--- OA_place: publisher _id: '14510' abstract: - lang: eng text: "Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. " 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. corr_author: '1' date_created: 2023-11-10T09:10:06Z date_published: 2023-11-10T00:00:00Z date_updated: 2026-05-15T22:30:39Z 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: 2024-11-23T23:30:38Z embargo_to: open_access file_id: '14567' file_name: Thesis_Gnyliukh_final_08_11_23.docx file_size: 20824903 relation: source_file - access_level: open_access checksum: bfc96d47fc4e7e857dd71656097214a4 content_type: application/pdf creator: ngnyliuk date_created: 2023-11-20T09:23:11Z date_updated: 2024-11-23T23:30:38Z embargo: 2024-11-23 file_id: '14568' file_name: Thesis_Gnyliukh_final_20_11_23.pdf file_size: 24871844 relation: main_file file_date_updated: 2024-11-23T23:30:38Z 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 license: https://creativecommons.org/licenses/by/4.0/ month: '11' oa: 1 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2023-01-31T15:10:53Z date_published: 2023-01-09T00:00:00Z date_updated: 2026-04-07T14:11:10Z 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 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _id: '14323' abstract: - lang: eng text: Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube. acknowledged_ssus: - _id: Bio - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Katarzyna full_name: Kuzmicz-Kowalska, Katarzyna id: 4CED352A-F248-11E8-B48F-1D18A9856A87 last_name: Kuzmicz-Kowalska citation: ama: Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323 apa: Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323 chicago: Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14323. ieee: K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023. ista: Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. mla: Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323. short: K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-09-13T10:07:18Z date_published: 2023-09-13T00:00:00Z date_updated: 2026-04-14T09:50:54Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi doi: 10.15479/at:ista:14323 file: - access_level: open_access checksum: bd83596869c814b24aeff7077d031c0e content_type: application/pdf creator: kkuzmicz date_created: 2023-09-13T09:52:52Z date_updated: 2025-03-13T23:30:05Z embargo: 2025-03-13 file_id: '14324' file_name: PhDThesis_KK_final_pdfA.pdf file_size: 10147911 relation: main_file - access_level: closed checksum: aa2757ae4c3478041fd7e62c587d3e4d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: kkuzmicz date_created: 2023-09-13T09:53:29Z date_updated: 2025-03-13T23:30:05Z embargo_to: open_access file_id: '14325' file_name: thesis_KK_final_corrections_092023.docx file_size: 103980668 relation: source_file file_date_updated: 2025-03-13T23:30:05Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version page: '151' project: - _id: 267AF0E4-B435-11E9-9278-68D0E5697425 name: The role of morphogens in the regulation of neural tube growth publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7883' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _id: '13081' abstract: - lang: eng text: During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis. acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Bocanegra, Laura id: 4896F754-F248-11E8-B48F-1D18A9856A87 last_name: Bocanegra citation: ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081 apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081 chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081. ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023. ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081. short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-05-23T19:10:42Z date_published: 2023-05-23T00:00:00Z date_updated: 2026-04-14T09:50:54Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi doi: 10.15479/at:ista:13081 file: - access_level: closed checksum: 74f3f89e59a0189bee53ebfad9c1b9af content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lbocaneg date_created: 2023-05-25T06:32:12Z date_updated: 2024-06-01T22:30:04Z embargo_to: open_access file_id: '13089' file_name: Thesis_final_LauraBocanegra.docx file_size: 25615534 relation: source_file - access_level: open_access checksum: c6cdef6323eacfb4b7a8af20f32eae97 content_type: application/pdf creator: lbocaneg date_created: 2023-05-25T06:32:16Z date_updated: 2024-06-01T22:30:04Z embargo: 2024-05-31 file_id: '13090' file_name: TotalFinal_Thesis_LauraBocanegraArx.pdf file_size: 12386046 relation: main_file file_date_updated: 2024-06-01T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '93' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9349' relation: part_of_dissertation status: public - id: '12837' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Epithelial dynamics during mouse neural tube development tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-04-07T08:19:54Z date_published: 2022-04-06T00:00:00Z date_updated: 2026-04-07T14:12:19Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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.' corr_author: '1' date_created: 2022-09-08T21:53:03Z date_published: 2022-09-08T00:00:00Z date_updated: 2026-04-07T14:13:35Z 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 license: https://creativecommons.org/licenses/by-nc-sa/4.0/ 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2023-01-25T10:43:24Z date_published: 2022-09-29T00:00:00Z date_updated: 2026-04-07T14:13:19Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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 Austria. 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 Austria, 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 Austria, 2022. ista: Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology Austria. mla: Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11777. short: P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2022-08-10T15:51:19Z date_published: 2022-08-11T00:00:00Z date_updated: 2026-04-07T14:18:26Z 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 Austria 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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.' corr_author: '1' date_created: 2022-06-30T12:15:03Z date_published: 2022-07-01T00:00:00Z date_updated: 2026-04-07T14:14:52Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-08-23T11:33:11Z date_published: 2022-08-23T00:00:00Z date_updated: 2026-04-07T14:17:59Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-07-20T11:21:53Z date_published: 2022-07-20T00:00:00Z date_updated: 2026-04-07T14:18:58Z 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: '8138' relation: part_of_dissertation status: public - id: '7142' relation: part_of_dissertation status: public - id: '6260' relation: part_of_dissertation status: public - id: '10411' relation: part_of_dissertation status: public - id: '8931' relation: part_of_dissertation status: public - id: '7465' relation: part_of_dissertation status: public - id: '9287' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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 orcid: 0009-0009-5204-7621 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. corr_author: '1' date_created: 2022-02-28T13:03:49Z date_published: 2022-03-08T00:00:00Z date_updated: 2026-04-07T14:19:48Z 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: '10802' relation: part_of_dissertation status: public - id: '10803' relation: part_of_dissertation status: public - id: '6590' relation: part_of_dissertation status: public - id: '8724' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-02-16T13:27:37Z date_published: 2022-02-21T00:00:00Z date_updated: 2026-04-07T14:20:12Z 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: '415' relation: part_of_dissertation status: public - id: '8644' relation: part_of_dissertation status: public - id: '7956' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2023-01-26T10:00:42Z date_published: 2022-12-15T00:00:00Z date_updated: 2026-04-16T08:20:52Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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.' corr_author: '1' date_created: 2023-01-24T10:49:46Z date_published: 2022-09-22T00:00:00Z date_updated: 2026-04-16T08:31:54Z 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: 'Big Splash: 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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 orcid: 0000-0003-2344-1039 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. corr_author: '1' date_created: 2022-04-20T09:47:12Z date_published: 2022-04-20T00:00:00Z date_updated: 2026-04-07T14:22:20Z 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 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 glutamatergic 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: Synaptic communication in neuronal microcircuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7473' relation: part_of_dissertation status: public - id: '11222' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-02-04T15:45:12Z date_published: 2022-02-07T00:00:00Z date_updated: 2026-04-07T14:30:18Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-08-17T07:58:53Z date_published: 2022-08-17T00:00:00Z date_updated: 2026-04-07T14:30:39Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2023-01-24T13:09:57Z date_published: 2022-09-19T00:00:00Z date_updated: 2026-04-07T14:30:57Z 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: '11160' relation: part_of_dissertation status: public - id: '3' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2022-05-17T08:57:41Z date_published: 2022-05-16T00:00:00Z date_updated: 2026-04-07T14:31:19Z 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ...