c49a8efc9d4b8bb3985 content_type: application/pdf creator: dernst date_created: 2020-01-28T07:32:42Z date_updated: 2020-07-14T12:47:52Z file_id: '7367' file_name: 2020_Tkadlec_Thesis.pdf file_size: 11670983 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '144' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '5751' relation: dissertation_contains status: public - id: '7210' relation: dissertation_contains status: public - id: '7212' relation: dissertation_contains status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: A role of graphs in evolutionary processes type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- OA_place: publisher _id: '7460' abstract: - lang: eng 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Katharina full_name: Ölsböck, Katharina id: 4D4AA390-F248-11E8-B48F-1D18A9856A87 last_name: Ölsböck orcid: 0000-0002-4672-8297 citation: ama: Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460 apa: Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460 chicago: Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460. 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. mla: Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460. short: K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-02-06T14:56:53Z date_published: 2020-02-10T00:00:00Z date_updated: 2026-04-08T07:23:21Z day: '10' ddc: - '514' degree_awarded: PhD department: - _id: HeEd - _id: GradSch doi: 10.15479/AT:ISTA:7460 file: - access_level: open_access checksum: 1df9f8c530b443c0e63a3f2e4fde412e content_type: application/pdf creator: koelsboe date_created: 2020-02-06T14:43:54Z date_updated: 2020-07-14T12:47:58Z file_id: '7461' file_name: thesis_ist-final_noack.pdf file_size: 76195184 relation: main_file - access_level: closed checksum: 7a52383c812b0be64d3826546509e5a4 content_type: application/x-zip-compressed creator: koelsboe date_created: 2020-02-06T14:52:45Z date_updated: 2020-07-14T12:47:58Z description: latex source files, figures file_id: '7462' file_name: latex-files.zip file_size: 122103715 relation: source_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' keyword: - shape reconstruction - hole manipulation - ordered complexes - Alpha complex - Wrap complex - computational topology - Bregman geometry language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '02' oa: 1 oa_version: Published Version page: '155' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6608' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: The hole system of triangulated shapes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ...