[{"language":[{"iso":"eng"}],"file":[{"creator":"pradler","date_updated":"2023-10-04T10:28:35Z","file_size":114932847,"date_created":"2023-10-04T10:11:53Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14390","checksum":"87eef11fbc5c7df0826f12a3a629b444"},{"date_updated":"2023-10-04T10:28:35Z","file_size":37838778,"creator":"pradler","date_created":"2023-10-04T10:11:21Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file","file_id":"14391","checksum":"3253e099b7126469d941fd9419d68b4f","embargo":"2024-10-04"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"11373","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7387"},{"relation":"research_data","status":"public","id":"10934"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"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.","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["572"],"date_updated":"2024-02-21T12:35:18Z","supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"file_date_updated":"2023-10-04T10:28:35Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"_id":"14280","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","day":"25","year":"2023","has_accepted_license":"1","date_created":"2023-09-06T10:58:25Z","doi":"10.15479/at:ista:14280","date_published":"2023-09-25T00:00:00Z","page":"156","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","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.","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","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280."},"title":"Spatiotemporal signaling during assembly of the bacterial divisome","article_processing_charge":"No","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler"}],"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"679239","name":"Self-Organization of the Bacterial Cell"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}]},{"month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"related_material":{"record":[{"id":"13312","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12118","status":"public"},{"id":"8910","status":"public","relation":"part_of_dissertation"},{"relation":"research_data","id":"12522","status":"public"}]},"ec_funded":1,"file":[{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"666ee31c7eade89679806287c062fa14","file_id":"14033","file_size":56121429,"date_updated":"2023-08-11T10:01:34Z","creator":"mvalenti","file_name":"PhD_thesis_Valentini_final.zip","date_created":"2023-08-11T09:27:39Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"0992f2ebef152dee8e70055350ebbb55","file_id":"14035","creator":"mvalenti","date_updated":"2023-08-11T14:39:17Z","file_size":38199711,"date_created":"2023-08-11T14:39:17Z","file_name":"PhD_thesis_Valentini_final_validated.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"13286","file_date_updated":"2023-08-11T14:39:17Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"ddc":["530"],"supervisor":[{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-21T12:35:34Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2023-07-21T00:00:00Z","doi":"10.15479/at:ista:13286","date_created":"2023-07-24T14:10:45Z","page":"184","day":"21","has_accepted_license":"1","year":"2023","project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Conventional and unconventional topological superconductors"}],"title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","full_name":"Valentini, Marco"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286","apa":"Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286","mla":"Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.","ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286."}},{"language":[{"iso":"eng"}],"file":[{"creator":"afransch","date_updated":"2024-03-01T08:51:42Z","file_size":10797612,"date_created":"2023-08-08T18:01:28Z","file_name":"Thesis_AnnaFranschitz_202308.pdf","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","file_id":"13986","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","embargo":"2024-08-08"},{"file_name":"Thesis_AnnaFranschitz_202308.docx","date_created":"2023-08-08T18:02:25Z","file_size":2619085,"date_updated":"2023-08-09T07:25:27Z","creator":"afransch","checksum":"40abf7ccca14a3893f72dc7fb88585d6","file_id":"13987","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"embargo":"2024-08-08","file_id":"15042","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","embargo_to":"open_access","description":"Minor modifications and clarifications - Feb 2024","content_type":"application/pdf","relation":"erratum","access_level":"closed","file_name":"Addendum_AnnaFranschitz202402.pdf","date_created":"2024-03-01T08:37:15Z","title":"Addendum","file_size":85956,"date_updated":"2024-03-01T12:13:29Z","creator":"cchlebak"},{"date_updated":"2024-03-01T08:51:42Z","file_size":11818,"creator":"cchlebak","date_created":"2024-03-01T08:39:20Z","title":"Addendum - source file","file_name":"Addendum_AnnaFranschitz202402.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"15043","checksum":"66745aa01f960f17472c024875c049ed"},{"title":"Print Version","date_created":"2024-03-01T08:56:06Z","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","date_updated":"2024-03-01T12:58:14Z","file_size":10416761,"creator":"cchlebak","file_id":"15044","checksum":"55c876b73d49db15228a7f571592ec77","content_type":"application/pdf","description":"For printing purposes","access_level":"closed","relation":"other"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663 - 337X"]},"month":"08","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"file_date_updated":"2024-03-01T12:58:14Z","ddc":["570","577"],"date_updated":"2024-03-01T15:25:17Z","supervisor":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"status":"public","type":"dissertation","_id":"13984","date_created":"2023-08-08T15:33:29Z","date_published":"2023-08-08T00:00:00Z","doi":"10.15479/at:ista:13984","page":"89","day":"08","year":"2023","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","title":"Individual and social immunity against viral infections in ants","article_processing_charge":"No","author":[{"full_name":"Franschitz, Anna","last_name":"Franschitz","first_name":"Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984."}},{"author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna"}],"article_processing_charge":"No","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","citation":{"short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323","apa":"Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323","mla":"Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14323."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"page":"151","date_published":"2023-09-13T00:00:00Z","doi":"10.15479/at:ista:14323","date_created":"2023-09-13T10:07:18Z","has_accepted_license":"1","year":"2023","day":"13","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-09-13T10:08:25Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"supervisor":[{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-07T15:02:59Z","ddc":["570"],"type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"14323","related_material":{"record":[{"status":"public","id":"7883","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"PhDThesis_KK_final_pdfA.pdf","date_created":"2023-09-13T09:52:52Z","creator":"kkuzmicz","file_size":10147911,"date_updated":"2023-09-13T10:08:25Z","embargo":"2025-03-13","file_id":"14324","checksum":"bd83596869c814b24aeff7077d031c0e","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf"},{"file_id":"14325","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","date_created":"2023-09-13T09:53:29Z","file_name":"thesis_KK_final_corrections_092023.docx","date_updated":"2023-09-13T09:53:29Z","file_size":103980668,"creator":"kkuzmicz"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube."}],"oa_version":"Published Version"},{"title":"Adaptive mutation in E. coli modulated by luxS","author":[{"full_name":"Hennessey-Wesen, Mike","last_name":"Hennessey-Wesen","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","first_name":"Mike"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). 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Institute of Science and Technology Austria."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.15479/at:ista:14641","date_published":"2023-11-30T00:00:00Z","date_created":"2023-12-04T13:17:37Z","page":"104","day":"30","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-03-20T13:19:36Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"ddc":["570"],"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"date_updated":"2024-03-22T13:21:17Z","status":"public","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"type":"dissertation","_id":"14641","ec_funded":1,"file":[{"content_type":"application/vnd.oasis.opendocument.text","access_level":"closed","relation":"source_file","file_id":"14648","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","date_updated":"2023-12-06T13:13:26Z","file_size":46405919,"creator":"mhenness","date_created":"2023-12-06T13:13:26Z","file_name":"mike_thesis_v06-12-2023.odt"},{"access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","file_id":"14649","checksum":"f5203a61eddaf35235bbc51904d73982","embargo":"2024-11-30","creator":"mhenness","date_updated":"2023-12-06T13:14:15Z","file_size":21282155,"date_created":"2023-12-06T13:14:15Z","file_name":"mike_thesis_v06-12-2023.pdf"},{"content_type":"application/pdf","relation":"other","access_level":"closed","file_id":"15145","checksum":"9f7b4d646f1cfb57e3b9106a8a9cdd9d","file_size":2930287,"date_updated":"2024-03-20T13:19:36Z","creator":"cchlebak","file_name":"2023_Hennessey_Michael_Thesis_from_source.pdf","date_created":"2024-03-20T13:19:36Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria."},"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","article_processing_charge":"No","author":[{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio","full_name":"Marveggio, Alice"}],"project":[{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"day":"21","year":"2023","has_accepted_license":"1","date_created":"2023-11-21T11:41:05Z","date_published":"2023-11-21T00:00:00Z","doi":"10.15479/at:ista:14587","page":"228","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["515"],"date_updated":"2024-03-22T13:21:28Z","supervisor":[{"last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"file_date_updated":"2024-03-20T12:28:32Z","_id":"14587","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"creator":"amarvegg","file_size":2881100,"date_updated":"2023-11-29T09:09:31Z","file_name":"thesis_Marveggio.pdf","date_created":"2023-11-29T09:09:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","file_id":"14626"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","file_id":"14627","date_updated":"2024-03-20T12:28:32Z","file_size":10189696,"creator":"amarvegg","date_created":"2023-11-29T09:10:19Z","file_name":"Thesis_Marveggio.zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"id":"11842","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"14597","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"month":"11","alternative_title":["ISTA Thesis"]},{"alternative_title":["ISTA Thesis"],"month":"02","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","related_material":{"record":[{"id":"8586","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2024-02-07","checksum":"069d87f025e0799bf9e3c375664264f2","file_id":"12527","creator":"bzens","file_size":23082464,"date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","date_created":"2023-02-07T13:07:38Z"},{"file_size":106169509,"date_updated":"2024-02-08T23:30:04Z","creator":"bzens","file_name":"PhDThesis_BettinaZens_2023_final.docx","date_created":"2023-02-07T13:09:05Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"8c66ed203495d6e078ed1002a866520c","file_id":"12528"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","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"],"_id":"12491","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"file_date_updated":"2024-02-08T23:30:04Z","supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"date_updated":"2024-03-25T23:30:05Z","ddc":["570"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"187","doi":"10.15479/at:ista:12491","date_published":"2023-02-02T00:00:00Z","date_created":"2023-02-02T14:50:20Z","has_accepted_license":"1","year":"2023","day":"02","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"author":[{"last_name":"Zens","full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","citation":{"ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","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.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"title":"Generalizing medial axes with homology switches","article_processing_charge":"No","author":[{"first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","last_name":"Stephenson"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226."},"date_created":"2023-08-24T13:01:18Z","date_published":"2023-08-24T00:00:00Z","doi":"10.15479/at:ista:14226","page":"43","day":"24","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"file_date_updated":"2024-02-26T23:30:03Z","ddc":["500"],"date_updated":"2024-02-26T23:30:04Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"status":"public","type":"dissertation","_id":"14226","language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","checksum":"453caf851d75c3478c10ed09bd242a91","file_id":"14227","creator":"cchlebak","file_size":15501411,"date_updated":"2024-02-26T23:30:03Z","file_name":"documents-export-2023-08-24.zip","date_created":"2023-08-24T13:02:49Z"},{"date_created":"2023-08-24T13:03:42Z","file_name":"thesis_pdf_a.pdf","creator":"cchlebak","date_updated":"2024-02-26T23:30:03Z","file_size":6854783,"checksum":"7349d29963d6695e555e171748648d9a","file_id":"14228","embargo":"2024-02-25","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"degree_awarded":"MS","publication_status":"published","publication_identifier":{"issn":["2791-4585"]},"month":"08","alternative_title":["ISTA Master's Thesis"],"oa_version":"Published Version","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}]},{"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"file_date_updated":"2023-07-27T22:30:54Z","ddc":["610"],"supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"date_updated":"2023-08-31T12:26:58Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12470","related_material":{"record":[{"status":"public","id":"11943","relation":"part_of_dissertation"},{"id":"11950","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_id":"12471","embargo":"2023-07-09","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-01-31T15:11:42Z","file_name":"20230109_PhD_thesis_JM_final.pdf","creator":"cchlebak","date_updated":"2023-07-27T22:30:54Z","file_size":41771714},{"file_name":"20230109_PhD_thesis_JM_final.docx","date_created":"2023-01-31T15:11:51Z","creator":"cchlebak","file_size":66983464,"date_updated":"2023-07-10T22:30:04Z","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_id":"12472","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":[" 978-3-99078-026-8"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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.","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.","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.","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","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi: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."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:12470","date_published":"2023-01-09T00:00:00Z","date_created":"2023-01-31T15:10:53Z","page":"201","day":"09","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1},{"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"08","page":"46","doi":"10.15479/at:ista:12531","date_published":"2023-02-08T00:00:00Z","date_created":"2023-02-09T07:45:05Z","citation":{"short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","full_name":"Kirillova, Kseniia","last_name":"Kirillova"}],"article_processing_charge":"No","title":"Panoramic functional gradients across the mouse retina","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Master's Thesis"],"month":"02","publication_identifier":{"issn":["2791-4585"]},"degree_awarded":"MS","publication_status":"published","file":[{"checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_id":"12532","embargo":"2024-02-08","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-02-09T08:03:32Z","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","date_updated":"2024-02-09T23:30:03Z","file_size":8369317,"creator":"cchlebak"},{"checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_id":"12535","embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","date_created":"2023-02-10T09:32:06Z","file_size":11204408,"date_updated":"2024-02-09T23:30:03Z","creator":"cchlebak"}],"language":[{"iso":"eng"}],"_id":"12531","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-09T23:30:04Z","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"file_date_updated":"2024-02-09T23:30:03Z"},{"publication_identifier":{"issn":["2791-4585"]},"degree_awarded":"MS","publication_status":"published","file":[{"date_created":"2023-04-06T06:09:40Z","file_name":"Dispersaldata.xlsx","date_updated":"2023-06-02T22:30:04Z","file_size":52795,"creator":"mjulseth","file_id":"12805","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","embargo_to":"open_access","access_level":"closed","relation":"supplementary_material"},{"file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_created":"2023-04-06T06:11:27Z","creator":"mjulseth","file_size":787239,"date_updated":"2023-06-02T22:30:04Z","embargo":"2023-06-01","file_id":"12806","checksum":"5a13b6d204371572e249f03795bc0d04","relation":"supplementary_material","access_level":"open_access","content_type":"application/vnd.wolfram.nb"},{"file_name":"ThesisMaraJulseth_04_23.docx","date_created":"2023-04-06T08:26:12Z","creator":"mjulseth","file_size":1061763,"date_updated":"2023-06-02T22:30:04Z","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_id":"12812","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2023-06-01","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_id":"12813","creator":"mjulseth","file_size":1741364,"date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.pdf","date_created":"2023-04-06T08:26:37Z"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"oa_version":"Published Version","alternative_title":["ISTA Master's Thesis"],"month":"04","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"date_updated":"2023-06-02T22:30:05Z","ddc":["576"],"file_date_updated":"2023-06-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"12800","type":"dissertation","status":"public","has_accepted_license":"1","year":"2023","day":"05","page":"21","date_published":"2023-04-05T00:00:00Z","doi":"10.15479/at:ista:12800","date_created":"2023-04-04T18:57:11Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Julseth, Mara","last_name":"Julseth","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara"}],"article_processing_charge":"No","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone"},{"publisher":"Institute of Science and Technology Austria","day":"10","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:14510","date_published":"2023-11-10T00:00:00Z","date_created":"2023-11-10T09:10:06Z","page":"180","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","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","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510"},"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","author":[{"orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"month":"11","alternative_title":["ISTA Thesis"],"file":[{"creator":"ngnyliuk","file_size":20824903,"date_updated":"2023-11-20T09:18:51Z","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_created":"2023-11-20T09:18:51Z","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14567","checksum":"3d5e680bfc61f98e308c434f45cc9bd6"},{"file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_created":"2023-11-20T09:23:11Z","creator":"ngnyliuk","file_size":24871844,"date_updated":"2023-11-23T13:10:55Z","embargo":"2024-11-23","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_id":"14568","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9887","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8139"}]},"ec_funded":1,"_id":"14510","status":"public","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"date_updated":"2024-03-27T23:30:45Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"file_date_updated":"2023-11-23T13:10:55Z"},{"has_accepted_license":"1","year":"2023","day":"05","page":"180","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12897","date_created":"2023-05-05T10:40:14Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","short":"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","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi: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.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","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."},"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hafner","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"article_processing_charge":"No","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"chafner","date_updated":"2023-12-08T23:30:04Z","file_size":50714445,"date_created":"2023-05-11T10:43:20Z","file_name":"thesis-hafner-2023may11-a2b.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"12942","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","embargo":"2023-12-07"},{"checksum":"a6b51334be2b81672357b1549afab40c","file_id":"12943","embargo_to":"open_access","content_type":"application/pdf","relation":"source_file","access_level":"closed","file_name":"thesis-release-form.pdf","date_created":"2023-05-11T10:43:44Z","file_size":265319,"date_updated":"2023-12-08T23:30:04Z","creator":"chafner"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9817"},{"status":"public","id":"7117","relation":"part_of_dissertation"},{"relation":"dissertation_contains","id":"13188","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","supervisor":[{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"date_updated":"2024-01-29T10:47:51Z","ddc":["516","004","518","531"],"file_date_updated":"2023-12-08T23:30:04Z","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"_id":"12897","type":"dissertation","status":"public"},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","date_created":"2022-09-08T21:53:03Z","doi":"10.15479/at:ista:12072","date_published":"2022-09-08T00:00:00Z","page":"208","day":"08","year":"2022","has_accepted_license":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","article_processing_charge":"No","author":[{"full_name":"Shute, Alec L","orcid":"0000-0002-1812-2810","last_name":"Shute","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. "}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"12076","status":"public"},{"relation":"part_of_dissertation","id":"12077","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2022-09-08T21:50:34Z","file_name":"Thesis_final_draft.pdf","creator":"ashute","date_updated":"2022-09-08T21:50:34Z","file_size":1907386,"file_id":"12073","checksum":"bf073344320e05d92c224786cec2e92d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_id":"12074","checksum":"b054ac6baa09f70e8235403a4abbed80","relation":"source_file","access_level":"closed","content_type":"application/octet-stream","file_name":"athesis.tex","date_created":"2022-09-08T21:50:42Z","creator":"ashute","file_size":495393,"date_updated":"2022-09-12T11:24:21Z"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"12078","checksum":"0a31e905f1cff5eb8110978cc90e1e79","creator":"ashute","file_size":944534,"date_updated":"2022-09-12T11:24:21Z","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","date_created":"2022-09-09T12:05:00Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","_id":"12072","file_date_updated":"2022-09-12T11:24:21Z","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"ddc":["512"],"date_updated":"2023-02-21T16:37:35Z","supervisor":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"}]},{"type":"dissertation","status":"public","_id":"11777","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"file_date_updated":"2022-08-11T16:09:19Z","supervisor":[{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"date_updated":"2023-06-22T09:56:36Z","ddc":["500","516","514"],"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2022-08-10T15:34:04Z","file_name":"flags.py","date_updated":"2022-08-10T15:34:04Z","file_size":16828,"creator":"pwild","file_id":"11780","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","content_type":"text/x-python","access_level":"open_access","relation":"supplementary_material"},{"file_name":"lowerbound.cpp","date_created":"2022-08-10T15:34:10Z","file_size":12226,"date_updated":"2022-08-10T15:34:10Z","creator":"pwild","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_id":"11781","description":"Code for proof of Lemma 8.20 in Thesis","content_type":"text/x-c++src","relation":"supplementary_material","access_level":"open_access"},{"file_size":3240,"date_updated":"2022-08-10T15:34:17Z","creator":"pwild","file_name":"upperbound.py","date_created":"2022-08-10T15:34:17Z","content_type":"text/x-python","description":"Code for proof of Proposition 7.9 in Thesis","relation":"supplementary_material","access_level":"open_access","file_id":"11782","checksum":"4cf81455c49e5dec3b9b2e3980137eeb"},{"file_name":"finalthesisPascalWildPDFA.pdf","date_created":"2022-08-11T16:08:33Z","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","creator":"pwild","file_size":5086282,"date_updated":"2022-08-11T16:08:33Z","checksum":"4e96575b10cbe4e0d0db2045b2847774","file_id":"11809","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_id":"11810","checksum":"92d94842a1fb6dca5808448137573b2e","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2022-08-11T16:09:19Z","file_name":"ThesisSubmission.zip","creator":"pwild","date_updated":"2022-08-11T16:09:19Z","file_size":18150068}],"language":[{"iso":"eng"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"last_name":"Wild","full_name":"Wild, Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","first_name":"Pascal"}],"article_processing_charge":"No","title":"High-dimensional expansion and crossing numbers of simplicial complexes","citation":{"ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","apa":"Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777","mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology","oa":1,"page":"170","doi":"10.15479/at:ista:11777","date_published":"2022-08-11T00:00:00Z","date_created":"2022-08-10T15:51:19Z","has_accepted_license":"1","year":"2022","day":"11"},{"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2022-04-07T08:11:51Z","ddc":["576","582"],"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-06-23T06:26:41Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"11128","file":[{"file_name":"LenkaPhD_Official_PDFA.pdf","date_created":"2022-04-07T08:11:34Z","creator":"cchlebak","file_size":11906472,"date_updated":"2022-04-07T08:11:34Z","file_id":"11129","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"creator":"cchlebak","date_updated":"2022-04-07T08:11:51Z","file_size":23036766,"date_created":"2022-04-07T08:11:51Z","file_name":"LenkaPhD Official_source.zip","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"99d67040432fd07a225643a212ee8588","file_id":"11130"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"04","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"title":"Genetic basis of flower colour as a model for adaptive evolution","author":[{"first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","last_name":"Matejovicova","full_name":"Matejovicova, Lenka"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","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","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022."},"date_published":"2022-04-06T00:00:00Z","doi":"10.15479/at:ista:11128","date_created":"2022-04-07T08:19:54Z","page":"112","day":"06","has_accepted_license":"1","year":"2022","publisher":"Institute of Science and Technology Austria","oa":1},{"project":[{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945.","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945","apa":"Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945","mla":"Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","last_name":"Schulz","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven"}],"title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2022","has_accepted_license":"1","day":"23","page":"133","date_created":"2022-08-23T11:33:11Z","doi":"10.15479/at:ista:11945","date_published":"2022-08-23T00:00:00Z","_id":"11945","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","date_updated":"2023-08-03T13:02:26Z","supervisor":[{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"file_date_updated":"2022-08-25T09:33:31Z","abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"08","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"61b1b666a210ff7cdd0e95ea75207a13","file_id":"11970","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-08-25T08:59:57Z","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","creator":"rschulz","date_updated":"2022-08-25T08:59:57Z","file_size":28079331},{"file_size":27226963,"date_updated":"2022-08-25T09:33:31Z","creator":"rschulz","file_name":"Thesis_Rouven_Schulz_2022_final.docx","date_created":"2022-08-25T09:00:11Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"11971","checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"11995","status":"public"}]}},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"15","year":"2022","has_accepted_license":"1","date_created":"2023-01-26T10:00:42Z","date_published":"2022-12-15T00:00:00Z","doi":"10.15479/at:ista:12390","page":"196","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","apa":"Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390"},"title":"Translation-invariant quantum systems with effectively broken symmetry","article_processing_charge":"No","author":[{"orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris","last_name":"Brooks","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"}],"oa_version":"Published Version","abstract":[{"text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n","lang":"eng"}],"month":"12","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","file_size":3095225,"date_updated":"2023-01-26T10:02:34Z","file_name":"Brooks_Thesis.pdf","date_created":"2023-01-26T10:02:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"b31460e937f33b557abb40ebef02b567","file_id":"12391"},{"file_name":"Brooks_Thesis.tex","date_created":"2023-01-26T10:02:42Z","creator":"cchlebak","file_size":809842,"date_updated":"2023-01-26T10:02:42Z","file_id":"12392","checksum":"9751869fa5e7981588ad4228f4fd4bd6","relation":"source_file","access_level":"closed","content_type":"application/octet-stream"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"id":"9005","status":"public","relation":"part_of_dissertation"}]},"_id":"12390","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","ddc":["500"],"date_updated":"2023-08-07T13:32:09Z","supervisor":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"file_date_updated":"2023-01-26T10:02:42Z"},{"abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":[" 978-3-99078-025-1 "],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12369","checksum":"e54a3e69b83ebf166544164afd25608e","success":1,"date_updated":"2023-01-25T10:52:46Z","file_size":14581024,"creator":"cchlebak","date_created":"2023-01-25T10:52:46Z","file_name":"THESIS_FINAL_FArslan_pdfa.pdf"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"9350","status":"public"}]},"_id":"12368","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","date_updated":"2023-08-08T13:14:10Z","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"file_date_updated":"2023-01-25T10:52:46Z","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2022","has_accepted_license":"1","day":"29","page":"113","date_created":"2023-01-25T10:43:24Z","doi":"10.15479/at:ista:12153","date_published":"2022-09-29T00:00:00Z","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"}],"title":"Remodeling of E-cadherin-mediated contacts via cortical flows"},{"_id":"11362","keyword":["neural networks","verification","machine learning"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"dissertation","ddc":["004"],"date_updated":"2023-08-17T06:58:38Z","supervisor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2022-05-17T15:19:39Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks."}],"month":"05","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"11378","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","file_size":13210143,"date_updated":"2022-05-13T12:49:00Z","creator":"mlechner","file_name":"src.zip","date_created":"2022-05-13T12:33:26Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11382","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","creator":"mlechner","date_updated":"2022-05-17T15:19:39Z","file_size":2732536,"date_created":"2022-05-16T08:02:28Z","file_name":"thesis_main-a2.pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-017-6"]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"10665","status":"public"},{"id":"10667","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"11366","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7808"},{"id":"10666","status":"public","relation":"part_of_dissertation"}]},"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","mla":"Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.","apa":"Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362","ama":"Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022."},"title":"Learning verifiable representations","article_processing_charge":"No","author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"12","year":"2022","has_accepted_license":"1","date_created":"2022-05-12T07:14:01Z","date_published":"2022-05-12T00:00:00Z","doi":"10.15479/at:ista:11362","page":"124"}]