[{"language":[{"iso":"eng"}],"month":"07","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","has_accepted_license":"1","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10564"},{"id":"8705","relation":"part_of_dissertation","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"11486","creator":"kmysliwy","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2022-07-05T08:12:56Z","content_type":"application/pdf","file_name":"thes1_no_isbn_2_1b.pdf","date_created":"2022-07-05T08:12:56Z","file_size":1830973,"checksum":"7970714a20a6052f75fb27a6c3e9976e"},{"file_id":"11487","creator":"kmysliwy","relation":"source_file","access_level":"closed","date_updated":"2022-07-05T08:17:12Z","file_name":"thes_source.zip","content_type":"application/zip","date_created":"2022-07-05T08:15:52Z","checksum":"647a2011fdf56277096c9350fefe1097","file_size":5831060}],"oa":1,"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2022-07-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-07-05T08:17:12Z","ec_funded":1,"page":"138","title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","alternative_title":["ISTA Thesis"],"date_created":"2022-06-30T12:15:03Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof"}],"_id":"11473","ddc":["515","539"],"abstract":[{"text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n","lang":"eng"}],"day":"01","doi":"10.15479/at:ista:11473","degree_awarded":"PhD","citation":{"ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","mla":"Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.","apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473"},"year":"2022","date_updated":"2023-09-07T13:43:52Z"},{"_id":"11626","author":[{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_created":"2022-07-20T11:21:53Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","page":"248","ec_funded":1,"file_date_updated":"2022-07-25T11:48:45Z","publisher":"Institute of Science and Technology Austria","date_updated":"2024-10-29T10:22:45Z","citation":{"apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria."},"year":"2022","degree_awarded":"PhD","doi":"10.15479/at:ista:11626","day":"20","abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"ddc":["575"],"has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"07","language":[{"iso":"eng"}],"date_published":"2022-07-20T00:00:00Z","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"}],"oa":1,"file":[{"date_updated":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf","content_type":"application/pdf","date_created":"2022-07-25T09:08:47Z","file_size":9730864,"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","file_id":"11645","creator":"mgallei","access_level":"open_access","relation":"main_file"},{"file_id":"11646","creator":"mgallei","access_level":"closed","relation":"source_file","date_updated":"2022-07-25T09:39:58Z","file_name":"Thesis_Gallei_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-07-25T09:09:09Z","file_size":19560720,"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb"},{"file_size":24542837,"checksum":"3994f7f20058941b5bb8a16886b21e71","date_created":"2022-07-25T09:09:32Z","file_name":"Thesis_Gallei_to_print.pdf","content_type":"application/pdf","date_updated":"2022-07-25T09:39:58Z","description":"This is the print version of the thesis including the full appendix","relation":"source_file","access_level":"closed","creator":"mgallei","file_id":"11647"},{"access_level":"open_access","relation":"main_file","file_id":"11650","creator":"mgallei","date_created":"2022-07-25T11:48:45Z","file_size":15435966,"checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","date_updated":"2022-07-25T11:48:45Z","content_type":"application/pdf","file_name":"Thesis_Gallei_Appendix.pdf"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"9287","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7142","status":"public"},{"relation":"part_of_dissertation","id":"7465","status":"public"},{"id":"8138","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6260"},{"status":"public","id":"8931","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10411","status":"public"}]}},{"ddc":["500","516","514"],"date_updated":"2023-06-22T09:56:36Z","citation":{"short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","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","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."},"year":"2022","degree_awarded":"PhD","doi":"10.15479/at:ista:11777","day":"11","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"}],"page":"170","ec_funded":1,"file_date_updated":"2022-08-11T16:09:19Z","publisher":"Institute of Science and Technology","_id":"11777","author":[{"id":"4C20D868-F248-11E8-B48F-1D18A9856A87","full_name":"Wild, Pascal","first_name":"Pascal","last_name":"Wild"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"article_processing_charge":"No","date_created":"2022-08-10T15:51:19Z","title":"High-dimensional expansion and crossing numbers of simplicial complexes","alternative_title":["ISTA Thesis"],"file":[{"checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","file_size":16828,"date_created":"2022-08-10T15:34:04Z","file_name":"flags.py","content_type":"text/x-python","date_updated":"2022-08-10T15:34:04Z","access_level":"open_access","relation":"supplementary_material","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","creator":"pwild","file_id":"11780"},{"access_level":"open_access","relation":"supplementary_material","description":"Code for proof of Lemma 8.20 in Thesis","creator":"pwild","file_id":"11781","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_size":12226,"date_created":"2022-08-10T15:34:10Z","file_name":"lowerbound.cpp","content_type":"text/x-c++src","date_updated":"2022-08-10T15:34:10Z"},{"file_name":"upperbound.py","content_type":"text/x-python","date_updated":"2022-08-10T15:34:17Z","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","file_size":3240,"date_created":"2022-08-10T15:34:17Z","creator":"pwild","file_id":"11782","description":"Code for proof of Proposition 7.9 in Thesis","relation":"supplementary_material","access_level":"open_access"},{"creator":"pwild","file_id":"11809","relation":"main_file","access_level":"open_access","file_name":"finalthesisPascalWildPDFA.pdf","content_type":"application/pdf","date_updated":"2022-08-11T16:08:33Z","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","checksum":"4e96575b10cbe4e0d0db2045b2847774","file_size":5086282,"date_created":"2022-08-11T16:08:33Z"},{"creator":"pwild","file_id":"11810","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"ThesisSubmission.zip","date_updated":"2022-08-11T16:09:19Z","checksum":"92d94842a1fb6dca5808448137573b2e","file_size":18150068,"date_created":"2022-08-11T16:09:19Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","date_published":"2022-08-11T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"supervisor":[{"first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"08"},{"citation":{"short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","mla":"Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11879.","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","apa":"Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11879","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:10.15479/at:ista:11879","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11879."},"year":"2022","date_updated":"2023-09-09T22:30:04Z","day":"17","degree_awarded":"PhD","doi":"10.15479/at:ista:11879","abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","ddc":["580"],"_id":"11879","author":[{"full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-08-17T07:58:53Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","page":"128","file_date_updated":"2023-09-09T22:30:03Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","date_published":"2022-08-17T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"file":[{"date_created":"2022-08-17T12:08:49Z","embargo":"2023-09-08","checksum":"a2c2fdc28002538840490bfa6a08b2cb","file_size":11113608,"date_updated":"2023-09-09T22:30:03Z","content_type":"application/pdf","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","access_level":"open_access","relation":"main_file","file_id":"11907","creator":"cartner"},{"file_id":"11908","creator":"cartner","relation":"source_file","access_level":"closed","date_updated":"2023-09-09T22:30:03Z","content_type":"application/octet-stream","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","date_created":"2022-08-17T12:08:59Z","checksum":"66b461c074b815fbe63481b3f46a9f43","file_size":19097730,"embargo_to":"open_access"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"oa_version":"Published Version","month":"08","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"language":[{"iso":"eng"}]},{"file":[{"creator":"mnardin","file_id":"11935","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","date_updated":"2023-06-20T22:30:04Z","file_size":13515457,"checksum":"2dbb70c74aaa3b64c1f463e943baf09c","embargo_to":"open_access","date_created":"2022-08-19T16:31:34Z"},{"file_id":"11941","creator":"mnardin","access_level":"open_access","relation":"main_file","date_updated":"2023-06-20T22:30:04Z","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","content_type":"application/pdf","date_created":"2022-08-22T09:43:50Z","embargo":"2023-06-19","file_size":9906458,"checksum":"0ec94035ea35a47a9f589ed168e60b48"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10077"},{"status":"public","id":"6194","relation":"part_of_dissertation"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-08-19T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"month":"08","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","ddc":["573"],"date_updated":"2023-09-05T12:02:14Z","year":"2022","citation":{"ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932","apa":"Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","mla":"Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria."},"doi":"10.15479/at:ista:11932","degree_awarded":"PhD","day":"19","abstract":[{"text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes.","lang":"eng"}],"page":"136","ec_funded":1,"file_date_updated":"2023-06-20T22:30:04Z","publisher":"Institute of Science and Technology Austria","_id":"11932","author":[{"first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_created":"2022-08-19T08:52:30Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"alternative_title":["ISTA Thesis"],"title":"On the encoding, transfer, and consolidation of spatial memories"},{"file_date_updated":"2022-08-25T09:33:31Z","page":"133","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Schulz","first_name":"Rouven","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"_id":"11945","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","alternative_title":["ISTA Thesis"],"date_created":"2022-08-23T11:33:11Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"article_processing_charge":"No","publication_status":"published","ddc":["570"],"citation":{"ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","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.","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","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.","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","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945"},"year":"2022","date_updated":"2023-08-03T13:02:26Z","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."}],"day":"23","degree_awarded":"PhD","doi":"10.15479/at:ista:11945","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"08","project":[{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"11995","status":"public"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_size":28079331,"checksum":"61b1b666a210ff7cdd0e95ea75207a13","date_created":"2022-08-25T08:59:57Z","content_type":"application/pdf","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","date_updated":"2022-08-25T08:59:57Z","access_level":"open_access","success":1,"relation":"main_file","creator":"rschulz","file_id":"11970"},{"file_name":"Thesis_Rouven_Schulz_2022_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-08-25T09:33:31Z","file_size":27226963,"checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","date_created":"2022-08-25T09:00:11Z","creator":"rschulz","file_id":"11971","relation":"source_file","access_level":"closed"}],"type":"dissertation","date_published":"2022-08-23T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"publication_identifier":{"issn":["2663-337X"]}},{"department":[{"_id":"GradSch"},{"_id":"TiBr"}],"date_created":"2022-09-08T21:53:03Z","article_processing_charge":"No","publication_status":"published","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"12072","author":[{"first_name":"Alec L","last_name":"Shute","orcid":"0000-0002-1812-2810","full_name":"Shute, Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"page":"208","file_date_updated":"2022-09-12T11:24:21Z","day":"08","doi":"10.15479/at:ista:12072","degree_awarded":"PhD","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. "}],"citation":{"mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","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."},"year":"2022","date_updated":"2023-02-21T16:37:35Z","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.","ddc":["512"],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","month":"09","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-023-7"]},"oa":1,"supervisor":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","date_published":"2022-09-08T00:00:00Z","file":[{"date_created":"2022-09-08T21:50:34Z","file_size":1907386,"checksum":"bf073344320e05d92c224786cec2e92d","date_updated":"2022-09-08T21:50:34Z","content_type":"application/pdf","file_name":"Thesis_final_draft.pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12073","creator":"ashute"},{"date_created":"2022-09-08T21:50:42Z","file_size":495393,"checksum":"b054ac6baa09f70e8235403a4abbed80","date_updated":"2022-09-12T11:24:21Z","file_name":"athesis.tex","content_type":"application/octet-stream","access_level":"closed","relation":"source_file","file_id":"12074","creator":"ashute"},{"creator":"ashute","file_id":"12078","relation":"source_file","access_level":"closed","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","content_type":"application/x-zip-compressed","date_updated":"2022-09-12T11:24:21Z","checksum":"0a31e905f1cff5eb8110978cc90e1e79","file_size":944534,"date_created":"2022-09-09T12:05:00Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"12076","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12077"}]},"status":"public"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"month":"09","file":[{"content_type":"application/pdf","file_name":"thesis_gsperl.pdf","date_updated":"2023-02-02T09:29:57Z","title":"Thesis","checksum":"083722acbb8115e52e3b0fdec6226769","file_size":104497530,"date_created":"2023-01-25T12:04:41Z","creator":"cchlebak","file_id":"12371","relation":"main_file","access_level":"open_access","description":"This is the main PDF file of the thesis. File size: 105 MB"},{"creator":"cchlebak","file_id":"12483","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_gsperl_compressed.pdf","date_updated":"2023-02-02T09:33:37Z","checksum":"511f82025e5fcb70bff4731d6896ca07","file_size":23183710,"title":"Thesis (compressed 23MB)","date_created":"2023-02-02T09:33:37Z"},{"date_created":"2023-02-02T09:39:25Z","file_size":98382247,"checksum":"ed4cb85225eedff761c25bddfc37a2ed","date_updated":"2023-02-02T09:39:25Z","file_name":"thesis-source.zip","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"open_access","file_id":"12484","creator":"cchlebak"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11736","status":"public"},{"status":"public","id":"9818","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8385","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","type":"dissertation","date_published":"2022-09-22T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]},"oa":1,"supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan"}],"ec_funded":1,"page":"138","file_date_updated":"2023-02-02T09:39:25Z","publisher":"Institute of Science and Technology Austria","_id":"12358","author":[{"full_name":"Sperl, Georg","last_name":"Sperl","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_created":"2023-01-24T10:49:46Z","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","ddc":["000","620"],"year":"2022","citation":{"ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103","apa":"Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria."},"date_updated":"2024-02-28T12:57:46Z","day":"22","doi":"10.15479/at:ista:12103","degree_awarded":"PhD","abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}]},{"ddc":["570"],"degree_awarded":"PhD","doi":"10.15479/at:ista:12094","day":"19","abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"date_updated":"2023-11-16T13:10:22Z","citation":{"short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094","apa":"Dotter, C. (2022). Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12094","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094."},"year":"2022","publisher":"Institute of Science and Technology Austria","page":"152","ec_funded":1,"file_date_updated":"2023-09-20T22:30:03Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"article_processing_charge":"No","date_created":"2023-01-24T13:09:57Z","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","alternative_title":["ISTA Thesis"],"_id":"12364","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph"}],"file":[{"file_id":"12365","creator":"cchlebak","access_level":"open_access","relation":"main_file","date_updated":"2023-09-20T22:30:03Z","file_name":"220923_Thesis_CDotter_Final.pdf","content_type":"application/pdf","embargo":"2023-09-19","date_created":"2023-01-24T13:15:45Z","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","file_size":20457465},{"file_id":"12482","creator":"cchlebak","relation":"source_file","access_level":"closed","date_updated":"2023-09-20T22:30:03Z","file_name":"latex_source_CDotter_Thesis_2022.zip","content_type":"application/x-zip-compressed","date_created":"2023-02-02T09:15:35Z","embargo_to":"open_access","file_size":22433512,"checksum":"ad01bb20da163be6893b7af832e58419"}],"status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"3"},{"status":"public","id":"11160","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"}],"oa":1,"date_published":"2022-09-19T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"month":"09","has_accepted_license":"1"},{"ddc":["530"],"date_updated":"2024-08-07T07:11:56Z","citation":{"mla":"Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:10.15479/at:ista:12132","apa":"Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022."},"year":"2022","doi":"10.15479/at:ista:12132","degree_awarded":"PhD","day":"26","abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"page":"168","ec_funded":1,"file_date_updated":"2023-01-26T23:30:44Z","publisher":"Institute of Science and Technology Austria","_id":"12366","author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena"}],"publication_status":"published","article_processing_charge":"No","date_created":"2023-01-25T09:17:02Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"title":"Controllable states of superconducting Qubit ensembles","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2023-01-26T23:30:44Z","file_name":"Final_Thesis_ES_Redchenko.pdf","content_type":"application/pdf","date_created":"2023-01-25T09:41:49Z","embargo":"2022-12-28","checksum":"39eabb1e006b41335f17f3b29af09648","file_size":56076868,"file_id":"12367","creator":"cchlebak","relation":"main_file","access_level":"open_access"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-09-26T00:00:00Z","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]},"supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies"}],"month":"09"},{"related_material":{"record":[{"status":"public","id":"9350","relation":"part_of_dissertation"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2023-01-25T10:52:46Z","file_size":14581024,"checksum":"e54a3e69b83ebf166544164afd25608e","date_updated":"2023-01-25T10:52:46Z","content_type":"application/pdf","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","success":1,"relation":"main_file","access_level":"open_access","file_id":"12369","creator":"cchlebak"}],"supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"oa":1,"publication_identifier":{"isbn":[" 978-3-99078-025-1 "],"issn":["2663-337X"]},"date_published":"2022-09-29T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"month":"09","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"has_accepted_license":"1","ddc":["570"],"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"}],"doi":"10.15479/at:ista:12153","degree_awarded":"PhD","day":"29","date_updated":"2023-08-08T13:14:10Z","citation":{"ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria.","mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153"},"year":"2022","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-01-25T10:52:46Z","page":"113","ec_funded":1,"alternative_title":["ISTA Thesis"],"title":"Remodeling of E-cadherin-mediated contacts via cortical flows","publication_status":"published","date_created":"2023-01-25T10:43:24Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"author":[{"first_name":"Feyza N","last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"}],"_id":"12368"},{"author":[{"first_name":"Gloria","last_name":"Colombo","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"}],"_id":"12378","alternative_title":["ISTA Thesis"],"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"article_processing_charge":"No","date_created":"2023-01-25T14:27:43Z","publication_status":"published","file_date_updated":"2023-04-12T22:30:03Z","ec_funded":1,"page":"142","publisher":"Institute of Science and Technology Austria","year":"2022","citation":{"ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378","apa":"Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","mla":"Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria."},"date_updated":"2023-08-04T09:40:37Z","abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia.","lang":"eng"}],"day":"11","doi":"10.15479/at:ista:12378","degree_awarded":"PhD","ddc":["570"],"has_accepted_license":"1","month":"11","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"type":"dissertation","date_published":"2022-11-11T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"12244","relation":"part_of_dissertation","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"access_level":"closed","relation":"source_file","file_id":"12379","creator":"cchlebak","date_created":"2023-01-25T14:31:32Z","file_size":23890382,"checksum":"8cd3ddfe9b53381dcf086023d8d8893a","embargo_to":"open_access","date_updated":"2023-04-12T22:30:03Z","file_name":"Gloria_Colombo_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","access_level":"open_access","creator":"cchlebak","file_id":"12380","file_size":13802421,"checksum":"8af4319c18b516e8758e9a6cb02b103b","date_created":"2023-01-25T14:31:36Z","embargo":"2023-04-11","file_name":"Gloria_Colombo_Thesis.pdf","content_type":"application/pdf","date_updated":"2023-04-12T22:30:03Z"}]},{"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"oa_version":"Published Version","month":"12","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","date_published":"2022-12-15T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2023-01-26T10:02:34Z","file_name":"Brooks_Thesis.pdf","content_type":"application/pdf","date_created":"2023-01-26T10:02:34Z","file_size":3095225,"checksum":"b31460e937f33b557abb40ebef02b567","file_id":"12391","creator":"cchlebak","access_level":"open_access","success":1,"relation":"main_file"},{"date_updated":"2023-01-26T10:02:42Z","content_type":"application/octet-stream","file_name":"Brooks_Thesis.tex","date_created":"2023-01-26T10:02:42Z","checksum":"9751869fa5e7981588ad4228f4fd4bd6","file_size":809842,"file_id":"12392","creator":"cchlebak","access_level":"closed","relation":"source_file"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9005"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","_id":"12390","author":[{"id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris","last_name":"Brooks","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"No","date_created":"2023-01-26T10:00:42Z","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Translation-invariant quantum systems with effectively broken symmetry","ec_funded":1,"page":"196","file_date_updated":"2023-01-26T10:02:42Z","publisher":"Institute of Science and Technology Austria","year":"2022","citation":{"ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390","apa":"Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","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.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria."},"date_updated":"2023-08-07T13:32:09Z","day":"15","degree_awarded":"PhD","doi":"10.15479/at:ista:12390","abstract":[{"lang":"eng","text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n"}],"ddc":["500"]},{"date_published":"2022-12-22T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"access_level":"open_access","relation":"main_file","creator":"cchlebak","file_id":"12402","file_size":42059787,"checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","embargo":"2023-12-20","date_created":"2023-01-26T11:58:14Z","content_type":"application/pdf","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","date_updated":"2023-12-21T23:30:03Z"},{"relation":"source_file","access_level":"closed","creator":"cchlebak","file_id":"12403","file_size":261256696,"checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","embargo_to":"open_access","date_created":"2023-01-26T12:00:10Z","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","content_type":"application/x-zip-compressed","date_updated":"2023-12-21T23:30:03Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"679","status":"public"},{"status":"public","id":"10703","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7885","status":"public"},{"status":"public","id":"9429","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","has_accepted_license":"1","oa_version":"Published Version","month":"12","language":[{"iso":"eng"}],"date_updated":"2024-09-10T12:04:26Z","citation":{"ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria."},"year":"2022","doi":"10.15479/at:ista:12401","degree_awarded":"PhD","day":"22","abstract":[{"lang":"eng","text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening."}],"ddc":["610"],"_id":"12401","author":[{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"date_created":"2023-01-26T11:55:16Z","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"title":"Role of microenvironment heterogeneity in cancer cell invasion","page":"105","file_date_updated":"2023-12-21T23:30:03Z","publisher":"Institute of Science and Technology Austria"},{"date_published":"2021-01-01T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","related_material":{"record":[{"id":"1386","relation":"part_of_dissertation","status":"public"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"id":"639","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"6918","status":"public"},{"id":"6490","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7158","status":"public"},{"status":"public","id":"6009","relation":"part_of_dissertation"},{"id":"949","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"311"},{"id":"7810","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8089"},{"relation":"part_of_dissertation","id":"8728","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"id":"6175","relation":"part_of_dissertation","status":"public"},{"id":"6340","relation":"part_of_dissertation","status":"public"},{"id":"6378","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"6380","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"66","status":"public"},{"id":"6780","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7014","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_updated":"2021-12-23T23:30:04Z","content_type":"application/pdf","file_name":"Thesis-pdfa.pdf","embargo":"2021-12-22","date_created":"2020-12-22T20:08:44Z","file_size":5251507,"checksum":"d1b9db3725aed34dadd81274aeb9426c","file_id":"8969","creator":"akafshda","relation":"main_file","access_level":"open_access"},{"file_id":"8970","creator":"akafshda","relation":"source_file","access_level":"closed","date_updated":"2021-03-04T23:30:04Z","file_name":"source.zip","content_type":"application/zip","date_created":"2020-12-22T20:08:50Z","checksum":"1661df7b393e6866d2460eba3c905130","file_size":10636756,"embargo_to":"open_access"}],"has_accepted_license":"1","month":"01","oa_version":"Published Version","project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"date_updated":"2025-06-02T08:53:47Z","year":"2021","citation":{"chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934."},"abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8934","day":"01","ddc":["005"],"acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","author":[{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"_id":"8934","license":"https://creativecommons.org/publicdomain/zero/1.0/","title":"Parameterized and algebro-geometric advances in static program analysis","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2020-12-10T12:17:07Z","article_processing_charge":"No","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2021-12-23T23:30:04Z","page":"278","publisher":"Institute of Science and Technology Austria"},{"file":[{"file_id":"9043","creator":"gcipollo","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2021-01-25T14:19:03Z","content_type":"application/pdf","file_name":"thesis.pdf","date_created":"2021-01-25T14:19:03Z","file_size":4127796,"checksum":"5a93658a5f19478372523ee232887e2b"},{"date_updated":"2021-01-25T14:19:10Z","content_type":"application/zip","file_name":"Thesis_files.zip","date_created":"2021-01-25T14:19:10Z","file_size":12775206,"checksum":"e8270eddfe6a988e92a53c88d1d19b8c","file_id":"9044","creator":"gcipollo","relation":"source_file","access_level":"closed"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László"}],"oa":1,"date_published":"2021-01-25T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"month":"01","has_accepted_license":"1","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","ddc":["510"],"doi":"10.15479/AT:ISTA:9022","degree_awarded":"PhD","day":"25","abstract":[{"text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.","lang":"eng"}],"date_updated":"2023-09-07T13:29:32Z","year":"2021","citation":{"mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","apa":"Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022."},"publisher":"Institute of Science and Technology Austria","page":"380","ec_funded":1,"file_date_updated":"2021-01-25T14:19:10Z","publication_status":"published","date_created":"2021-01-21T18:16:54Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"alternative_title":["ISTA Thesis"],"title":"Fluctuations in the spectrum of random matrices","_id":"9022","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"}]},{"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","month":"02","file":[{"date_updated":"2021-02-03T10:37:28Z","content_type":"application/zip","file_name":"thesis_source.zip","date_created":"2021-02-02T14:09:25Z","checksum":"bcf27986147cab0533b6abadd74e7629","file_size":13446994,"file_id":"9063","creator":"patrickd","relation":"source_file","access_level":"closed"},{"creator":"patrickd","file_id":"9064","relation":"main_file","access_level":"open_access","success":1,"file_name":"thesis_pdfA2b.pdf","content_type":"application/pdf","date_updated":"2021-02-02T14:09:18Z","file_size":5210329,"checksum":"9cc8af266579a464385bbe2aff6af606","date_created":"2021-02-02T14:09:18Z"}],"place":"Klosterneuburg","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"187","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8703","relation":"part_of_dissertation"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2021-02-01T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"}],"oa":1,"page":"134","file_date_updated":"2021-02-03T10:37:28Z","publisher":"Institute of Science and Technology Austria","_id":"9056","author":[{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116"}],"publication_status":"published","date_created":"2021-02-02T14:11:06Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"article_processing_charge":"No","title":"Multi-cover persistence and Delaunay mosaics","alternative_title":["ISTA Thesis"],"ddc":["006","514","516"],"date_updated":"2023-09-07T13:29:01Z","citation":{"short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056."},"year":"2021","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:9056","day":"01","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}]},{"type":"dissertation","date_published":"2021-05-18T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"file":[{"embargo_to":"open_access","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_size":47799741,"date_created":"2021-05-17T12:29:12Z","file_name":"KHuljev_Thesis_corrections.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-05-21T22:30:04Z","relation":"source_file","access_level":"closed","creator":"khuljev","file_id":"9398"},{"file_id":"9401","creator":"khuljev","relation":"main_file","access_level":"open_access","date_updated":"2022-05-21T22:30:04Z","file_name":"new_KHuljev_Thesis_corrections.pdf","content_type":"application/pdf","date_created":"2021-05-18T14:50:28Z","embargo":"2022-05-20","file_size":16542131,"checksum":"bf512f8a1e572a543778fc4b227c01ba"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","has_accepted_license":"1","oa_version":"Published Version","month":"05","language":[{"iso":"eng"}],"year":"2021","citation":{"ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria."},"date_updated":"2023-09-07T13:32:32Z","day":"18","doi":"10.15479/at:ista:9397","degree_awarded":"PhD","abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"ddc":["571"],"_id":"9397","author":[{"first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"date_created":"2021-05-17T12:31:30Z","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","page":"101","file_date_updated":"2022-05-21T22:30:04Z","publisher":"Institute of Science and Technology Austria"},{"day":"30","doi":"10.15479/AT:ISTA:9418","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"citation":{"chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021."},"year":"2021","date_updated":"2023-09-08T11:11:12Z","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_created":"2021-05-24T13:06:23Z","article_processing_charge":"No","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Underspecification in deep learning","_id":"9418","author":[{"last_name":"Bui Thi Mai","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","page":"125","file_date_updated":"2021-05-24T11:56:02Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"type":"dissertation","date_published":"2021-05-30T00:00:00Z","file":[{"checksum":"4f0abe64114cfed264f9d36e8d1197e3","file_size":2673905,"date_created":"2021-05-24T11:22:29Z","content_type":"application/pdf","file_name":"mph-thesis-v519-pdfimages.pdf","date_updated":"2021-05-24T11:22:29Z","relation":"main_file","success":1,"access_level":"open_access","creator":"bphuong","file_id":"9419"},{"access_level":"closed","relation":"source_file","creator":"bphuong","file_id":"9420","file_size":92995100,"checksum":"f5699e876bc770a9b0df8345a77720a2","date_created":"2021-05-24T11:56:02Z","file_name":"thesis.zip","content_type":"application/zip","date_updated":"2021-05-24T11:56:02Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"7435","status":"deleted"},{"relation":"part_of_dissertation","id":"7481","status":"public"},{"relation":"part_of_dissertation","id":"9416","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7479"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"month":"05","has_accepted_license":"1","language":[{"iso":"eng"}]},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-07-02T22:30:04Z","page":"124","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","alternative_title":["ISTA Thesis"],"publication_status":"published","article_processing_charge":"No","date_created":"2021-06-17T14:10:47Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"author":[{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"}],"_id":"9562","ddc":["570"],"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"doi":"10.15479/at:ista:9562","degree_awarded":"PhD","day":"01","date_updated":"2023-09-11T12:55:53Z","year":"2021","citation":{"chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021."},"language":[{"iso":"eng"}],"month":"06","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","has_accepted_license":"1","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9756"},{"status":"public","relation":"part_of_dissertation","id":"9437"},{"id":"8532","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"612","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"embargo":"2022-07-01","date_created":"2021-06-17T14:03:14Z","checksum":"659df5518db495f679cb1df9e9bd1d94","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z","file_name":"Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9563","creator":"dkleindienst"},{"creator":"dkleindienst","file_id":"9564","relation":"source_file","access_level":"closed","file_name":"Thesis_source.zip","content_type":"application/zip","date_updated":"2022-07-02T22:30:04Z","file_size":369804895,"checksum":"3bcf63a2b19e5b6663be051bea332748","embargo_to":"open_access","date_created":"2021-06-17T14:04:30Z"}],"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_published":"2021-06-01T00:00:00Z","type":"dissertation"}]