[{"date_published":"2023-11-10T00:00:00Z","date_created":"2023-11-10T09:10:06Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2023","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"id":"9887","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8139"}]},"page":"180","date_updated":"2024-03-25T23:30:25Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","citation":{"ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 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.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","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.","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."},"day":"10","ddc":["570"],"month":"11","file_date_updated":"2023-11-23T13:10:55Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-11-20T09:18:51Z","file_id":"14567","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-11-20T09:18:51Z","relation":"source_file","file_size":20824903,"creator":"ngnyliuk","file_name":"Thesis_Gnyliukh_final_08_11_23.docx"},{"file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","relation":"main_file","file_size":24871844,"creator":"ngnyliuk","embargo":"2024-11-23","access_level":"closed","checksum":"bfc96d47fc4e7e857dd71656097214a4","content_type":"application/pdf","date_updated":"2023-11-23T13:10:55Z","embargo_to":"open_access","file_id":"14568","date_created":"2023-11-20T09:23:11Z"}],"doi":"10.15479/at:ista:14510","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"author":[{"orcid":"0000-0002-2198-0509","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia"}],"_id":"14510","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}]},{"related_material":{"record":[{"id":"11458","status":"public","relation":"part_of_dissertation"},{"id":"13053","relation":"part_of_dissertation","status":"public"},{"id":"12299","relation":"part_of_dissertation","status":"public"}]},"page":"147","date_updated":"2023-08-04T10:33:27Z","alternative_title":["ISTA Thesis"],"year":"2023","oa":1,"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2023-05-23T00:00:00Z","date_created":"2023-05-23T17:07:53Z","acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"abstract":[{"text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.","lang":"eng"}],"doi":"10.15479/at:ista:13074","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"title":"Efficiency and generalization of sparse neural networks","author":[{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"}],"_id":"13074","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"13087","date_created":"2023-05-24T16:11:16Z","access_level":"open_access","content_type":"application/pdf","checksum":"6b3354968403cb9d48cc5a83611fb571","success":1,"date_updated":"2023-05-24T16:11:16Z","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","file_size":2152072,"relation":"main_file","creator":"epeste"},{"date_created":"2023-05-24T16:12:59Z","file_id":"13088","relation":"source_file","creator":"epeste","file_size":1658293,"file_name":"PhD_Thesis_APeste.zip","date_updated":"2023-05-24T16:12:59Z","content_type":"application/zip","checksum":"8d0df94bbcf4db72c991f22503b3fd60","access_level":"closed"}],"oa_version":"Published Version","citation":{"mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria."},"day":"23","file_date_updated":"2023-05-24T16:12:59Z","ddc":["000"],"month":"05"},{"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"date_created":"2023-08-15T10:20:40Z","date_published":"2023-08-15T00:00:00Z","date_updated":"2023-12-13T12:15:36Z","page":"230","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"12933"},{"id":"6831","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14077"}]},"oa":1,"year":"2023","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2023-08-17T06:55:24Z","access_level":"closed","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","content_type":"application/zip","file_name":"Thesis_latex_forpdfa.zip","creator":"gpuixeus","relation":"source_file","file_size":10891454,"file_id":"14075","date_created":"2023-08-16T18:15:17Z"},{"relation":"main_file","file_size":19856686,"creator":"gpuixeus","file_name":"PhDThesis_PuixeuG.pdf","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-18T10:47:55Z","success":1,"date_created":"2023-08-18T10:47:55Z","file_id":"14079"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","month":"08","file_date_updated":"2023-08-18T10:47:55Z","ddc":["576"],"citation":{"mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023."},"day":"15","oa_version":"Published Version","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"14058","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","supervisor":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"author":[{"orcid":"0000-0001-8330-1754","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma"}],"doi":"10.15479/at:ista:14058","abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}]},{"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2023-09-25T00:00:00Z","date_created":"2023-09-06T10:58:25Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"11373","relation":"part_of_dissertation","status":"public"},{"id":"7387","status":"public","relation":"part_of_dissertation"},{"relation":"research_data","status":"public","id":"10934"}]},"page":"156","date_updated":"2024-02-21T12:35:18Z","alternative_title":["ISTA Thesis"],"year":"2023","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2023-10-04T10:28:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"87eef11fbc5c7df0826f12a3a629b444","access_level":"closed","relation":"source_file","creator":"pradler","file_size":114932847,"file_name":"PhD Thesis_Philipp Radler_20231004.docx","date_created":"2023-10-04T10:11:53Z","file_id":"14390"},{"embargo_to":"open_access","file_id":"14391","date_created":"2023-10-04T10:11:21Z","access_level":"closed","checksum":"3253e099b7126469d941fd9419d68b4f","content_type":"application/pdf","date_updated":"2023-10-04T10:28:35Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","file_size":37838778,"relation":"main_file","creator":"pradler","embargo":"2024-10-04"}],"oa_version":"Published Version","citation":{"ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280."},"day":"25","ddc":["572"],"file_date_updated":"2023-10-04T10:28:35Z","month":"09","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis"}],"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"doi":"10.15479/at:ista:14280","supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","author":[{"last_name":"Radler","full_name":"Radler, Philipp","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "}],"_id":"14280"},{"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_published":"2023-01-09T00:00:00Z","date_created":"2023-01-31T15:10:53Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11943"},{"id":"11950","relation":"part_of_dissertation","status":"public"}]},"page":"201","date_updated":"2023-08-31T12:26:58Z","alternative_title":["ISTA Thesis"],"year":"2023","oa":1,"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","checksum":"1a2306e5f59f52df598e7ecfadf921ac","access_level":"open_access","date_updated":"2023-07-27T22:30:54Z","creator":"cchlebak","file_size":41771714,"relation":"main_file","file_name":"20230109_PhD_thesis_JM_final.pdf","embargo":"2023-07-09","date_created":"2023-01-31T15:11:42Z","file_id":"12471"},{"embargo_to":"open_access","date_created":"2023-01-31T15:11:51Z","file_id":"12472","checksum":"0bebbdee0773443959e1f6ab8caf281f","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-07-10T22:30:04Z","file_size":66983464,"relation":"source_file","creator":"cchlebak","file_name":"20230109_PhD_thesis_JM_final.docx"}],"oa_version":"Published Version","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","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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.","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","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.","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.","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."},"day":"09","file_date_updated":"2023-07-27T22:30:54Z","ddc":["610"],"month":"01","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"abstract":[{"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\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved 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.","lang":"eng"}],"doi":"10.15479/at:ista:12470","supervisor":[{"full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","author":[{"orcid":"0000-0003-3862-1235","last_name":"Michalska","full_name":"Michalska, Julia M","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"}],"_id":"12470"},{"supervisor":[{"orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","full_name":"Zens, Bettina","last_name":"Zens"}],"_id":"12491","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"doi":"10.15479/at:ista:12491","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"publication_status":"published","status":"public","citation":{"mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491"},"day":"02","month":"02","ddc":["570"],"file_date_updated":"2024-02-08T23:30:04Z","oa_version":"Published Version","degree_awarded":"PhD","file":[{"content_type":"application/pdf","checksum":"069d87f025e0799bf9e3c375664264f2","access_level":"open_access","date_updated":"2024-02-08T23:30:04Z","file_size":23082464,"relation":"main_file","creator":"bzens","file_name":"PhDThesis_BettinaZens_2023_final.pdf","embargo":"2024-02-07","date_created":"2023-02-07T13:07:38Z","file_id":"12527"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"8c66ed203495d6e078ed1002a866520c","access_level":"closed","date_updated":"2024-02-08T23:30:04Z","creator":"bzens","relation":"source_file","file_size":106169509,"file_name":"PhDThesis_BettinaZens_2023_final.docx","embargo_to":"open_access","date_created":"2023-02-07T13:09:05Z","file_id":"12528"}],"has_accepted_license":"1","article_processing_charge":"No","oa":1,"alternative_title":["ISTA Thesis"],"year":"2023","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"date_updated":"2024-02-08T23:30:05Z","related_material":{"record":[{"id":"8586","relation":"part_of_dissertation","status":"public"}]},"page":"187","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2023-02-02T00:00:00Z","date_created":"2023-02-02T14:50:20Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation"},{"oa_version":"Published Version","month":"03","file_date_updated":"2023-03-08T15:08:46Z","ddc":["599","573"],"citation":{"ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716."},"day":"10","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"Burnett_Thesis_2023.docx","file_size":23029260,"relation":"source_file","creator":"lburnett","date_updated":"2023-03-08T15:08:46Z","access_level":"closed","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12717","date_created":"2023-03-08T15:08:46Z"},{"date_updated":"2023-03-08T15:08:46Z","success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","content_type":"application/pdf","access_level":"open_access","file_size":11959869,"creator":"lburnett","relation":"main_file","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_created":"2023-03-08T15:08:46Z","file_id":"12718"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:12716","abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"_id":"12716","title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","supervisor":[{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"author":[{"orcid":"0000-0002-8937-410X","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","last_name":"Burnett"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"date_created":"2023-03-08T15:19:45Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"date_published":"2023-03-10T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","year":"2023","alternative_title":["ISTA Thesis"],"oa":1,"page":"178","date_updated":"2023-04-05T10:59:04Z"},{"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2023-03-15T13:22:13Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"date_published":"2023-03-23T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"page":"260","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10703"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"status":"public","relation":"part_of_dissertation","id":"7932"},{"status":"public","relation":"part_of_dissertation","id":"461"},{"id":"14530","relation":"new_edition","status":"public"}]},"date_updated":"2023-11-30T10:55:13Z","year":"2023","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2023-03-23T12:49:23Z","file_id":"12745","date_updated":"2023-11-24T11:57:46Z","content_type":"application/pdf","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","access_level":"closed","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_size":63734746,"relation":"main_file","creator":"cchlebak","file_name":"Thesis_Riedl_2023.pdf"},{"file_name":"Thesis_Riedl_2023_source.rar","file_size":339473651,"creator":"cchlebak","relation":"source_file","access_level":"closed","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","content_type":"application/octet-stream","date_updated":"2023-09-24T22:30:03Z","embargo_to":"open_access","file_id":"12746","date_created":"2023-03-23T12:54:34Z"}],"degree_awarded":"PhD","oa_version":"None","file_date_updated":"2023-11-24T11:57:46Z","month":"03","ddc":["530"],"citation":{"mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023."},"day":"23","publication_status":"published","status":"public","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12726","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"_id":"12726","supervisor":[{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"title":"Synchronization in collectively moving active matter","author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}]},{"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"12732","author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","orcid":"0000-0002-7969-2729"}],"supervisor":[{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","doi":"10.15479/at:ista:12732","abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"file":[{"date_updated":"2023-03-23T16:42:56Z","checksum":"5d2de651ef9449c1b8dc27148ca74777","content_type":"application/zip","access_level":"closed","relation":"source_file","file_size":42167561,"creator":"pbrighi","file_name":"Thesis_sub_PBrighi.zip","date_created":"2023-03-23T16:42:56Z","file_id":"12753"},{"creator":"pbrighi","file_size":13977000,"relation":"main_file","file_name":"Thesis_PBrighi.pdf","date_updated":"2023-03-23T16:43:14Z","success":1,"checksum":"7caa153d4a5b0873a79358787d2dfe1e","content_type":"application/pdf","access_level":"open_access","date_created":"2023-03-23T16:43:14Z","file_id":"12754"}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2023-03-23T16:43:14Z","ddc":["530"],"month":"03","day":"21","citation":{"mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732.","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria."},"oa_version":"None","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_updated":"2023-09-20T10:44:12Z","page":"158","related_material":{"record":[{"id":"11470","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8308"},{"id":"11469","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12750"}]},"oa":1,"year":"2023","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2023-03-17T13:30:48Z","date_published":"2023-03-21T00:00:00Z"},{"alternative_title":["ISTA Thesis"],"year":"2023","related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"page":"127","date_updated":"2023-08-04T08:54:51Z","date_published":"2023-03-23T00:00:00Z","date_created":"2023-03-31T12:24:42Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"doi":"10.15479/at:ista:12781","supervisor":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk"}],"_id":"12781","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines"}],"oa_version":"Published Version","citation":{"chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781"},"day":"23","month":"03","ddc":["570","572"],"file_date_updated":"2023-04-20T07:02:59Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"content_type":"application/pdf","checksum":"5ebb6345cb4119f93460c81310265a6d","access_level":"closed","date_updated":"2023-04-19T14:33:41Z","relation":"main_file","file_size":6071553,"creator":"vkravchu","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo":"2024-04-20","embargo_to":"local","date_created":"2023-04-19T14:33:41Z","file_id":"12852"},{"date_created":"2023-04-19T14:33:52Z","file_id":"12853","embargo_to":"local","date_updated":"2023-04-20T07:02:59Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"c12055c48411d030d2afa51de2166221","access_level":"closed","embargo":"2024-04-20","relation":"source_file","file_size":19468766,"creator":"vkravchu","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx"}]},{"day":"28","citation":{"mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885"},"month":"04","ddc":["546","541"],"file_date_updated":"2023-05-02T07:43:18Z","oa_version":"Published Version","degree_awarded":"PhD","file":[{"date_updated":"2023-05-02T07:43:18Z","checksum":"9347b0e09425f56fdcede5d3528404dc","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"mcalcabr","file_size":99627036,"relation":"source_file","file_name":"Thesis_Calcabrini.docx","date_created":"2023-05-02T07:43:18Z","file_id":"12887"},{"date_created":"2023-05-02T07:42:45Z","file_id":"12888","creator":"mcalcabr","file_size":8742220,"relation":"main_file","file_name":"Thesis_Calcabrini_pdfa.pdf","content_type":"application/pdf","checksum":"2d188b76621086cd384f0b9264b0a576","access_level":"open_access","date_updated":"2023-05-02T07:42:45Z","success":1}],"has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Calcabrini","full_name":"Calcabrini, Mariano","first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877"}],"supervisor":[{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"}],"title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","_id":"12885","abstract":[{"text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"doi":"10.15479/at:ista:12885","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"status":"public","publication_status":"published","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2023-04-28T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"date_created":"2023-05-02T07:58:57Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"alternative_title":["ISTA Thesis"],"year":"2023","date_updated":"2023-08-14T07:25:26Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10806"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"relation":"part_of_dissertation","status":"public","id":"12237"},{"id":"9118","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10123"}]},"page":"82"},{"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2023-05-11T10:43:20Z","file_id":"12942","embargo":"2023-12-07","creator":"chafner","relation":"main_file","file_size":50714445,"file_name":"thesis-hafner-2023may11-a2b.pdf","date_updated":"2023-12-08T23:30:04Z","content_type":"application/pdf","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","access_level":"open_access"},{"creator":"chafner","relation":"source_file","file_size":265319,"file_name":"thesis-release-form.pdf","date_updated":"2023-12-08T23:30:04Z","checksum":"a6b51334be2b81672357b1549afab40c","content_type":"application/pdf","access_level":"closed","date_created":"2023-05-11T10:43:44Z","file_id":"12943","embargo_to":"open_access"}],"degree_awarded":"PhD","oa_version":"Published Version","file_date_updated":"2023-12-08T23:30:04Z","ddc":["516","004","518","531"],"month":"05","day":"05","citation":{"ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897."},"ec_funded":1,"status":"public","publication_status":"published","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:12897","abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"_id":"12897","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"M-Shop"}],"date_created":"2023-05-05T10:40:14Z","date_published":"2023-05-05T00:00:00Z","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"page":"180","related_material":{"record":[{"id":"9817","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7117"},{"status":"public","relation":"dissertation_contains","id":"13188"}]},"date_updated":"2024-01-29T10:47:51Z","alternative_title":["ISTA Thesis"],"year":"2023","oa":1},{"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2023-05-15T14:52:36Z","date_published":"2023-05-17T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"page":"146","related_material":{"record":[{"id":"8602","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-08-04T11:02:40Z","alternative_title":["ISTA Thesis"],"year":"2023","article_processing_charge":"No","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"embargo_to":"open_access","date_created":"2023-05-17T13:39:54Z","file_id":"12988","content_type":"application/pdf","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","access_level":"closed","date_updated":"2023-05-19T07:04:25Z","creator":"dboocock","file_size":40414730,"relation":"main_file","file_name":"thesis_boocock.pdf","embargo":"2024-05-17"},{"file_id":"12989","date_created":"2023-05-17T13:39:53Z","date_updated":"2023-05-17T14:35:13Z","access_level":"closed","checksum":"581a2313ffeb40fe77e8a122a25a7795","content_type":"application/zip","file_name":"thesis_boocock.zip","file_size":34338567,"relation":"source_file","creator":"dboocock"}],"degree_awarded":"PhD","oa_version":"Published Version","file_date_updated":"2023-05-19T07:04:25Z","ddc":["530"],"month":"05","day":"17","citation":{"apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964."},"ec_funded":1,"publication_status":"published","status":"public","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"doi":"10.15479/at:ista:12964","abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"_id":"12964","author":[{"orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R"}],"supervisor":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"title":"Mechanochemical pattern formation across biological scales"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"date_created":"2022-02-04T15:45:12Z","date_published":"2022-02-07T00:00:00Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T13:43:23Z","month":"02","file_date_updated":"2023-02-04T23:30:03Z","ddc":["570"],"day":"07","citation":{"ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","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.","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."},"oa_version":"Published Version","file":[{"embargo_to":"open_access","date_created":"2022-02-04T15:36:12Z","file_id":"10728","relation":"source_file","creator":"smetzler","file_size":6757886,"file_name":"Thesis_Sina_Metzler.docx","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-02-03T23:30:03Z"},{"file_id":"10730","date_created":"2022-02-04T15:36:43Z","date_updated":"2023-02-03T23:30:03Z","access_level":"open_access","content_type":"application/pdf","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","embargo":"2023-02-02","file_name":"Thesis_Sina_Metzler_A2.pdf","file_size":6314921,"creator":"smetzler","relation":"main_file"},{"file_id":"10742","date_created":"2022-02-07T10:35:02Z","file_name":"Thesis_Sina_Metzler_print.pdf","file_size":6882557,"relation":"main_file","creator":"smetzler","embargo":"2023-02-02","access_level":"open_access","checksum":"dedd14b7be7a75d63018dbfc68dd8113","content_type":"application/pdf","date_updated":"2023-02-04T23:30:03Z"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"10727","author":[{"full_name":"Metzler, Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","orcid":"0000-0002-9547-2494"}],"title":"Pathogen-mediated sexual selection and immunization in ant colonies","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"doi":"10.15479/AT:ISTA:10727","abstract":[{"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.","lang":"eng"}],"project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"publication_status":"published","status":"public"},{"alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"page":"120","related_material":{"record":[{"id":"10762","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7956"},{"status":"public","relation":"part_of_dissertation","id":"415"},{"status":"public","relation":"part_of_dissertation","id":"8644"}]},"date_updated":"2024-08-07T07:16:53Z","date_created":"2022-02-16T13:27:37Z","date_published":"2022-02-21T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:10759","abstract":[{"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.","lang":"eng"}],"_id":"10759","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","orcid":"0000-0002-1106-4419"}],"supervisor":[{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"title":"Analytic and machine learning approaches to composite quantum impurities","ec_funded":1,"status":"public","publication_status":"published","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","ddc":["530"],"file_date_updated":"2022-02-22T07:20:12Z","month":"02","day":"21","citation":{"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.","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.","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","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","short":"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.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759"},"article_processing_charge":"No","has_accepted_license":"1","file":[{"content_type":"application/zip","checksum":"0fc54ad1eaede879c665ac9b53c93e22","access_level":"closed","date_updated":"2022-02-22T07:20:12Z","file_size":17668233,"relation":"source_file","creator":"wrzadkow","file_name":"Rzadkowski_thesis_final_source.zip","date_created":"2022-02-21T13:58:16Z","file_id":"10785"},{"file_name":"Rzadkowski_thesis_final.pdf","creator":"wrzadkow","relation":"main_file","file_size":13307331,"access_level":"open_access","checksum":"22d2d7af37ca31f6b1730c26cac7bced","content_type":"application/pdf","success":1,"date_updated":"2022-02-21T14:02:54Z","file_id":"10786","date_created":"2022-02-21T14:02:54Z"}],"degree_awarded":"PhD"},{"ddc":["000"],"file_date_updated":"2022-03-10T12:11:48Z","month":"03","citation":{"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.","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.","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","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"},"day":"08","oa_version":"Published Version","file":[{"file_id":"10823","date_created":"2022-03-06T11:42:54Z","success":1,"date_updated":"2022-03-06T11:42:54Z","access_level":"open_access","content_type":"application/pdf","checksum":"626bc523ae8822d20e635d0e2d95182e","file_name":"thesis.pdf","relation":"main_file","file_size":4204905,"creator":"nkonstan"},{"file_id":"10824","date_created":"2022-03-06T11:42:57Z","file_name":"thesis.zip","file_size":22841103,"relation":"source_file","creator":"nkonstan","date_updated":"2022-03-10T12:11:48Z","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"e2ca2b88350ac8ea1515b948885cbcb1"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"10799","title":"Robustness and fairness in machine learning","supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H"}],"doi":"10.15479/at:ista:10799","abstract":[{"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.","lang":"eng"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-015-2"]},"ec_funded":1,"publication_status":"published","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_created":"2022-02-28T13:03:49Z","date_published":"2022-03-08T00:00:00Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"oa":1,"keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"alternative_title":["ISTA Thesis"],"year":"2022","date_updated":"2023-10-17T12:31:54Z","page":"176","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8724"},{"id":"10803","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10802"},{"relation":"part_of_dissertation","status":"public","id":"6590"}]}},{"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-04-06T00:00:00Z","date_created":"2022-04-07T08:19:54Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"date_updated":"2023-06-23T06:26:41Z","page":"112","citation":{"ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","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","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","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.","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."},"day":"06","month":"04","file_date_updated":"2022-04-07T08:11:51Z","ddc":["576","582"],"oa_version":"Published Version","degree_awarded":"PhD","file":[{"file_name":"LenkaPhD_Official_PDFA.pdf","relation":"main_file","file_size":11906472,"creator":"cchlebak","access_level":"open_access","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","content_type":"application/pdf","date_updated":"2022-04-07T08:11:34Z","file_id":"11129","date_created":"2022-04-07T08:11:34Z"},{"date_updated":"2022-04-07T08:11:51Z","access_level":"closed","checksum":"99d67040432fd07a225643a212ee8588","content_type":"application/x-zip-compressed","file_name":"LenkaPhD Official_source.zip","file_size":23036766,"relation":"source_file","creator":"cchlebak","file_id":"11130","date_created":"2022-04-07T08:11:51Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Genetic basis of flower colour as a model for adaptive evolution","author":[{"last_name":"Matejovicova","full_name":"Matejovicova, Lenka","first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87"}],"_id":"11128","abstract":[{"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.","lang":"eng"}],"doi":"10.15479/at:ista:11128","publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"publication_status":"published","status":"public"},{"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_published":"2022-04-20T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"}],"date_created":"2022-04-20T08:59:07Z","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10614"},{"id":"544","relation":"part_of_dissertation","status":"public"}]},"page":"170","date_updated":"2023-09-19T10:15:54Z","alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"11195","date_created":"2022-04-20T09:03:57Z","access_level":"open_access","content_type":"application/pdf","checksum":"999ab16884c4522486136ebc5ae8dbff","date_updated":"2023-04-21T22:30:03Z","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","file_size":8820951,"creator":"cchlebak","relation":"main_file","embargo":"2023-04-20"},{"content_type":"application/x-zip-compressed","checksum":"fd92b1e38d53bdf8b458213882d41383","access_level":"closed","date_updated":"2023-04-21T22:30:03Z","relation":"source_file","creator":"cchlebak","file_size":65864612,"file_name":"Thesis_Stephanie_Wachner_20200414.zip","embargo_to":"open_access","date_created":"2022-04-22T12:41:00Z","file_id":"11329"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","day":"20","citation":{"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.","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.","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","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 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."},"file_date_updated":"2023-04-21T22:30:03Z","ddc":["570"],"month":"04","publication_status":"published","status":"public","publication_identifier":{"issn":["2663-337X"]},"project":[{"name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"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"}],"doi":"10.15479/at:ista:11193","author":[{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","full_name":"Wachner, Stephanie","last_name":"Wachner"}],"supervisor":[{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","_id":"11193"},{"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_created":"2022-04-20T14:21:56Z","file_id":"11220","checksum":"1616a8bf6f13a57c892dac873dcd0936","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-04-20T22:30:03Z","file_size":21273537,"relation":"main_file","creator":"okim","file_name":"Olena_KIM_thesis_final.pdf","embargo":"2023-04-19"},{"date_created":"2022-04-20T14:22:56Z","file_id":"11221","embargo_to":"open_access","date_updated":"2023-04-20T22:30:03Z","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","creator":"okim","file_size":59248569,"file_name":"KIM_thesis_final.zip"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","citation":{"ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 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.","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","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","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.","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."},"day":"20","file_date_updated":"2023-04-20T22:30:03Z","ddc":["570"],"month":"04","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497"},{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"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"}],"doi":"10.15479/at:ista:11196","title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","supervisor":[{"last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"author":[{"last_name":"Kim","full_name":"Kim, Olena","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"}],"_id":"11196","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2022-04-20T00:00:00Z","date_created":"2022-04-20T09:47:12Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"department":[{"_id":"PeJo"},{"_id":"GradSch"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11222"},{"id":"7473","relation":"part_of_dissertation","status":"public"}]},"page":"132","date_updated":"2023-08-18T06:31:52Z","year":"2022","alternative_title":["ISTA Thesis"],"oa":1},{"oa_version":"Published Version","file_date_updated":"2023-05-17T22:30:03Z","ddc":["570"],"month":"05","day":"16","citation":{"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.","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.","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","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.","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.","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"},"article_processing_charge":"No","has_accepted_license":"1","file":[{"embargo_to":"open_access","file_id":"11395","date_created":"2022-05-17T09:08:06Z","file_name":"MJ thesis.docx","relation":"source_file","file_size":56427603,"creator":"cchlebak","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"8fc695d88020d70d231dad0e9f10b138","date_updated":"2023-05-17T22:30:03Z"},{"file_id":"11397","date_created":"2022-05-17T12:09:25Z","date_updated":"2023-05-17T22:30:03Z","access_level":"open_access","content_type":"application/pdf","checksum":"c1dd20a1aece521b3500607b00e463d6","embargo":"2023-05-16","file_name":"MJ_thesis_PDFA.pdf","relation":"main_file","file_size":4351981,"creator":"cchlebak"}],"degree_awarded":"PhD","doi":"10.15479/at:ista: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."}],"_id":"11393","author":[{"first_name":"Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","last_name":"Jevtic","full_name":"Jevtic, Marijo"}],"title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","supervisor":[{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"publication_status":"published","status":"public","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2022-05-17T08:57:41Z","date_published":"2022-05-16T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"RySh"}],"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"page":"108","related_material":{"record":[{"id":"7391","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T14:53:44Z"}]