[{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_processing_charge":"No","author":[{"last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"title":"On the encoding, transfer, and consolidation of spatial memories","citation":{"ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932","apa":"Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932","mla":"Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","page":"136","date_created":"2022-08-19T08:52:30Z","doi":"10.15479/at:ista:11932","date_published":"2022-08-19T00:00:00Z","year":"2022","has_accepted_license":"1","day":"19","type":"dissertation","status":"public","_id":"11932","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"file_date_updated":"2023-06-20T22:30:04Z","date_updated":"2023-09-05T12:02:14Z","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"ddc":["573"],"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10077","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6194"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"source_file","content_type":"application/zip","embargo_to":"open_access","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","file_id":"11935","creator":"mnardin","date_updated":"2023-06-20T22:30:04Z","file_size":13515457,"date_created":"2022-08-19T16:31:34Z","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0ec94035ea35a47a9f589ed168e60b48","file_id":"11941","embargo":"2023-06-19","date_updated":"2023-06-20T22:30:04Z","file_size":9906458,"creator":"mnardin","date_created":"2022-08-22T09:43:50Z","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf"}]},{"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2023-04-12T22:30:03Z","file_size":23890382,"date_created":"2023-01-25T14:31:32Z","file_name":"Gloria_Colombo_Thesis.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"12379","checksum":"8cd3ddfe9b53381dcf086023d8d8893a"},{"date_updated":"2023-04-12T22:30:03Z","file_size":13802421,"creator":"cchlebak","date_created":"2023-01-25T14:31:36Z","file_name":"Gloria_Colombo_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8af4319c18b516e8758e9a6cb02b103b","file_id":"12380","embargo":"2023-04-11"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"id":"12244","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"month":"11","alternative_title":["ISTA Thesis"],"ddc":["570"],"date_updated":"2023-08-04T09:40:37Z","supervisor":[{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"file_date_updated":"2023-04-12T22:30:03Z","_id":"12378","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","day":"11","year":"2022","has_accepted_license":"1","date_created":"2023-01-25T14:27:43Z","doi":"10.15479/at:ista:12378","date_published":"2022-11-11T00:00:00Z","page":"142","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","mla":"Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","apa":"Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378"},"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","article_processing_charge":"No","author":[{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022."},"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","author":[{"id":"43FE426A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","last_name":"Belohlavy"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"18","has_accepted_license":"1","year":"2022","date_published":"2022-05-18T00:00:00Z","doi":"10.15479/at:ista:11388","date_created":"2022-05-16T16:49:18Z","page":"98","_id":"11388","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-29T06:41:51Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2023-05-20T22:30:03Z","oa_version":"Published Version","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"file_id":"11398","checksum":"4d75e6a619df7e8a9d6e840aee182380","embargo":"2023-05-19","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-19T13:03:13Z","file_name":"thesis_sb_final_pdfa.pdf","date_updated":"2023-05-20T22:30:03Z","file_size":8247240,"creator":"sbelohla"},{"file_name":"thesis_sb_final.zip","date_created":"2022-05-19T13:07:47Z","creator":"sbelohla","file_size":7094,"date_updated":"2023-05-20T22:30:03Z","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","file_id":"11399","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-018-3"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"status":"public","id":"6713","relation":"part_of_dissertation"}]}},{"year":"2022","has_accepted_license":"1","day":"22","page":"105","date_created":"2023-01-26T11:55:16Z","doi":"10.15479/at:ista:12401","date_published":"2022-12-22T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401.","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"}],"title":"Role of microenvironment heterogeneity in cancer cell invasion","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"embargo":"2023-12-20","file_id":"12402","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","date_created":"2023-01-26T11:58:14Z","file_size":42059787,"date_updated":"2023-12-21T23:30:03Z","creator":"cchlebak"},{"date_created":"2023-01-26T12:00:10Z","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","date_updated":"2023-12-21T23:30:03Z","file_size":261256696,"creator":"cchlebak","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","file_id":"12403","content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"679"},{"status":"public","id":"10703","relation":"part_of_dissertation"},{"status":"public","id":"9429","relation":"part_of_dissertation"},{"status":"public","id":"7885","relation":"part_of_dissertation"}]},"abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"12","date_updated":"2023-12-21T23:30:04Z","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"ddc":["610"],"file_date_updated":"2023-12-21T23:30:03Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"_id":"12401","type":"dissertation","status":"public"},{"project":[{"name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","author":[{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","full_name":"Wachner, Stephanie","last_name":"Wachner"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11193.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","apa":"Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11193","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193.","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2022-04-20T00:00:00Z","doi":"10.15479/at:ista:11193","date_created":"2022-04-20T08:59:07Z","page":"170","day":"20","has_accepted_license":"1","year":"2022","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"11193","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"file_date_updated":"2023-04-21T22:30:03Z","ddc":["570"],"supervisor":[{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"date_updated":"2023-09-19T10:15:54Z","month":"04","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis.","lang":"eng"}],"related_material":{"record":[{"id":"10614","status":"public","relation":"part_of_dissertation"},{"id":"544","status":"public","relation":"part_of_dissertation"}]},"file":[{"creator":"cchlebak","date_updated":"2023-04-21T22:30:03Z","file_size":8820951,"date_created":"2022-04-20T09:03:57Z","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11195","checksum":"999ab16884c4522486136ebc5ae8dbff","embargo":"2023-04-20"},{"checksum":"fd92b1e38d53bdf8b458213882d41383","file_id":"11329","content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2022-04-22T12:41:00Z","file_name":"Thesis_Stephanie_Wachner_20200414.zip","date_updated":"2023-04-21T22:30:03Z","file_size":65864612,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD"},{"_id":"12364","type":"dissertation","status":"public","date_updated":"2023-11-16T13:10:22Z","supervisor":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"ddc":["570"],"file_date_updated":"2023-09-20T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized 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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","file_id":"12365","embargo":"2023-09-19","date_updated":"2023-09-20T22:30:03Z","file_size":20457465,"creator":"cchlebak","date_created":"2023-01-24T13:15:45Z","file_name":"220923_Thesis_CDotter_Final.pdf"},{"embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"12482","checksum":"ad01bb20da163be6893b7af832e58419","file_size":22433512,"date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","file_name":"latex_source_CDotter_Thesis_2022.zip","date_created":"2023-02-02T09:15:35Z"}],"ec_funded":1,"related_material":{"record":[{"id":"3","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11160","status":"public"}]},"project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"},{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","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.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","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","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph"}],"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2022","has_accepted_license":"1","day":"19","page":"152","date_created":"2023-01-24T13:09:57Z","doi":"10.15479/at:ista:12094","date_published":"2022-09-19T00:00:00Z"},{"related_material":{"record":[{"id":"187","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8703"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"checksum":"bcf27986147cab0533b6abadd74e7629","file_id":"9063","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2021-02-02T14:09:25Z","file_name":"thesis_source.zip","creator":"patrickd","date_updated":"2021-02-03T10:37:28Z","file_size":13446994},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9064","checksum":"9cc8af266579a464385bbe2aff6af606","success":1,"creator":"patrickd","date_updated":"2021-02-02T14:09:18Z","file_size":5210329,"date_created":"2021-02-02T14:09:18Z","file_name":"thesis_pdfA2b.pdf"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"place":"Klosterneuburg","month":"02","abstract":[{"lang":"eng","text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets."}],"oa_version":"Published Version","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2021-02-03T10:37:28Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"date_updated":"2023-09-07T13:29:01Z","ddc":["006","514","516"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9056","page":"134","date_published":"2021-02-01T00:00:00Z","doi":"10.15479/AT:ISTA:9056","date_created":"2021-02-02T14:11:06Z","has_accepted_license":"1","year":"2021","day":"01","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"last_name":"Osang","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"article_processing_charge":"No","title":"Multi-cover persistence and Delaunay mosaics","citation":{"ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"ec_funded":1,"language":[{"iso":"eng"}],"file":[{"file_size":4127796,"date_updated":"2021-01-25T14:19:03Z","creator":"gcipollo","file_name":"thesis.pdf","date_created":"2021-01-25T14:19:03Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9043","checksum":"5a93658a5f19478372523ee232887e2b"},{"creator":"gcipollo","date_updated":"2021-01-25T14:19:10Z","file_size":12775206,"date_created":"2021-01-25T14:19:10Z","file_name":"Thesis_files.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"9044","checksum":"e8270eddfe6a988e92a53c88d1d19b8c"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"status":"public","type":"dissertation","_id":"9022","file_date_updated":"2021-01-25T14:19:10Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2023-09-07T13:29:32Z","supervisor":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"}],"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","date_created":"2021-01-21T18:16:54Z","date_published":"2021-01-25T00:00:00Z","doi":"10.15479/AT:ISTA:9022","page":"380","day":"25","year":"2021","has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"title":"Fluctuations in the spectrum of random matrices","article_processing_charge":"No","author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","last_name":"Cipolloni"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","apa":"Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022."}},{"date_created":"2021-09-13T11:12:34Z","date_published":"2021-09-14T00:00:00Z","doi":"10.15479/at:ista:10007","page":"300","day":"14","year":"2021","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","article_processing_charge":"No","author":[{"last_name":"Hensel","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10012","status":"public"},{"relation":"part_of_dissertation","id":"10013","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7489"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-13T11:03:24Z","file_name":"thesis_final_Hensel.zip","creator":"shensel","date_updated":"2021-09-15T14:37:30Z","file_size":15022154,"file_id":"10008","checksum":"c8475faaf0b680b4971f638f1db16347","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed"},{"file_name":"thesis_final_Hensel.pdf","date_created":"2021-09-13T14:18:56Z","creator":"shensel","file_size":6583638,"date_updated":"2021-09-14T09:52:47Z","checksum":"1a609937aa5275452822f45f2da17f07","file_id":"10014","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"file_date_updated":"2021-09-15T14:37:30Z","ddc":["515"],"date_updated":"2023-09-07T13:30:45Z","supervisor":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"dissertation","_id":"10007"},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","date_created":"2021-09-21T09:14:15Z","date_published":"2021-09-22T00:00:00Z","doi":"10.15479/at:ista:10030","day":"22","year":"2021","has_accepted_license":"1","project":[{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","article_processing_charge":"No","author":[{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"related_material":{"record":[{"id":"10022","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9792","status":"public"},{"relation":"part_of_dissertation","id":"7573","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"8cd60dcb8762e8f21867e21e8001e183","file_id":"10032","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2021-09-21T09:17:34Z","file_name":"tex_and_pictures.zip","creator":"cchlebak","date_updated":"2022-03-10T12:14:42Z","file_size":3876668},{"file_name":"thesis_portinale_Final (1).pdf","date_created":"2021-09-27T11:14:31Z","file_size":2532673,"date_updated":"2021-09-27T11:14:31Z","creator":"cchlebak","checksum":"9789e9d967c853c1503ec7f307170279","file_id":"10047","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"10030","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"file_date_updated":"2022-03-10T12:14:42Z","ddc":["515"],"date_updated":"2023-09-07T13:31:06Z","supervisor":[{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"}]}]