--- _id: '14587' abstract: - lang: eng text: "This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero." acknowledgement: The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alice full_name: Marveggio, Alice id: 25647992-AA84-11E9-9D75-8427E6697425 last_name: Marveggio citation: ama: Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587 apa: Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587 chicago: Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587. ieee: A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023. ista: Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. mla: Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587. short: A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023. date_created: 2023-11-21T11:41:05Z date_published: 2023-11-21T00:00:00Z date_updated: 2024-03-22T13:21:28Z day: '21' ddc: - '515' degree_awarded: PhD department: - _id: GradSch - _id: JuFi doi: 10.15479/at:ista:14587 ec_funded: 1 file: - access_level: open_access checksum: 6c7db4cc86da6cdc79f7f358dc7755d4 content_type: application/pdf creator: amarvegg date_created: 2023-11-29T09:09:31Z date_updated: 2023-11-29T09:09:31Z file_id: '14626' file_name: thesis_Marveggio.pdf file_size: 2881100 relation: main_file success: 1 - access_level: closed checksum: 52f28bdf95ec82cff39f3685f9c48e7d content_type: application/zip creator: amarvegg date_created: 2023-11-29T09:10:19Z date_updated: 2024-03-20T12:28:32Z file_id: '14627' file_name: Thesis_Marveggio.zip file_size: 10189696 relation: source_file file_date_updated: 2024-03-20T12:28:32Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: '228' project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11842' relation: part_of_dissertation status: public - id: '14597' relation: part_of_dissertation status: public status: public supervisor: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X title: Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12491' abstract: - lang: eng text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 citation: ama: Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491 apa: Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491 chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491. ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023. ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491. short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023. date_created: 2023-02-02T14:50:20Z date_published: 2023-02-02T00:00:00Z date_updated: 2024-03-25T23:30:05Z day: '02' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:12491 file: - access_level: open_access checksum: 069d87f025e0799bf9e3c375664264f2 content_type: application/pdf creator: bzens date_created: 2023-02-07T13:07:38Z date_updated: 2024-02-08T23:30:04Z embargo: 2024-02-07 file_id: '12527' file_name: PhDThesis_BettinaZens_2023_final.pdf file_size: 23082464 relation: main_file - access_level: closed checksum: 8c66ed203495d6e078ed1002a866520c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: bzens date_created: 2023-02-07T13:09:05Z date_updated: 2024-02-08T23:30:04Z embargo_to: open_access file_id: '12528' file_name: PhDThesis_BettinaZens_2023_final.docx file_size: 106169509 relation: source_file file_date_updated: 2024-02-08T23:30:04Z has_accepted_license: '1' keyword: - cryo-EM - cryo-ET - FIB milling - method development - FIBSEM - extracellular matrix - ECM - cell-derived matrices - CDMs - cell culture - high pressure freezing - HPF - structural biology - tomography - collagen language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '187' project: - _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3 name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions - _id: 059B463C-7A3F-11EA-A408-12923DDC885E name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria publication_identifier: isbn: - 978-3-99078-027-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8586' relation: part_of_dissertation status: public status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 title: Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14226' abstract: - lang: eng text: "We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes." alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Elizabeth R full_name: Stephenson, Elizabeth R id: 2D04F932-F248-11E8-B48F-1D18A9856A87 last_name: Stephenson orcid: 0000-0002-6862-208X citation: ama: Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226 apa: Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226 chicago: Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226. ieee: E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023. ista: Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria. mla: Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226. short: E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023. date_created: 2023-08-24T13:01:18Z date_published: 2023-08-24T00:00:00Z date_updated: 2024-02-26T23:30:04Z day: '24' ddc: - '500' degree_awarded: MS department: - _id: GradSch - _id: HeEd doi: 10.15479/at:ista:14226 file: - access_level: closed checksum: 453caf851d75c3478c10ed09bd242a91 content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-08-24T13:02:49Z date_updated: 2024-02-26T23:30:03Z embargo_to: open_access file_id: '14227' file_name: documents-export-2023-08-24.zip file_size: 15501411 relation: source_file - access_level: open_access checksum: 7349d29963d6695e555e171748648d9a content_type: application/pdf creator: cchlebak date_created: 2023-08-24T13:03:42Z date_updated: 2024-02-26T23:30:03Z embargo: 2024-02-25 file_id: '14228' file_name: thesis_pdf_a.pdf file_size: 6854783 relation: main_file file_date_updated: 2024-02-26T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '43' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria 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: Generalizing medial axes with homology switches type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12470' abstract: - lang: eng text: "The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\x02resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\x02resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl - _id: EM-Fac - _id: M-Shop - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia M full_name: Michalska, Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska orcid: 0000-0003-3862-1235 citation: ama: Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470 apa: Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470 chicago: Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470. ieee: J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023. ista: Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. mla: Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470. short: J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023. date_created: 2023-01-31T15:10:53Z date_published: 2023-01-09T00:00:00Z date_updated: 2023-08-31T12:26:58Z day: '09' ddc: - '610' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:12470 ec_funded: 1 file: - access_level: open_access checksum: 1a2306e5f59f52df598e7ecfadf921ac content_type: application/pdf creator: cchlebak date_created: 2023-01-31T15:11:42Z date_updated: 2023-07-27T22:30:54Z embargo: 2023-07-09 file_id: '12471' file_name: 20230109_PhD_thesis_JM_final.pdf file_size: 41771714 relation: main_file - access_level: closed checksum: 0bebbdee0773443959e1f6ab8caf281f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-01-31T15:11:51Z date_updated: 2023-07-10T22:30:04Z embargo_to: open_access file_id: '12472' file_name: 20230109_PhD_thesis_JM_final.docx file_size: 66983464 relation: source_file file_date_updated: 2023-07-27T22:30:54Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version page: '201' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication_identifier: isbn: - ' 978-3-99078-026-8' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11943' relation: part_of_dissertation status: public - id: '11950' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12531' abstract: - lang: eng text: "All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics." alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Kseniia full_name: Kirillova, Kseniia id: 8e3f931e-dc85-11ea-9058-e7b957bf23f0 last_name: Kirillova citation: ama: Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531 apa: Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531 chicago: Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531. ieee: K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023. ista: Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. mla: Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531. short: K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023. date_created: 2023-02-09T07:45:05Z date_published: 2023-02-08T00:00:00Z date_updated: 2024-02-09T23:30:04Z day: '08' ddc: - '570' degree_awarded: MS department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:12531 file: - access_level: open_access checksum: 57d8da3a6c749eb1556b7435fe266a5f content_type: application/pdf creator: cchlebak date_created: 2023-02-09T08:03:32Z date_updated: 2024-02-09T23:30:03Z embargo: 2024-02-08 file_id: '12532' file_name: Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf file_size: 8369317 relation: main_file - access_level: closed checksum: 87fb44318e4f9eb9da2ad9ad6ca8e76f content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-02-10T09:32:06Z date_updated: 2024-02-09T23:30:03Z embargo_to: open_access file_id: '12535' file_name: Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip file_size: 11204408 relation: source_file file_date_updated: 2024-02-09T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '46' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: Panoramic functional gradients across the mouse retina 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2023' ... --- _id: '12800' abstract: - lang: eng text: 'The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ' alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth citation: ama: Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800 apa: Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800 chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800. ieee: M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023. ista: Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800. short: M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023. date_created: 2023-04-04T18:57:11Z date_published: 2023-04-05T00:00:00Z date_updated: 2023-06-02T22:30:05Z day: '05' ddc: - '576' degree_awarded: MS department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:12800 file: - access_level: closed checksum: b76cf6d69f2093d8248f6a3f9d4654a4 content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: mjulseth date_created: 2023-04-06T06:09:40Z date_updated: 2023-06-02T22:30:04Z embargo_to: open_access file_id: '12805' file_name: Dispersaldata.xlsx file_size: 52795 relation: supplementary_material - access_level: open_access checksum: 5a13b6d204371572e249f03795bc0d04 content_type: application/vnd.wolfram.nb creator: mjulseth date_created: 2023-04-06T06:11:27Z date_updated: 2023-06-02T22:30:04Z embargo: 2023-06-01 file_id: '12806' file_name: 2023_MSc_ThesisMaraJulseth_Notebook.nb file_size: 787239 relation: supplementary_material - access_level: closed checksum: c3ec842839ed1e66bf2618ae33047df8 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mjulseth date_created: 2023-04-06T08:26:12Z date_updated: 2023-06-02T22:30:04Z embargo_to: open_access file_id: '12812' file_name: ThesisMaraJulseth_04_23.docx file_size: 1061763 relation: source_file - access_level: open_access checksum: 3132cc998fbe3ae2a3a83c2a69367f37 content_type: application/pdf creator: mjulseth date_created: 2023-04-06T08:26:37Z date_updated: 2023-06-02T22:30:04Z embargo: 2023-06-01 file_id: '12813' file_name: ThesisMaraJulseth_04_23.pdf file_size: 1741364 relation: main_file file_date_updated: 2023-06-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '21' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14510' acknowledged_ssus: - _id: EM-Fac - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 citation: ama: Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510 apa: Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510 chicago: Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510. ieee: N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023. ista: Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria. mla: Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510. short: N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023. date_created: 2023-11-10T09:10:06Z date_published: 2023-11-10T00:00:00Z date_updated: 2024-03-27T23:30:45Z day: '10' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: MaLo doi: 10.15479/at:ista:14510 ec_funded: 1 file: - access_level: closed checksum: 3d5e680bfc61f98e308c434f45cc9bd6 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ngnyliuk date_created: 2023-11-20T09:18:51Z date_updated: 2023-11-20T09:18:51Z file_id: '14567' file_name: Thesis_Gnyliukh_final_08_11_23.docx file_size: 20824903 relation: source_file - access_level: closed checksum: bfc96d47fc4e7e857dd71656097214a4 content_type: application/pdf creator: ngnyliuk date_created: 2023-11-20T09:23:11Z date_updated: 2023-11-23T13:10:55Z embargo: 2024-11-23 embargo_to: open_access file_id: '14568' file_name: Thesis_Gnyliukh_final_20_11_23.pdf file_size: 24871844 relation: main_file file_date_updated: 2023-11-23T13:10:55Z has_accepted_license: '1' keyword: - Clathrin-Mediated Endocytosis - vesicle scission - Dynamin-Related Protein 2 - SH3P2 - TPLATE complex - Total internal reflection fluorescence microscopy - Arabidopsis thaliana language: - iso: eng month: '11' oa_version: Published Version page: '180' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-037-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14591' relation: part_of_dissertation status: public - id: '9887' relation: part_of_dissertation status: public - id: '8139' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Mechanism of clathrin-coated vesicle formation during endocytosis in plants tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12897' abstract: - lang: eng text: "Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner citation: ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897' apa: 'Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897' chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.' ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.' ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.' mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.' short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-05T10:40:14Z date_published: 2023-05-05T00:00:00Z date_updated: 2024-01-29T10:47:51Z day: '05' ddc: - '516' - '004' - '518' - '531' degree_awarded: PhD department: - _id: GradSch - _id: BeBi doi: 10.15479/at:ista:12897 ec_funded: 1 file: - access_level: open_access checksum: cc2094e92fa27000b70eb4bfb76d6b5a content_type: application/pdf creator: chafner date_created: 2023-05-11T10:43:20Z date_updated: 2023-12-08T23:30:04Z embargo: 2023-12-07 file_id: '12942' file_name: thesis-hafner-2023may11-a2b.pdf file_size: 50714445 relation: main_file - access_level: closed checksum: a6b51334be2b81672357b1549afab40c content_type: application/pdf creator: chafner date_created: 2023-05-11T10:43:44Z date_updated: 2023-12-08T23:30:04Z embargo_to: open_access file_id: '12943' file_name: thesis-release-form.pdf file_size: 265319 relation: source_file file_date_updated: 2023-12-08T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '180' project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: isbn: - 978-3-99078-031-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9817' relation: part_of_dissertation status: public - id: '7117' relation: part_of_dissertation status: public - id: '13188' relation: dissertation_contains status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models' type: dissertation user_id: 400429CC-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12072' abstract: - lang: eng text: "In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. " acknowledgement: I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alec L full_name: Shute, Alec L id: 440EB050-F248-11E8-B48F-1D18A9856A87 last_name: Shute orcid: 0000-0002-1812-2810 citation: ama: 'Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072' apa: 'Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072' chicago: 'Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072.' ieee: 'A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.' ista: 'Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.' mla: 'Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.' short: 'A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.' date_created: 2022-09-08T21:53:03Z date_published: 2022-09-08T00:00:00Z date_updated: 2023-02-21T16:37:35Z day: '08' ddc: - '512' degree_awarded: PhD department: - _id: GradSch - _id: TiBr doi: 10.15479/at:ista:12072 ec_funded: 1 file: - access_level: open_access checksum: bf073344320e05d92c224786cec2e92d content_type: application/pdf creator: ashute date_created: 2022-09-08T21:50:34Z date_updated: 2022-09-08T21:50:34Z file_id: '12073' file_name: Thesis_final_draft.pdf file_size: 1907386 relation: main_file success: 1 - access_level: closed checksum: b054ac6baa09f70e8235403a4abbed80 content_type: application/octet-stream creator: ashute date_created: 2022-09-08T21:50:42Z date_updated: 2022-09-12T11:24:21Z file_id: '12074' file_name: athesis.tex file_size: 495393 relation: source_file - access_level: closed checksum: 0a31e905f1cff5eb8110978cc90e1e79 content_type: application/x-zip-compressed creator: ashute date_created: 2022-09-09T12:05:00Z date_updated: 2022-09-12T11:24:21Z file_id: '12078' file_name: qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip file_size: 944534 relation: source_file file_date_updated: 2022-09-12T11:24:21Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '208' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-023-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12076' relation: part_of_dissertation status: public - id: '12077' relation: part_of_dissertation status: public status: public supervisor: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 title: 'Existence and density problems in Diophantine geometry: From norm forms to Campana points' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11777' abstract: - lang: eng text: "In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pascal full_name: Wild, Pascal id: 4C20D868-F248-11E8-B48F-1D18A9856A87 last_name: Wild citation: ama: Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777 apa: Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777 chicago: Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777. ieee: P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022. ista: Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. mla: Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777. short: P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022. date_created: 2022-08-10T15:51:19Z date_published: 2022-08-11T00:00:00Z date_updated: 2023-06-22T09:56:36Z day: '11' ddc: - '500' - '516' - '514' degree_awarded: PhD department: - _id: GradSch - _id: UlWa doi: 10.15479/at:ista:11777 ec_funded: 1 file: - access_level: open_access checksum: f5f3af1fb7c8a24b71ddc88ad7f7c5b4 content_type: text/x-python creator: pwild date_created: 2022-08-10T15:34:04Z date_updated: 2022-08-10T15:34:04Z description: Code for computer-assisted proofs in Section 8.4.7 in Thesis file_id: '11780' file_name: flags.py file_size: 16828 relation: supplementary_material - access_level: open_access checksum: 1f7c12dfe3bdaa9b147e4fbc3d34e3d5 content_type: text/x-c++src creator: pwild date_created: 2022-08-10T15:34:10Z date_updated: 2022-08-10T15:34:10Z description: Code for proof of Lemma 8.20 in Thesis file_id: '11781' file_name: lowerbound.cpp file_size: 12226 relation: supplementary_material - access_level: open_access checksum: 4cf81455c49e5dec3b9b2e3980137eeb content_type: text/x-python creator: pwild date_created: 2022-08-10T15:34:17Z date_updated: 2022-08-10T15:34:17Z description: Code for proof of Proposition 7.9 in Thesis file_id: '11782' file_name: upperbound.py file_size: 3240 relation: supplementary_material - access_level: open_access checksum: 4e96575b10cbe4e0d0db2045b2847774 content_type: application/pdf creator: pwild date_created: 2022-08-11T16:08:33Z date_updated: 2022-08-11T16:08:33Z file_id: '11809' file_name: finalthesisPascalWildPDFA.pdf file_size: 5086282 relation: main_file title: High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes - access_level: closed checksum: 92d94842a1fb6dca5808448137573b2e content_type: application/zip creator: pwild date_created: 2022-08-11T16:09:19Z date_updated: 2022-08-11T16:09:19Z file_id: '11810' file_name: ThesisSubmission.zip file_size: 18150068 relation: source_file file_date_updated: 2022-08-11T16:09:19Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '170' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-021-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: High-dimensional expansion and crossing numbers of simplicial complexes type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11128' abstract: - lang: eng text: "Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline." acknowledged_ssus: - _id: ScienComp - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lenka full_name: Matejovicova, Lenka id: 2DFDEC72-F248-11E8-B48F-1D18A9856A87 last_name: Matejovicova citation: ama: Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128 apa: Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128 chicago: Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128. ieee: L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022. ista: Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. mla: Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128. short: L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022. date_created: 2022-04-07T08:19:54Z date_published: 2022-04-06T00:00:00Z date_updated: 2023-06-23T06:26:41Z day: '06' ddc: - '576' - '582' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11128 file: - access_level: open_access checksum: e9609bc4e8f8e20146fc1125fd4f1bf7 content_type: application/pdf creator: cchlebak date_created: 2022-04-07T08:11:34Z date_updated: 2022-04-07T08:11:34Z file_id: '11129' file_name: LenkaPhD_Official_PDFA.pdf file_size: 11906472 relation: main_file - access_level: closed checksum: 99d67040432fd07a225643a212ee8588 content_type: application/x-zip-compressed creator: cchlebak date_created: 2022-04-07T08:11:51Z date_updated: 2022-04-07T08:11:51Z file_id: '11130' file_name: LenkaPhD Official_source.zip file_size: 23036766 relation: source_file file_date_updated: 2022-04-07T08:11:51Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '112' publication_identifier: isbn: - 978-3-99078-016-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Genetic basis of flower colour as a model for adaptive evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11945' abstract: - lang: eng text: "G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level." acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rouven full_name: Schulz, Rouven id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87 last_name: Schulz orcid: 0000-0001-5297-733X citation: ama: Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945 apa: Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945 chicago: Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945. ieee: R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022. ista: Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. mla: Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945. short: R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022. date_created: 2022-08-23T11:33:11Z date_published: 2022-08-23T00:00:00Z date_updated: 2023-08-03T13:02:26Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/at:ista:11945 file: - access_level: open_access checksum: 61b1b666a210ff7cdd0e95ea75207a13 content_type: application/pdf creator: rschulz date_created: 2022-08-25T08:59:57Z date_updated: 2022-08-25T08:59:57Z file_id: '11970' file_name: Thesis_Rouven_Schulz_2022_final.pdf file_size: 28079331 relation: main_file success: 1 - access_level: closed checksum: 2b8f95ea1c134dbdb927b41b1dbeeeb5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rschulz date_created: 2022-08-25T09:00:11Z date_updated: 2022-08-25T09:33:31Z file_id: '11971' file_name: Thesis_Rouven_Schulz_2022_final.docx file_size: 27226963 relation: source_file file_date_updated: 2022-08-25T09:33:31Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '133' project: - _id: 267F75D8-B435-11E9-9278-68D0E5697425 name: Modulating microglia through G protein-coupled receptor (GPCR) signaling publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11995' relation: dissertation_contains status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12390' abstract: - lang: eng text: "The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 citation: ama: Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390 apa: Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390 chicago: Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390. ieee: M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022. ista: Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. mla: Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390. short: M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022. date_created: 2023-01-26T10:00:42Z date_published: 2022-12-15T00:00:00Z date_updated: 2023-08-07T13:32:09Z day: '15' ddc: - '500' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:12390 ec_funded: 1 file: - access_level: open_access checksum: b31460e937f33b557abb40ebef02b567 content_type: application/pdf creator: cchlebak date_created: 2023-01-26T10:02:34Z date_updated: 2023-01-26T10:02:34Z file_id: '12391' file_name: Brooks_Thesis.pdf file_size: 3095225 relation: main_file success: 1 - access_level: closed checksum: 9751869fa5e7981588ad4228f4fd4bd6 content_type: application/octet-stream creator: cchlebak date_created: 2023-01-26T10:02:42Z date_updated: 2023-01-26T10:02:42Z file_id: '12392' file_name: Brooks_Thesis.tex file_size: 809842 relation: source_file file_date_updated: 2023-01-26T10:02:42Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '196' project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9005' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Translation-invariant quantum systems with effectively broken symmetry 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12368' abstract: - lang: eng text: "Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\x02mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\x02cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts." acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 citation: ama: Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:10.15479/at:ista:12153 apa: Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153 chicago: Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153. ieee: F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022. ista: Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria. mla: Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153. short: F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022. date_created: 2023-01-25T10:43:24Z date_published: 2022-09-29T00:00:00Z date_updated: 2023-08-08T13:14:10Z day: '29' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:12153 ec_funded: 1 file: - access_level: open_access checksum: e54a3e69b83ebf166544164afd25608e content_type: application/pdf creator: cchlebak date_created: 2023-01-25T10:52:46Z date_updated: 2023-01-25T10:52:46Z file_id: '12369' file_name: THESIS_FINAL_FArslan_pdfa.pdf file_size: 14581024 relation: main_file success: 1 file_date_updated: 2023-01-25T10:52:46Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '113' project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication_identifier: isbn: - ' 978-3-99078-025-1 ' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9350' 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: Remodeling of E-cadherin-mediated contacts via cortical 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11362' abstract: - lang: eng text: "Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks." alternative_title: - ISTA Thesis 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 verifiable representations. 2022. doi:10.15479/at:ista:11362 apa: Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362 chicago: Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362. ieee: M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022. ista: Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria. mla: Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362. short: M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022. date_created: 2022-05-12T07:14:01Z date_published: 2022-05-12T00:00:00Z date_updated: 2023-08-17T06:58:38Z day: '12' ddc: - '004' degree_awarded: PhD department: - _id: GradSch - _id: ToHe doi: 10.15479/at:ista:11362 ec_funded: 1 file: - access_level: closed checksum: 8eefa9c7c10ca7e1a2ccdd731962a645 content_type: application/zip creator: mlechner date_created: 2022-05-13T12:33:26Z date_updated: 2022-05-13T12:49:00Z file_id: '11378' file_name: src.zip file_size: 13210143 relation: source_file - access_level: open_access checksum: 1b9e1e5a9a83ed9d89dad2f5133dc026 content_type: application/pdf creator: mlechner date_created: 2022-05-16T08:02:28Z date_updated: 2022-05-17T15:19:39Z file_id: '11382' file_name: thesis_main-a2.pdf file_size: 2732536 relation: main_file file_date_updated: 2022-05-17T15:19:39Z has_accepted_license: '1' keyword: - neural networks - verification - machine learning language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: '124' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication_identifier: isbn: - 978-3-99078-017-6 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10665' relation: part_of_dissertation status: public - id: '10667' relation: part_of_dissertation status: public - id: '11366' relation: part_of_dissertation status: public - id: '7808' relation: part_of_dissertation status: public - id: '10666' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: Learning verifiable representations tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11473' abstract: - lang: eng text: "The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n" acknowledged_ssus: - _id: SSU alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy citation: ama: 'Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473' apa: 'Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473' chicago: 'Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.' ieee: 'K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.' ista: 'Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.' mla: 'Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.' short: 'K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.' date_created: 2022-06-30T12:15:03Z date_published: 2022-07-01T00:00:00Z date_updated: 2023-09-07T13:43:52Z day: '01' ddc: - '515' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:11473 ec_funded: 1 file: - access_level: open_access checksum: 7970714a20a6052f75fb27a6c3e9976e content_type: application/pdf creator: kmysliwy date_created: 2022-07-05T08:12:56Z date_updated: 2022-07-05T08:12:56Z file_id: '11486' file_name: thes1_no_isbn_2_1b.pdf file_size: 1830973 relation: main_file success: 1 - access_level: closed checksum: 647a2011fdf56277096c9350fefe1097 content_type: application/zip creator: kmysliwy date_created: 2022-07-05T08:15:52Z date_updated: 2022-07-05T08:17:12Z file_id: '11487' file_name: thes_source.zip file_size: 5831060 relation: source_file file_date_updated: 2022-07-05T08:17:12Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '138' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10564' relation: part_of_dissertation status: public - id: '8705' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: 'Polarons in Bose gases and polar crystals: Some rigorous energy estimates' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2022' ... --- _id: '10799' abstract: - lang: eng text: "Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nikola H full_name: Konstantinov, Nikola H id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87 last_name: Konstantinov citation: ama: Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799 apa: Konstantinov, N. H. (2022). Robustness and fairness in machine learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799 chicago: Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799. ieee: N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022. ista: Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria. mla: Konstantinov, Nikola H. Robustness and Fairness in Machine Learning. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799. short: N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022. date_created: 2022-02-28T13:03:49Z date_published: 2022-03-08T00:00:00Z date_updated: 2023-10-17T12:31:54Z day: '08' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/at:ista:10799 ec_funded: 1 file: - access_level: open_access checksum: 626bc523ae8822d20e635d0e2d95182e content_type: application/pdf creator: nkonstan date_created: 2022-03-06T11:42:54Z date_updated: 2022-03-06T11:42:54Z file_id: '10823' file_name: thesis.pdf file_size: 4204905 relation: main_file success: 1 - access_level: closed checksum: e2ca2b88350ac8ea1515b948885cbcb1 content_type: application/x-zip-compressed creator: nkonstan date_created: 2022-03-06T11:42:57Z date_updated: 2022-03-10T12:11:48Z file_id: '10824' file_name: thesis.zip file_size: 22841103 relation: source_file file_date_updated: 2022-03-10T12:11:48Z has_accepted_license: '1' keyword: - robustness - fairness - machine learning - PAC learning - adversarial learning language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '176' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-015-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8724' relation: part_of_dissertation status: public - id: '10803' relation: part_of_dissertation status: public - id: '10802' relation: part_of_dissertation status: public - id: '6590' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Robustness and fairness in machine learning type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2022' ... --- _id: '11626' abstract: - lang: eng text: Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 citation: ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626 apa: Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626 chicago: Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626. ieee: M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022. ista: Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. mla: Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626. short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022. date_created: 2022-07-20T11:21:53Z date_published: 2022-07-20T00:00:00Z date_updated: 2023-11-07T08:20:13Z day: '20' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:11626 ec_funded: 1 file: - access_level: open_access checksum: bd7ac35403cf5b4b2607287d2a104b3a content_type: application/pdf creator: mgallei date_created: 2022-07-25T09:08:47Z date_updated: 2022-07-25T09:08:47Z file_id: '11645' file_name: Thesis_Gallei.pdf file_size: 9730864 relation: main_file - access_level: closed checksum: a9e54fe5471ba25dc13c2150c1b8ccbb content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mgallei date_created: 2022-07-25T09:09:09Z date_updated: 2022-07-25T09:39:58Z file_id: '11646' file_name: Thesis_Gallei_source.docx file_size: 19560720 relation: source_file - access_level: closed checksum: 3994f7f20058941b5bb8a16886b21e71 content_type: application/pdf creator: mgallei date_created: 2022-07-25T09:09:32Z date_updated: 2022-07-25T09:39:58Z description: This is the print version of the thesis including the full appendix file_id: '11647' file_name: Thesis_Gallei_to_print.pdf file_size: 24542837 relation: source_file - access_level: open_access checksum: f24acd3c0d864f4c6676e8b0d7bfa76b content_type: application/pdf creator: mgallei date_created: 2022-07-25T11:48:45Z date_updated: 2022-07-25T11:48:45Z file_id: '11650' file_name: Thesis_Gallei_Appendix.pdf file_size: 15435966 relation: main_file file_date_updated: 2022-07-25T11:48:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '248' project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication_identifier: isbn: - 978-3-99078-019-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8931' relation: part_of_dissertation status: public - id: '9287' relation: part_of_dissertation status: public - id: '7142' relation: part_of_dissertation status: public - id: '7465' relation: part_of_dissertation status: public - id: '8138' relation: part_of_dissertation status: public - id: '6260' relation: part_of_dissertation status: public - id: '10411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Eilon full_name: Shani, Eilon last_name: Shani title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12358' abstract: - lang: eng text: "The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n" acknowledged_ssus: - _id: SSU alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg full_name: Sperl, Georg id: 4DD40360-F248-11E8-B48F-1D18A9856A87 last_name: Sperl citation: ama: 'Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103' apa: 'Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103' chicago: 'Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103.' ieee: 'G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.' ista: 'Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.' mla: 'Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.' short: 'G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.' date_created: 2023-01-24T10:49:46Z date_published: 2022-09-22T00:00:00Z date_updated: 2024-02-28T12:57:46Z day: '22' ddc: - '000' - '620' degree_awarded: PhD department: - _id: GradSch - _id: ChWo doi: 10.15479/at:ista:12103 ec_funded: 1 file: - access_level: open_access checksum: 083722acbb8115e52e3b0fdec6226769 content_type: application/pdf creator: cchlebak date_created: 2023-01-25T12:04:41Z date_updated: 2023-02-02T09:29:57Z description: 'This is the main PDF file of the thesis. File size: 105 MB' file_id: '12371' file_name: thesis_gsperl.pdf file_size: 104497530 relation: main_file title: Thesis - access_level: open_access checksum: 511f82025e5fcb70bff4731d6896ca07 content_type: application/pdf creator: cchlebak date_created: 2023-02-02T09:33:37Z date_updated: 2023-02-02T09:33:37Z description: This version of the thesis uses stronger image compression for a smaller file size of 23MB. file_id: '12483' file_name: thesis_gsperl_compressed.pdf file_size: 23183710 relation: main_file title: Thesis (compressed 23MB) - access_level: open_access checksum: ed4cb85225eedff761c25bddfc37a2ed content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-02-02T09:39:25Z date_updated: 2023-02-02T09:39:25Z file_id: '12484' file_name: thesis-source.zip file_size: 98382247 relation: source_file file_date_updated: 2023-02-02T09:39:25Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '138' project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_identifier: isbn: - 978-3-99078-020-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11736' relation: part_of_dissertation status: public - id: '9818' relation: part_of_dissertation status: public - id: '8385' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 title: 'Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '10759' abstract: - lang: eng text: In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 citation: ama: Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759 apa: Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759 chicago: Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759. ieee: W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022. ista: Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. mla: Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759. short: W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022. date_created: 2022-02-16T13:27:37Z date_published: 2022-02-21T00:00:00Z date_updated: 2024-02-28T13:01:59Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MiLe doi: 10.15479/at:ista:10759 ec_funded: 1 file: - access_level: closed checksum: 0fc54ad1eaede879c665ac9b53c93e22 content_type: application/zip creator: wrzadkow date_created: 2022-02-21T13:58:16Z date_updated: 2022-02-22T07:20:12Z file_id: '10785' file_name: Rzadkowski_thesis_final_source.zip file_size: 17668233 relation: source_file - access_level: open_access checksum: 22d2d7af37ca31f6b1730c26cac7bced content_type: application/pdf creator: wrzadkow date_created: 2022-02-21T14:02:54Z date_updated: 2022-02-21T14:02:54Z file_id: '10786' file_name: Rzadkowski_thesis_final.pdf file_size: 13307331 relation: main_file success: 1 file_date_updated: 2022-02-22T07:20:12Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '120' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10762' relation: part_of_dissertation status: public - id: '8644' relation: part_of_dissertation status: public - id: '7956' relation: part_of_dissertation status: public - id: '415' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Analytic and machine learning approaches to composite quantum impurities type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2022' ... --- _id: '11196' abstract: - lang: eng text: "One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n" acknowledged_ssus: - _id: EM-Fac - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim citation: ama: Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:10.15479/at:ista:11196 apa: Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196 chicago: Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196. ieee: O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022. ista: Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. mla: Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196. short: O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022. date_created: 2022-04-20T09:47:12Z date_published: 2022-04-20T00:00:00Z date_updated: 2023-08-18T06:31:52Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: PeJo - _id: GradSch doi: 10.15479/at:ista:11196 ec_funded: 1 file: - access_level: open_access checksum: 1616a8bf6f13a57c892dac873dcd0936 content_type: application/pdf creator: okim date_created: 2022-04-20T14:21:56Z date_updated: 2023-04-20T22:30:03Z embargo: 2023-04-19 file_id: '11220' file_name: Olena_KIM_thesis_final.pdf file_size: 21273537 relation: main_file - access_level: closed checksum: 1acb433f98dc42abb0b4b0cbb0c4b918 content_type: application/x-zip-compressed creator: okim date_created: 2022-04-20T14:22:56Z date_updated: 2023-04-20T22:30:03Z embargo_to: open_access file_id: '11221' file_name: KIM_thesis_final.zip file_size: 59248569 relation: source_file file_date_updated: 2023-04-20T22:30:03Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: '132' project: - _id: 25BAF7B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '708497' name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C3DBB6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01205 name: Zellkommunikation in Gesundheit und Krankheit - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11222' relation: part_of_dissertation status: public - id: '7473' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '10727' abstract: - lang: eng text: "Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 citation: ama: Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727 apa: Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727 chicago: Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727. ieee: S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022. ista: Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. mla: Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727. short: S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022. date_created: 2022-02-04T15:45:12Z date_published: 2022-02-07T00:00:00Z date_updated: 2023-09-07T13:43:23Z day: '07' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/AT:ISTA:10727 ec_funded: 1 file: - access_level: closed checksum: 47ba18bb270dd6cc266e0a3f7c69d0e4 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: smetzler date_created: 2022-02-04T15:36:12Z date_updated: 2023-02-03T23:30:03Z embargo_to: open_access file_id: '10728' file_name: Thesis_Sina_Metzler.docx file_size: 6757886 relation: source_file - access_level: open_access checksum: f3ec07d5d6b20ae6e46bfeedebce9027 content_type: application/pdf creator: smetzler date_created: 2022-02-04T15:36:43Z date_updated: 2023-02-03T23:30:03Z embargo: 2023-02-02 file_id: '10730' file_name: Thesis_Sina_Metzler_A2.pdf file_size: 6314921 relation: main_file - access_level: open_access checksum: dedd14b7be7a75d63018dbfc68dd8113 content_type: application/pdf creator: smetzler date_created: 2022-02-07T10:35:02Z date_updated: 2023-02-04T23:30:03Z embargo: 2023-02-02 file_id: '10742' file_name: Thesis_Sina_Metzler_print.pdf file_size: 6882557 relation: main_file file_date_updated: 2023-02-04T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Pathogen-mediated sexual selection and immunization in ant colonies type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2022' ... --- _id: '11879' abstract: - lang: eng text: "As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: SSU acknowledgement: I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christina full_name: Artner, Christina id: 45DF286A-F248-11E8-B48F-1D18A9856A87 last_name: Artner citation: ama: Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:10.15479/at:ista:11879 apa: Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11879 chicago: Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11879. ieee: C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022. ista: Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. mla: Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11879. short: C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022. date_created: 2022-08-17T07:58:53Z date_published: 2022-08-17T00:00:00Z date_updated: 2023-09-09T22:30:04Z day: '17' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:11879 file: - access_level: open_access checksum: a2c2fdc28002538840490bfa6a08b2cb content_type: application/pdf creator: cartner date_created: 2022-08-17T12:08:49Z date_updated: 2023-09-09T22:30:03Z embargo: 2023-09-08 file_id: '11907' file_name: ChristinaArtner_PhD_Thesis_2022.pdf file_size: 11113608 relation: main_file - access_level: closed checksum: 66b461c074b815fbe63481b3f46a9f43 content_type: application/octet-stream creator: cartner date_created: 2022-08-17T12:08:59Z date_updated: 2023-09-09T22:30:03Z embargo_to: open_access file_id: '11908' file_name: ChristinaArtner_PhD_Thesis_2022.7z file_size: 19097730 relation: source_file file_date_updated: 2023-09-09T22:30:03Z has_accepted_license: '1' keyword: - high ambient temperature - auxin - PINs - Zinc-Finger proteins - thermomorphogenesis - stress language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '128' project: - _id: 2685A872-B435-11E9-9278-68D0E5697425 name: Hormonal regulation of plant adaptive responses to environmental signals publication_identifier: isbn: - 978-3-99078-022-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria 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: Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11393' abstract: - lang: eng text: "AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits." acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marijo full_name: Jevtic, Marijo id: 4BE3BC94-F248-11E8-B48F-1D18A9856A87 last_name: Jevtic citation: ama: Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393 apa: Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11393 chicago: Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393. ieee: M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022. ista: Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. mla: Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11393. short: M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022. date_created: 2022-05-17T08:57:41Z date_published: 2022-05-16T00:00:00Z date_updated: 2023-09-07T14:53:44Z day: '16' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:11393 file: - access_level: closed checksum: 8fc695d88020d70d231dad0e9f10b138 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2022-05-17T09:08:06Z date_updated: 2023-05-17T22:30:03Z embargo_to: open_access file_id: '11395' file_name: MJ thesis.docx file_size: 56427603 relation: source_file - access_level: open_access checksum: c1dd20a1aece521b3500607b00e463d6 content_type: application/pdf creator: cchlebak date_created: 2022-05-17T12:09:25Z date_updated: 2023-05-17T22:30:03Z embargo: 2023-05-16 file_id: '11397' file_name: MJ_thesis_PDFA.pdf file_size: 4351981 relation: main_file file_date_updated: 2023-05-17T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '108' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7391' 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: Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12366' abstract: - lang: eng text: "Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko citation: ama: Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:10.15479/at:ista:12132 apa: Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132 chicago: Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132. ieee: E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022. ista: Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. mla: Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132. short: E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022. date_created: 2023-01-25T09:17:02Z date_published: 2022-09-26T00:00:00Z date_updated: 2023-05-26T09:29:07Z day: '26' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:12132 ec_funded: 1 file: - access_level: open_access checksum: 39eabb1e006b41335f17f3b29af09648 content_type: application/pdf creator: cchlebak date_created: 2023-01-25T09:41:49Z date_updated: 2023-01-26T23:30:44Z embargo: 2022-12-28 file_id: '12367' file_name: Final_Thesis_ES_Redchenko.pdf file_size: 56076868 relation: main_file file_date_updated: 2023-01-26T23:30:44Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '168' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies publication_identifier: isbn: - 978-3-99078-024-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Controllable states of superconducting Qubit ensembles type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11932' abstract: - lang: eng text: "The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes." acknowledgement: I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. alternative_title: - ISTA Thesis 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 citation: ama: Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932 apa: Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932 chicago: Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932. ieee: M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022. ista: Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. mla: Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932. short: M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022. date_created: 2022-08-19T08:52:30Z date_published: 2022-08-19T00:00:00Z date_updated: 2023-09-05T12:02:14Z day: '19' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:11932 ec_funded: 1 file: - access_level: closed checksum: 2dbb70c74aaa3b64c1f463e943baf09c content_type: application/zip creator: mnardin date_created: 2022-08-19T16:31:34Z date_updated: 2023-06-20T22:30:04Z embargo_to: open_access file_id: '11935' file_name: Michele Nardin, Ph.D. Thesis - ISTA (1).zip file_size: 13515457 relation: source_file - access_level: open_access checksum: 0ec94035ea35a47a9f589ed168e60b48 content_type: application/pdf creator: mnardin date_created: 2022-08-22T09:43:50Z date_updated: 2023-06-20T22:30:04Z embargo: 2023-06-19 file_id: '11941' file_name: Michele_Nardin_Phd_Thesis_PDFA.pdf file_size: 9906458 relation: main_file file_date_updated: 2023-06-20T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '136' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10077' relation: part_of_dissertation status: public - id: '6194' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: On the encoding, transfer, and consolidation of spatial memories type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12378' abstract: - lang: eng text: "Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\x02automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\x02like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 citation: ama: Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378 apa: Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378 chicago: Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378. ieee: G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022. ista: Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. mla: Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378. short: G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022. date_created: 2023-01-25T14:27:43Z date_published: 2022-11-11T00:00:00Z date_updated: 2023-08-04T09:40:37Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/at:ista:12378 ec_funded: 1 file: - access_level: closed checksum: 8cd3ddfe9b53381dcf086023d8d8893a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-01-25T14:31:32Z date_updated: 2023-04-12T22:30:03Z embargo_to: open_access file_id: '12379' file_name: Gloria_Colombo_Thesis.docx file_size: 23890382 relation: source_file - access_level: open_access checksum: 8af4319c18b516e8758e9a6cb02b103b content_type: application/pdf creator: cchlebak date_created: 2023-01-25T14:31:36Z date_updated: 2023-04-12T22:30:03Z embargo: 2023-04-11 file_id: '12380' file_name: Gloria_Colombo_Thesis.pdf file_size: 13802421 relation: main_file file_date_updated: 2023-04-12T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '142' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12244' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11388' abstract: - lang: eng text: "In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefanie full_name: Belohlavy, Stefanie id: 43FE426A-F248-11E8-B48F-1D18A9856A87 last_name: Belohlavy orcid: 0000-0002-9849-498X citation: ama: Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388 apa: Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388 chicago: Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388. ieee: S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022. ista: Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. mla: Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388. short: S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022. date_created: 2022-05-16T16:49:18Z date_published: 2022-05-18T00:00:00Z date_updated: 2023-08-29T06:41:51Z day: '18' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11388 file: - access_level: open_access checksum: 4d75e6a619df7e8a9d6e840aee182380 content_type: application/pdf creator: sbelohla date_created: 2022-05-19T13:03:13Z date_updated: 2023-05-20T22:30:03Z embargo: 2023-05-19 file_id: '11398' file_name: thesis_sb_final_pdfa.pdf file_size: 8247240 relation: main_file - access_level: closed checksum: 7a5d8b6dd0ca00784f860075b0a7d8f0 content_type: application/x-zip-compressed creator: sbelohla date_created: 2022-05-19T13:07:47Z date_updated: 2023-05-20T22:30:03Z embargo_to: open_access file_id: '11399' file_name: thesis_sb_final.zip file_size: 7094 relation: source_file file_date_updated: 2023-05-20T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '98' publication_identifier: isbn: - 978-3-99078-018-3 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6713' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The genetic basis of complex traits studied via analysis of evolve and resequence experiments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12401' abstract: - lang: eng text: "Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X citation: ama: Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401 apa: Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401 chicago: Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401. ieee: S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022. ista: Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. mla: Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401. short: S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022. date_created: 2023-01-26T11:55:16Z date_published: 2022-12-22T00:00:00Z date_updated: 2023-12-21T23:30:04Z day: '22' ddc: - '610' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/at:ista:12401 file: - access_level: open_access checksum: cc4a2b4a7e3c4ee8ef7f2dbf909b12bd content_type: application/pdf creator: cchlebak date_created: 2023-01-26T11:58:14Z date_updated: 2023-12-21T23:30:03Z embargo: 2023-12-20 file_id: '12402' file_name: PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf file_size: 42059787 relation: main_file - access_level: closed checksum: f1b4ca98b8ab0cb043b1830971e9bd9c content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-01-26T12:00:10Z date_updated: 2023-12-21T23:30:03Z embargo_to: open_access file_id: '12403' file_name: Source Files - Saren Tasciyan - PhD Thesis.zip file_size: 261256696 relation: source_file file_date_updated: 2023-12-21T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '105' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '679' relation: part_of_dissertation status: public - id: '10703' relation: part_of_dissertation status: public - id: '9429' relation: part_of_dissertation status: public - id: '7885' 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: 0000-0002-6620-9179 title: Role of microenvironment heterogeneity in cancer cell invasion type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11193' abstract: - lang: eng text: "The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stephanie full_name: Wachner, Stephanie id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87 last_name: Wachner citation: ama: Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193 apa: Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11193 chicago: Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193. ieee: S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022. ista: Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. mla: Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11193. short: S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022. date_created: 2022-04-20T08:59:07Z date_published: 2022-04-20T00:00:00Z date_updated: 2023-09-19T10:15:54Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: DaSi doi: 10.15479/at:ista:11193 file: - access_level: open_access checksum: 999ab16884c4522486136ebc5ae8dbff content_type: application/pdf creator: cchlebak date_created: 2022-04-20T09:03:57Z date_updated: 2023-04-21T22:30:03Z embargo: 2023-04-20 file_id: '11195' file_name: Thesis_Stephanie_Wachner_20200414_formatted.pdf file_size: 8820951 relation: main_file - access_level: closed checksum: fd92b1e38d53bdf8b458213882d41383 content_type: application/x-zip-compressed creator: cchlebak date_created: 2022-04-22T12:41:00Z date_updated: 2023-04-21T22:30:03Z embargo_to: open_access file_id: '11329' file_name: Thesis_Stephanie_Wachner_20200414.zip file_size: 65864612 relation: source_file file_date_updated: 2023-04-21T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '170' project: - _id: 26199CA4-B435-11E9-9278-68D0E5697425 grant_number: '24800' name: Tissue barrier penetration is crucial for immunity and metastasis publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10614' relation: part_of_dissertation status: public - id: '544' relation: part_of_dissertation status: public status: public supervisor: - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 title: Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12364' abstract: - lang: eng text: "Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\x02ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 citation: ama: Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094 apa: Dotter, C. (2022). Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12094 chicago: Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094. ieee: C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022. ista: Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. mla: Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094. short: C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022. date_created: 2023-01-24T13:09:57Z date_published: 2022-09-19T00:00:00Z date_updated: 2023-11-16T13:10:22Z day: '19' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/at:ista:12094 ec_funded: 1 file: - access_level: open_access checksum: 896f4cac9adb6d3f26a6605772f4e1a3 content_type: application/pdf creator: cchlebak date_created: 2023-01-24T13:15:45Z date_updated: 2023-09-20T22:30:03Z embargo: 2023-09-19 file_id: '12365' file_name: 220923_Thesis_CDotter_Final.pdf file_size: 20457465 relation: main_file - access_level: closed checksum: ad01bb20da163be6893b7af832e58419 content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-02-02T09:15:35Z date_updated: 2023-09-20T22:30:03Z embargo_to: open_access file_id: '12482' file_name: latex_source_CDotter_Thesis_2022.zip file_size: 22433512 relation: source_file file_date_updated: 2023-09-20T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '152' project: - _id: 254BA948-B435-11E9-9278-68D0E5697425 grant_number: '401299' name: Probing development and reversibility of autism spectrum disorders - _id: 9B91375C-BA93-11EA-9121-9846C619BF3A grant_number: '707964' name: Critical windows and reversibility of ASD associated with mutations in chromatin remodelers - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2690FEAC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I04205 name: Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '3' relation: part_of_dissertation status: public - id: '11160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '9056' abstract: - lang: eng text: "In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 citation: ama: Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056 apa: Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056 chicago: Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056. ieee: G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021. ista: 'Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.' mla: Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056. short: G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021. date_created: 2021-02-02T14:11:06Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-09-07T13:29:01Z day: '01' ddc: - '006' - '514' - '516' degree_awarded: PhD department: - _id: HeEd - _id: GradSch doi: 10.15479/AT:ISTA:9056 file: - access_level: closed checksum: bcf27986147cab0533b6abadd74e7629 content_type: application/zip creator: patrickd date_created: 2021-02-02T14:09:25Z date_updated: 2021-02-03T10:37:28Z file_id: '9063' file_name: thesis_source.zip file_size: 13446994 relation: source_file - access_level: open_access checksum: 9cc8af266579a464385bbe2aff6af606 content_type: application/pdf creator: patrickd date_created: 2021-02-02T14:09:18Z date_updated: 2021-02-02T14:09:18Z file_id: '9064' file_name: thesis_pdfA2b.pdf file_size: 5210329 relation: main_file success: 1 file_date_updated: 2021-02-03T10:37:28Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '134' place: Klosterneuburg publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '187' relation: part_of_dissertation status: public - id: '8703' 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: Multi-cover persistence and Delaunay mosaics 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9022' abstract: - lang: eng text: "In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices." acknowledgement: I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 citation: ama: Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022 apa: Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022 chicago: Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022. ieee: G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021. ista: Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. mla: Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022. short: G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021. date_created: 2021-01-21T18:16:54Z date_published: 2021-01-25T00:00:00Z date_updated: 2023-09-07T13:29:32Z day: '25' ddc: - '510' degree_awarded: PhD department: - _id: GradSch - _id: LaEr doi: 10.15479/AT:ISTA:9022 ec_funded: 1 file: - access_level: open_access checksum: 5a93658a5f19478372523ee232887e2b content_type: application/pdf creator: gcipollo date_created: 2021-01-25T14:19:03Z date_updated: 2021-01-25T14:19:03Z file_id: '9043' file_name: thesis.pdf file_size: 4127796 relation: main_file success: 1 - access_level: closed checksum: e8270eddfe6a988e92a53c88d1d19b8c content_type: application/zip creator: gcipollo date_created: 2021-01-25T14:19:10Z date_updated: 2021-01-25T14:19:10Z file_id: '9044' file_name: Thesis_files.zip file_size: 12775206 relation: source_file file_date_updated: 2021-01-25T14:19:10Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '380' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 title: Fluctuations in the spectrum of random matrices type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10007' abstract: - lang: eng text: The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 citation: ama: 'Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007' apa: 'Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007' chicago: 'Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.' ieee: 'S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.' ista: 'Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.' mla: 'Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.' short: 'S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.' date_created: 2021-09-13T11:12:34Z date_published: 2021-09-14T00:00:00Z date_updated: 2023-09-07T13:30:45Z day: '14' ddc: - '515' degree_awarded: PhD department: - _id: GradSch - _id: JuFi doi: 10.15479/at:ista:10007 ec_funded: 1 file: - access_level: closed checksum: c8475faaf0b680b4971f638f1db16347 content_type: application/x-zip-compressed creator: shensel date_created: 2021-09-13T11:03:24Z date_updated: 2021-09-15T14:37:30Z file_id: '10008' file_name: thesis_final_Hensel.zip file_size: 15022154 relation: source_file - access_level: open_access checksum: 1a609937aa5275452822f45f2da17f07 content_type: application/pdf creator: shensel date_created: 2021-09-13T14:18:56Z date_updated: 2021-09-14T09:52:47Z file_id: '10014' file_name: thesis_final_Hensel.pdf file_size: 6583638 relation: main_file file_date_updated: 2021-09-15T14:37:30Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '300' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10012' relation: part_of_dissertation status: public - id: '10013' relation: part_of_dissertation status: public - id: '7489' relation: part_of_dissertation status: public status: public supervisor: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X title: 'Curvature driven interface evolution: Uniqueness properties of weak solution concepts' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10030' abstract: - lang: eng text: "This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces." acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030 apa: Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030 chicago: Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030. ieee: L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021. ista: Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. mla: Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030. short: L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021. date_created: 2021-09-21T09:14:15Z date_published: 2021-09-22T00:00:00Z date_updated: 2023-09-07T13:31:06Z day: '22' ddc: - '515' degree_awarded: PhD department: - _id: GradSch - _id: JaMa doi: 10.15479/at:ista:10030 file: - access_level: closed checksum: 8cd60dcb8762e8f21867e21e8001e183 content_type: application/x-zip-compressed creator: cchlebak date_created: 2021-09-21T09:17:34Z date_updated: 2022-03-10T12:14:42Z file_id: '10032' file_name: tex_and_pictures.zip file_size: 3876668 relation: source_file - access_level: open_access checksum: 9789e9d967c853c1503ec7f307170279 content_type: application/pdf creator: cchlebak date_created: 2021-09-27T11:14:31Z date_updated: 2021-09-27T11:14:31Z file_id: '10047' file_name: thesis_portinale_Final (1).pdf file_size: 2532673 relation: main_file file_date_updated: 2022-03-10T12:14:42Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260788DE-B435-11E9-9278-68D0E5697425 call_identifier: FWF name: Dissipation and Dispersion in Nonlinear Partial Differential Equations - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10022' relation: part_of_dissertation status: public - id: '9792' relation: part_of_dissertation status: public - id: '7573' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: Discrete-to-continuum limits of transport problems and gradient flows in the space of measures 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9920' abstract: - lang: eng text: 'This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.' acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 citation: ama: Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920 apa: Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920 chicago: Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920. ieee: M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021. ista: Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. mla: Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920. short: M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021. date_created: 2021-08-16T09:44:09Z date_published: 2021-08-19T00:00:00Z date_updated: 2023-09-07T13:31:22Z day: '19' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:9920 file: - access_level: closed checksum: 3cd1986efde5121d7581f6fcf9090da8 content_type: application/x-zip-compressed creator: mperuzzo date_created: 2021-08-16T09:33:21Z date_updated: 2021-09-06T08:39:47Z file_id: '9924' file_name: GeometricSuperinductorsForCQED.zip file_size: 151387283 relation: source_file - access_level: open_access checksum: 50928c621cdf0775d7a5906b9dc8602c content_type: application/pdf creator: mperuzzo date_created: 2021-08-18T14:20:06Z date_updated: 2021-09-06T08:39:47Z file_id: '9939' file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf file_size: 17596344 relation: main_file - access_level: closed checksum: 37f486aa1b622fe44af00d627ec13f6c content_type: application/pdf creator: mperuzzo date_created: 2021-08-18T14:20:09Z date_updated: 2021-09-06T08:39:47Z description: Extra copy of the thesis as PDF/A-2b file_id: '9940' file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf file_size: 17592425 relation: other file_date_updated: 2021-09-06T08:39:47Z has_accepted_license: '1' keyword: - quantum computing - superinductor - quantum metrology language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '149' publication_identifier: isbn: - 978-3-99078-013-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9928' relation: part_of_dissertation status: public - id: '8755' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Geometric superinductors and their applications in circuit quantum electrodynamics type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10422' abstract: - lang: eng text: Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems. alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Anton full_name: Piankov, Anton id: 865E3C26-AA8C-11E9-A409-C4C4E5697425 last_name: Piankov citation: ama: Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422 apa: Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422 chicago: Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422. ieee: A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021. ista: Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. mla: Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422. short: A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021. date_created: 2021-12-07T10:48:06Z date_published: 2021-12-07T00:00:00Z date_updated: 2023-09-07T13:34:12Z day: '07' ddc: - '530' degree_awarded: MS department: - _id: GradSch - _id: CaGo doi: 10.15479/at:ista:10422 file: - access_level: closed checksum: 114e8f4b2c002c6c352416c12de2c695 content_type: application/x-zip-compressed creator: cchlebak date_created: 2021-12-07T11:13:52Z date_updated: 2022-03-10T12:10:25Z file_id: '10424' file_name: Thesis.zip file_size: 394018 relation: source_file - access_level: closed checksum: cd15ae991ced352a9959815f794e657c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2021-12-07T11:14:01Z date_updated: 2022-03-10T12:10:25Z file_id: '10425' file_name: Preliminary_pages_Piankov.docx file_size: 47638 relation: source_file - access_level: open_access checksum: e6899c798b75ba42fab9822bce309050 content_type: application/pdf creator: cchlebak date_created: 2021-12-07T11:20:35Z date_updated: 2021-12-07T11:20:35Z file_id: '10426' file_name: 2021_Piankov_combined.pdf file_size: 484965 relation: main_file success: 1 file_date_updated: 2022-03-10T12:10:25Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 title: Towards designer materials using customizable particle shape type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9418' abstract: - lang: eng text: "Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models." acknowledged_ssus: - _id: ScienComp - _id: CampIT - _id: E-Lib alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai citation: ama: Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418 apa: Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418 chicago: Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418. ieee: M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021. ista: Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria. mla: Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418. short: M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021. date_created: 2021-05-24T13:06:23Z date_published: 2021-05-30T00:00:00Z date_updated: 2023-09-08T11:11:12Z day: '30' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/AT:ISTA:9418 file: - access_level: open_access checksum: 4f0abe64114cfed264f9d36e8d1197e3 content_type: application/pdf creator: bphuong date_created: 2021-05-24T11:22:29Z date_updated: 2021-05-24T11:22:29Z file_id: '9419' file_name: mph-thesis-v519-pdfimages.pdf file_size: 2673905 relation: main_file success: 1 - access_level: closed checksum: f5699e876bc770a9b0df8345a77720a2 content_type: application/zip creator: bphuong date_created: 2021-05-24T11:56:02Z date_updated: 2021-05-24T11:56:02Z file_id: '9420' file_name: thesis.zip file_size: 92995100 relation: source_file file_date_updated: 2021-05-24T11:56:02Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '125' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7435' relation: part_of_dissertation status: deleted - id: '7481' relation: part_of_dissertation status: public - id: '9416' relation: part_of_dissertation status: public - id: '7479' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Underspecification in deep learning type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10199' abstract: - lang: eng text: The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness. acknowledged_ssus: - _id: SSU alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199 apa: Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199 chicago: Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199. ieee: V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021. ista: Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. mla: Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199. short: V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021. date_created: 2021-10-29T20:09:01Z date_published: 2021-10-31T00:00:00Z date_updated: 2023-09-19T09:59:54Z day: '31' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/at:ista:10199 ec_funded: 1 file: - access_level: open_access checksum: 4f412a1ee60952221b499a4b1268df35 content_type: application/pdf creator: vtoman date_created: 2021-11-08T14:12:22Z date_updated: 2021-11-08T14:12:22Z file_id: '10225' file_name: toman_th_final.pdf file_size: 2915234 relation: main_file - access_level: closed checksum: 9584943f99127be2dd2963f6784c37d4 content_type: application/zip creator: vtoman date_created: 2021-11-08T14:12:46Z date_updated: 2021-11-09T09:00:50Z file_id: '10226' file_name: toman_thesis.zip file_size: 8616056 relation: source_file file_date_updated: 2021-11-09T09:00:50Z has_accepted_license: '1' keyword: - concurrency - verification - model checking language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '166' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10190' relation: part_of_dissertation status: public - id: '10191' relation: part_of_dissertation status: public - id: '9987' relation: part_of_dissertation status: public - id: '141' 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: Improved verification techniques for concurrent systems type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10035' abstract: - lang: eng text: 'Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for "graph-building" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).' acknowledgement: "I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein citation: ama: Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035 apa: Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035 chicago: Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035. ieee: K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021. ista: Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria. mla: Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035. short: K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021. date_created: 2021-09-23T07:31:44Z date_published: 2021-09-23T00:00:00Z date_updated: 2023-10-17T09:24:07Z day: '23' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/at:ista:10035 ec_funded: 1 file: - access_level: open_access checksum: 73a44345c683e81f3e765efbf86fdcc5 content_type: application/pdf creator: cchlebak date_created: 2021-10-04T12:22:33Z date_updated: 2021-10-04T12:22:33Z file_id: '10082' file_name: thesis_pdfa.pdf file_size: 2104726 relation: main_file success: 1 - access_level: closed checksum: 7b80df30a0e686c3ef6a56d4e1c59e29 content_type: application/x-zip-compressed creator: cchlebak date_created: 2021-10-05T07:04:37Z date_updated: 2022-03-10T12:15:18Z file_id: '10085' file_name: thesis_final (1).zip file_size: 9538359 relation: source_file file_date_updated: 2022-03-10T12:15:18Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '276' project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10044' relation: part_of_dissertation status: public - id: '10049' relation: part_of_dissertation status: public - id: '637' relation: part_of_dissertation status: public - id: '10041' relation: part_of_dissertation status: public - id: '6430' relation: part_of_dissertation status: public - id: '10048' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: On the adaptive security of graph-based games 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10429' abstract: - lang: eng text: "The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 citation: ama: Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429 apa: Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429 chicago: Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429. ieee: G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021. ista: Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria. mla: Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429. short: G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021. date_created: 2021-12-08T21:52:28Z date_published: 2021-12-09T00:00:00Z date_updated: 2023-10-17T11:48:55Z day: '09' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/at:ista:10429 ec_funded: 1 file: - access_level: open_access checksum: 6bf14e9a523387328f016c0689f5e10e content_type: application/pdf creator: gnadirad date_created: 2021-12-09T17:47:49Z date_updated: 2021-12-09T17:47:49Z file_id: '10436' file_name: Thesis_Final_09_12_2021.pdf file_size: 2370859 relation: main_file success: 1 - access_level: closed checksum: 914d6c5ca86bd0add471971a8f4c4341 content_type: application/zip creator: gnadirad date_created: 2021-12-09T17:47:49Z date_updated: 2022-03-28T12:55:12Z file_id: '10437' file_name: Thesis_Final_09_12_2021.zip file_size: 2596924 relation: source_file file_date_updated: 2022-03-28T12:55:12Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '132' project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10432' relation: part_of_dissertation status: public - id: '6673' relation: part_of_dissertation status: public - id: '5965' relation: part_of_dissertation status: public - id: '10435' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: On achieving scalability through relaxation type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9733' abstract: - lang: eng text: This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 citation: ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733 apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733 chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733. ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021. ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria. mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733. short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021. date_created: 2021-07-27T15:48:30Z date_published: 2021-08-20T00:00:00Z date_updated: 2024-03-06T12:30:44Z day: '20' ddc: - '515' - '519' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe - _id: JaMa doi: 10.15479/at:ista:9733 ec_funded: 1 file: - access_level: open_access checksum: e88bb8ca43948abe060eb2d2fa719881 content_type: application/pdf creator: dfelicia date_created: 2021-08-19T14:03:48Z date_updated: 2021-09-06T09:28:56Z file_id: '9944' file_name: Thesis_FeliciangeliA.pdf file_size: 1958710 relation: main_file - access_level: closed checksum: 72810843abee83705853505b3f8348aa content_type: application/octet-stream creator: dfelicia date_created: 2021-08-19T14:06:35Z date_updated: 2022-03-10T12:13:57Z file_id: '9945' file_name: thesis.7z file_size: 3771669 relation: source_file file_date_updated: 2022-03-10T12:13:57Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '180' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9787' relation: part_of_dissertation status: public - id: '9792' relation: part_of_dissertation status: public - id: '9225' relation: part_of_dissertation status: public - id: '9781' relation: part_of_dissertation status: public - id: '9791' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: The polaron at strong coupling tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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. date_created: 2021-09-09T07:37:20Z date_published: 2021-09-13T00:00:00Z date_updated: 2023-09-07T13:38:33Z 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: '6351' relation: part_of_dissertation status: public - id: '6943' relation: part_of_dissertation status: public - id: '8002' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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. date_created: 2021-07-01T14:50:17Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-09-07T13:33:27Z 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: '9750' relation: part_of_dissertation status: public - id: '9006' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10058' abstract: - lang: eng text: 'Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.' acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 citation: ama: Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058 apa: Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058 chicago: Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058. ieee: D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021. ista: Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. mla: Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058. short: D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021. date_created: 2021-09-30T07:53:49Z date_published: 2021-10-05T00:00:00Z date_updated: 2023-09-08T11:41:08Z day: '05' ddc: - '621' - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:10058 file: - access_level: closed checksum: ad6bcb24083ed7c02baaf1885c9ea3d5 content_type: application/x-zip-compressed creator: djirovec date_created: 2021-09-30T14:29:14Z date_updated: 2022-12-20T23:30:07Z embargo_to: open_access file_id: '10061' file_name: PHD_Thesis_Jirovec_Source.zip file_size: 32397600 relation: source_file - access_level: open_access checksum: 5fbe08d4f66d1153e04c47971538fae8 content_type: application/pdf creator: djirovec date_created: 2021-10-05T07:56:49Z date_updated: 2022-12-20T23:30:07Z embargo: 2022-10-06 file_id: '10087' file_name: PHD_Thesis_pdfa2b_1.pdf file_size: 26910829 relation: main_file file_date_updated: 2022-12-20T23:30:07Z has_accepted_license: '1' keyword: - qubits - quantum computing - holes language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '151' project: - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8831' relation: part_of_dissertation status: public - id: '10065' relation: part_of_dissertation status: public - id: '10066' relation: part_of_dissertation status: public - id: '8909' relation: part_of_dissertation status: public - id: '5816' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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. date_created: 2021-05-17T12:31:30Z date_published: 2021-05-18T00:00:00Z date_updated: 2023-09-07T13:32:32Z 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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.' date_created: 2021-06-17T14:10:47Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-09-11T12:55:53Z 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: '9756' relation: part_of_dissertation status: public - id: '9437' relation: part_of_dissertation status: public - id: '8532' relation: part_of_dissertation status: public - id: '612' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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. date_created: 2020-12-10T12:17:07Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-09-22T10:03:21Z 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 Probablistic 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: '1386' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '311' relation: part_of_dissertation status: public - id: '6056' relation: part_of_dissertation status: public - id: '6380' relation: part_of_dissertation status: public - id: '639' relation: part_of_dissertation status: public - id: '66' relation: part_of_dissertation status: public - id: '6780' relation: part_of_dissertation status: public - id: '6918' relation: part_of_dissertation status: public - id: '7810' relation: part_of_dissertation status: public - id: '6175' relation: part_of_dissertation status: public - id: '6378' relation: part_of_dissertation status: public - id: '6490' relation: part_of_dissertation status: public - id: '7014' relation: part_of_dissertation status: public - id: '8089' relation: part_of_dissertation status: public - id: '8728' relation: part_of_dissertation status: public - id: '7158' relation: part_of_dissertation status: public - id: '5977' relation: part_of_dissertation status: public - id: '6009' relation: part_of_dissertation status: public - id: '6340' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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. date_created: 2021-11-18T15:05:06Z date_published: 2021-11-18T00:00:00Z date_updated: 2023-09-07T13:34:38Z 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _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. date_created: 2021-11-18T11:20:59Z date_published: 2021-11-22T00:00:00Z date_updated: 2023-09-19T14:42:45Z 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: '9010' relation: part_of_dissertation status: public - id: '9913' relation: part_of_dissertation status: public - id: '47' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ...