[{"supervisor":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-20T10:44:12Z","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2023-03-23T16:43:14Z","_id":"12732","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"12753","checksum":"5d2de651ef9449c1b8dc27148ca74777","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis_sub_PBrighi.zip","date_created":"2023-03-23T16:42:56Z","creator":"pbrighi","file_size":42167561,"date_updated":"2023-03-23T16:42:56Z"},{"success":1,"file_id":"12754","checksum":"7caa153d4a5b0873a79358787d2dfe1e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_PBrighi.pdf","date_created":"2023-03-23T16:43:14Z","file_size":13977000,"date_updated":"2023-03-23T16:43:14Z","creator":"pbrighi"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"11470","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8308","status":"public"},{"status":"public","id":"11469","relation":"part_of_dissertation"},{"id":"12750","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"03","citation":{"mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732.","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"}],"article_processing_charge":"No","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"has_accepted_license":"1","year":"2023","day":"21","page":"158","date_published":"2023-03-21T00:00:00Z","doi":"10.15479/at:ista:12732","date_created":"2023-03-17T13:30:48Z","publisher":"Institute of Science and Technology Austria","oa":1},{"_id":"13081","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","status":"public","date_updated":"2023-10-04T11:14:04Z","supervisor":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"file_date_updated":"2023-05-25T06:32:16Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","file_id":"13089","creator":"lbocaneg","file_size":25615534,"date_updated":"2023-05-25T06:32:12Z","file_name":"Thesis_final_LauraBocanegra.docx","date_created":"2023-05-25T06:32:12Z"},{"embargo":"2024-05-31","file_id":"13090","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","date_created":"2023-05-25T06:32:16Z","file_size":12386046,"date_updated":"2023-05-25T06:32:16Z","creator":"lbocaneg"}],"related_material":{"record":[{"id":"9349","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"12837","relation":"part_of_dissertation"}]},"citation":{"mla":"Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081","apa":"Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"}],"title":"Epithelial dynamics during mouse neural tube development","publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"23","page":"93","date_created":"2023-05-23T19:10:42Z","doi":"10.15479/at:ista:13081","date_published":"2023-05-23T00:00:00Z"},{"ddc":["510","516"],"date_updated":"2023-10-04T11:54:56Z","supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"file_date_updated":"2023-08-03T15:28:55Z","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"_id":"13331","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"13333","checksum":"96ee518d796d02af71395622c45de03c","file_size":28684,"date_updated":"2023-07-31T10:16:32Z","creator":"skoese","file_name":"Exterior Algebra and Combinatorics.zip","date_created":"2023-07-31T10:16:32Z"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13480","checksum":"f610f4713f88bc477de576aaa46b114e","file_size":4953418,"date_updated":"2023-08-03T15:28:55Z","creator":"skoese","file_name":"thesis-pdfa.pdf","date_created":"2023-08-03T15:28:55Z"}],"degree_awarded":"MS","publication_status":"published","publication_identifier":{"issn":["2791-4585"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"12680","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"month":"07","alternative_title":["ISTA Master's Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13331","ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","mla":"Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13331.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331."},"title":"Exterior algebra and combinatorics","article_processing_charge":"No","author":[{"last_name":"Köse","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda"}],"day":"31","year":"2023","has_accepted_license":"1","date_created":"2023-07-31T10:20:55Z","doi":"10.15479/at:ista:13331","date_published":"2023-07-31T00:00:00Z","page":"26","oa":1,"publisher":"Institute of Science and Technology Austria"},{"project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","mla":"Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422."},"title":"Synapseek: Meta-learning synaptic plasticity rules","author":[{"id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","full_name":"Confavreux, Basile J","last_name":"Confavreux"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","day":"12","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:14422","date_published":"2023-10-12T00:00:00Z","date_created":"2023-10-12T14:13:25Z","page":"148","_id":"14422","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"ddc":["610"],"supervisor":[{"last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"}],"date_updated":"2023-10-18T09:20:56Z","file_date_updated":"2023-10-18T07:56:08Z","department":[{"_id":"GradSch"},{"_id":"TiVo"}],"oa_version":"Published Version","abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"month":"10","alternative_title":["ISTA Thesis"],"file":[{"embargo":"2024-10-12","file_id":"14424","checksum":"7f636555eae7803323df287672fd13ed","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","file_name":"Confavreux_Thesis_2A.pdf","date_created":"2023-10-12T14:53:50Z","file_size":30599717,"date_updated":"2023-10-12T14:54:52Z","creator":"cchlebak"},{"file_id":"14440","checksum":"725e85946db92290a4583a0de9779e1b","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2023-10-18T07:38:34Z","file_name":"Confavreux Thesis.zip","creator":"cchlebak","date_updated":"2023-10-18T07:56:08Z","file_size":68406739}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9633"}]},"ec_funded":1},{"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/at:ista:14374","date_published":"2023-09-30T00:00:00Z","date_created":"2023-09-28T14:23:04Z","page":"206","day":"30","has_accepted_license":"1","year":"2023","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"title":"Boundary superconductivity in BCS theory","author":[{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","last_name":"Roos"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","mla":"Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14374.","apa":"Roos, B. (2023). Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"13207","status":"public"},{"relation":"part_of_dissertation","id":"10850","status":"public"}]},"ec_funded":1,"file":[{"file_size":2365702,"date_updated":"2023-10-06T11:35:56Z","creator":"broos","file_name":"phd-thesis-draft_pdfa_acrobat.pdf","date_created":"2023-10-06T11:35:56Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"14398","checksum":"ef039ffc3de2cb8dee5b14110938e9b6"},{"file_id":"14399","checksum":"81dcac33daeefaf0111db52f41bb1fd0","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"Version5.zip","date_created":"2023-10-06T11:38:01Z","file_size":4691734,"date_updated":"2023-10-06T11:38:01Z","creator":"broos"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"14374","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"file_date_updated":"2023-10-06T11:38:01Z","ddc":["515","539"],"supervisor":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-10-27T10:37:30Z"},{"alternative_title":["ISTA Thesis"],"month":"11","abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"9969","relation":"part_of_dissertation"},{"status":"public","id":"13238","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14490","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"14598","checksum":"521c72818d720a52b377207b2ee87b6a","creator":"cchlebak","file_size":3037720,"date_updated":"2023-11-23T10:29:55Z","file_name":"thesis_yeo.zip","date_created":"2023-11-23T10:29:55Z"},{"file_id":"14599","checksum":"0ed5d16899687aecf13d843c9878c9f2","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-11-23T10:30:08Z","file_name":"thesis_yeo.pdf","creator":"cchlebak","date_updated":"2023-11-23T10:30:08Z","file_size":2717256}],"type":"dissertation","status":"public","_id":"14506","file_date_updated":"2023-11-23T10:30:08Z","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"date_updated":"2023-11-30T10:54:51Z","supervisor":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"}],"ddc":["000"],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"162","date_created":"2023-11-10T08:10:43Z","doi":"10.15479/14506","date_published":"2023-11-10T00:00:00Z","year":"2023","has_accepted_license":"1","day":"10","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","author":[{"first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","last_name":"Yeo"}],"title":"Advances in efficiency and privacy in payment channel network analysis","citation":{"ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506","apa":"Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","mla":"Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria.","chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2023-11-24T11:57:46Z","date_updated":"2023-11-30T10:55:13Z","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"type":"dissertation","status":"public","_id":"12726","related_material":{"record":[{"status":"public","id":"10703","relation":"part_of_dissertation"},{"status":"public","id":"10791","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"relation":"part_of_dissertation","status":"public","id":"461"},{"relation":"new_edition","status":"public","id":"14530"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2023-11-24T11:57:46Z","file_size":63734746,"date_created":"2023-03-23T12:49:23Z","file_name":"Thesis_Riedl_2023.pdf","access_level":"closed","relation":"main_file","content_type":"application/pdf","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","file_id":"12745"},{"creator":"cchlebak","date_updated":"2023-09-24T22:30:03Z","file_size":339473651,"date_created":"2023-03-23T12:54:34Z","file_name":"Thesis_Riedl_2023_source.rar","access_level":"closed","relation":"source_file","content_type":"application/octet-stream","embargo_to":"open_access","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","file_id":"12746"}],"alternative_title":["ISTA Thesis"],"month":"03","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"None","article_processing_charge":"No","author":[{"last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"}],"title":"Synchronization in collectively moving active matter","citation":{"ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"260","date_created":"2023-03-15T13:22:13Z","doi":"10.15479/at:ista:12726","date_published":"2023-03-23T00:00:00Z","year":"2023","has_accepted_license":"1","day":"23","publisher":"Institute of Science and Technology Austria"},{"citation":{"ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"title":"Synchronization in collectively moving active matter","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"16","page":"260","date_created":"2023-11-15T09:59:03Z","date_published":"2023-11-16T00:00:00Z","doi":"10.15479/14530","_id":"14530","type":"dissertation","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"status":"public","date_updated":"2023-11-30T10:55:13Z","supervisor":[{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"ddc":["530","570"],"file_date_updated":"2023-11-15T09:52:54Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. "}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"Updated Version","alternative_title":["ISTA Thesis"],"month":"11","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","file_id":"14536","file_size":36743942,"date_updated":"2023-11-15T09:52:54Z","creator":"mriedl","file_name":"Thesis_Riedl_2023_corr.pdf","date_created":"2023-11-15T09:52:54Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10703","status":"public"},{"id":"10791","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"relation":"part_of_dissertation","id":"461","status":"public"},{"status":"public","id":"12726","relation":"old_edition"}]}},{"ddc":["530"],"date_updated":"2023-11-30T10:56:04Z","supervisor":[{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"file_date_updated":"2023-11-22T09:46:06Z","_id":"14547","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"date_created":"2023-11-17T13:36:44Z","file_name":"Phan_Thesis_pdfa.pdf","date_updated":"2023-11-22T09:46:06Z","file_size":34828019,"creator":"pduc","file_id":"14548","checksum":"db0c37d213bc002125bd59690e9db246","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"14549","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","creator":"pduc","date_updated":"2023-11-17T13:47:54Z","file_size":279319709,"date_created":"2023-11-17T13:44:53Z","file_name":"dissertation_src.zip"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"related_material":{"record":[{"status":"public","id":"10851","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"13264"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"month":"11","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","mla":"Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547.","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547","apa":"Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023."},"title":"Resonant microwave spectroscopy of Al-InAs","article_processing_charge":"No","author":[{"last_name":"Phan","full_name":"Phan, Duc T","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"}],"day":"16","year":"2023","has_accepted_license":"1","date_created":"2023-11-17T13:45:26Z","doi":"10.15479/14547","date_published":"2023-11-16T00:00:00Z","page":"80","oa":1,"publisher":"Institute of Science and Technology Austria"},{"publisher":"Institute of Science and Technology Austria","oa":1,"page":"230","date_published":"2023-08-15T00:00:00Z","doi":"10.15479/at:ista:14058","date_created":"2023-08-15T10:20:40Z","has_accepted_license":"1","year":"2023","day":"15","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"author":[{"last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","citation":{"mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"9803","status":"public"},{"id":"12933","status":"public","relation":"research_data"},{"status":"public","id":"6831","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14077","status":"public"}]},"ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"gpuixeus","date_updated":"2023-08-17T06:55:24Z","file_size":10891454,"date_created":"2023-08-16T18:15:17Z","file_name":"Thesis_latex_forpdfa.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_id":"14075"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","file_id":"14079","creator":"gpuixeus","file_size":19856686,"date_updated":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf","date_created":"2023-08-18T10:47:55Z"}],"language":[{"iso":"eng"}],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14058","file_date_updated":"2023-08-18T10:47:55Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-12-13T12:15:36Z","ddc":["576"]},{"_id":"14622","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"date_updated":"2023-12-13T14:47:25Z","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2023-12-01T11:10:46Z","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-11-30","file_id":"14635","checksum":"068fd3570506ec42b2faa390de784bc4","file_size":11947523,"date_updated":"2023-12-01T11:10:46Z","creator":"ssack","file_name":"PhD_Thesis.pdf","date_created":"2023-11-30T15:53:10Z"},{"date_created":"2023-11-30T15:54:11Z","file_name":"PhD Thesis (1).zip","date_updated":"2023-12-01T11:10:46Z","file_size":18422964,"creator":"ssack","file_id":"14636","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"11471","status":"public","relation":"part_of_dissertation"},{"id":"13125","status":"public","relation":"part_of_dissertation"},{"id":"9760","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"project":[{"name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"citation":{"short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan"}],"article_processing_charge":"No","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2023","day":"30","page":"142","doi":"10.15479/at:ista:14622","date_published":"2023-11-30T00:00:00Z","date_created":"2023-11-28T10:58:13Z"},{"file_date_updated":"2023-12-20T10:41:42Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-12-21T14:30:02Z","supervisor":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"status":"public","type":"dissertation","_id":"14697","ec_funded":1,"related_material":{"record":[{"status":"public","id":"6328","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7885","status":"public"},{"status":"public","id":"12272","relation":"part_of_dissertation"},{"status":"public","id":"14274","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14360"}]},"language":[{"iso":"eng"}],"file":[{"creator":"jstopp","file_size":51585778,"date_updated":"2023-12-20T09:35:34Z","file_name":"Thesis.pdf","date_created":"2023-12-20T09:35:34Z","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","embargo":"2024-12-20","file_id":"14699","checksum":"457927165d5d556305d3086f6b83e5c7"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950,"date_updated":"2023-12-20T10:41:42Z","creator":"jstopp","file_name":"Thesis.docx","date_created":"2023-12-20T09:35:35Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]},"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","article_processing_charge":"No","author":[{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697","apa":"Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"date_created":"2023-12-18T19:14:28Z","date_published":"2023-12-20T00:00:00Z","doi":"10.15479/at:ista:14697","page":"226","day":"20","year":"2023","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651."},"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","article_processing_charge":"No","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"12","year":"2023","has_accepted_license":"1","date_created":"2023-12-11T19:30:37Z","doi":"10.15479/at:ista:14651","date_published":"2023-12-12T00:00:00Z","page":"96","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["570"],"date_updated":"2023-12-22T11:04:45Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"file_date_updated":"2023-12-14T08:58:18Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"14651","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_name":"Phd_Thesis_LA.pdf","date_created":"2023-12-13T15:37:55Z","file_size":34101468,"date_updated":"2023-12-13T15:37:55Z","creator":"larathoo","success":1,"checksum":"520bdb61e95e66070e02824947d2c5fa","file_id":"14684","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"file_name":"Phd_Thesis_LA.zip","date_created":"2023-12-13T15:42:23Z","creator":"larathoo","file_size":31052872,"date_updated":"2023-12-14T08:58:18Z","checksum":"d8e59afd0817c98fba2564a264508e5c","file_id":"14685","relation":"source_file","access_level":"closed","content_type":"application/zip"},{"content_type":"application/zip","access_level":"closed","relation":"supplementary_material","file_id":"14681","checksum":"9a778c949932286f4519e1f1fca2820d","date_updated":"2023-12-14T08:58:18Z","file_size":10713896,"creator":"larathoo","date_created":"2023-12-11T19:24:59Z","file_name":"Supplementary_Materials.zip"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"id":"11411","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"12","alternative_title":["ISTA Thesis"]},{"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"date_updated":"2024-01-16T11:58:15Z","ddc":["000"],"file_date_updated":"2023-11-15T13:44:24Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"_id":"14539","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","publication_identifier":{"isbn":["978-3-99078-036-7"],"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"success":1,"checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_id":"14540","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"main.pdf","date_created":"2023-11-15T13:43:28Z","file_size":2116426,"date_updated":"2023-11-15T13:43:28Z","creator":"cchlebak"},{"date_created":"2023-11-15T13:44:24Z","file_name":"thesis_source.zip","date_updated":"2023-11-15T13:44:24Z","file_size":35884057,"creator":"cchlebak","checksum":"80ca37618a3c7b59866875f8be9b15ed","file_id":"14541","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1194","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"12000","relation":"part_of_dissertation"},{"status":"public","id":"9644","relation":"part_of_dissertation"},{"status":"public","id":"12511","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14600","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14601"},{"id":"10414","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","citation":{"chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14539.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","mla":"Zikelic, Dorde. Automated Verification and Control of Infinite State Stochastic Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/14539.","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","apa":"Zikelic, D. (2023). Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria. https://doi.org/10.15479/14539","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:10.15479/14539"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"article_processing_charge":"No","title":"Automated verification and control of infinite state stochastic systems","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2023","day":"15","page":"256","date_published":"2023-11-15T00:00:00Z","doi":"10.15479/14539","date_created":"2023-11-15T13:39:10Z","publisher":"Institute of Science and Technology Austria","oa":1},{"page":"147","date_created":"2023-06-01T09:05:24Z","date_published":"2023-05-31T00:00:00Z","doi":"10.15479/at:ista:13107","year":"2023","has_accepted_license":"1","day":"31","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"last_name":"Knaus","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa"}],"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","citation":{"apa":"Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","mla":"Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"12802","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-06-01T13:48:41Z","file_name":"Thesis_Lisa Knaus_approved_final.docx","date_updated":"2023-06-01T13:48:41Z","file_size":12991551,"creator":"lknaus","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","file_id":"13112","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"6903d152aa01181d87a696085af31c83","file_id":"13114","file_size":9309015,"date_updated":"2023-06-07T08:41:49Z","creator":"lknaus","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","date_created":"2023-06-02T09:47:29Z"}],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published Version","file_date_updated":"2023-06-07T08:41:49Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"date_updated":"2024-02-07T08:03:33Z","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"ddc":["570"],"type":"dissertation","status":"public","_id":"13107"},{"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","article_processing_charge":"No","author":[{"last_name":"Radler","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","date_created":"2023-09-06T10:58:25Z","doi":"10.15479/at:ista:14280","date_published":"2023-09-25T00:00:00Z","page":"156","day":"25","year":"2023","has_accepted_license":"1","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"14280","file_date_updated":"2023-10-04T10:28:35Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"ddc":["572"],"date_updated":"2024-02-21T12:35:18Z","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"}],"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11373"},{"relation":"part_of_dissertation","status":"public","id":"7387"},{"relation":"research_data","id":"10934","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"14390","checksum":"87eef11fbc5c7df0826f12a3a629b444","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-10-04T10:11:53Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","creator":"pradler","date_updated":"2023-10-04T10:28:35Z","file_size":114932847},{"file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_created":"2023-10-04T10:11:21Z","file_size":37838778,"date_updated":"2023-10-04T10:28:35Z","creator":"pradler","embargo":"2024-10-04","file_id":"14391","checksum":"3253e099b7126469d941fd9419d68b4f","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]}},{"_id":"13286","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","ddc":["530"],"date_updated":"2024-02-21T12:35:34Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"file_date_updated":"2023-08-11T14:39:17Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices.","lang":"eng"}],"month":"07","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_name":"PhD_thesis_Valentini_final.zip","date_created":"2023-08-11T09:27:39Z","file_size":56121429,"date_updated":"2023-08-11T10:01:34Z","creator":"mvalenti","checksum":"666ee31c7eade89679806287c062fa14","file_id":"14033","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"},{"file_id":"14035","checksum":"0992f2ebef152dee8e70055350ebbb55","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"PhD_thesis_Valentini_final_validated.pdf","date_created":"2023-08-11T14:39:17Z","file_size":38199711,"date_updated":"2023-08-11T14:39:17Z","creator":"mvalenti"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"13312","relation":"part_of_dissertation"},{"status":"public","id":"12118","relation":"part_of_dissertation"},{"id":"8910","status":"public","relation":"part_of_dissertation"},{"id":"12522","status":"public","relation":"research_data"}]},"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Conventional and unconventional topological superconductors","grant_number":"F8606"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286","apa":"Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","mla":"Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286."},"title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","article_processing_charge":"No","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco","last_name":"Valentini"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"21","year":"2023","has_accepted_license":"1","date_created":"2023-07-24T14:10:45Z","doi":"10.15479/at:ista:13286","date_published":"2023-07-21T00:00:00Z","page":"184"},{"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-034-3"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2023-08-08T18:01:28Z","file_name":"Thesis_AnnaFranschitz_202308.pdf","creator":"afransch","date_updated":"2024-03-01T08:51:42Z","file_size":10797612,"checksum":"27220243d5d51c3b0d7d61c0879d7a0c","file_id":"13986","embargo":"2024-08-08","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"13987","checksum":"40abf7ccca14a3893f72dc7fb88585d6","date_updated":"2023-08-09T07:25:27Z","file_size":2619085,"creator":"afransch","date_created":"2023-08-08T18:02:25Z","file_name":"Thesis_AnnaFranschitz_202308.docx"},{"embargo":"2024-08-08","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","file_id":"15042","relation":"erratum","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","description":"Minor modifications and clarifications - Feb 2024","file_name":"Addendum_AnnaFranschitz202402.pdf","title":"Addendum","date_created":"2024-03-01T08:37:15Z","creator":"cchlebak","file_size":85956,"date_updated":"2024-03-01T12:13:29Z"},{"date_updated":"2024-03-01T08:51:42Z","file_size":11818,"creator":"cchlebak","title":"Addendum - source file","date_created":"2024-03-01T08:39:20Z","file_name":"Addendum_AnnaFranschitz202402.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"15043","checksum":"66745aa01f960f17472c024875c049ed"},{"date_updated":"2024-03-01T12:58:14Z","file_size":10416761,"creator":"cchlebak","title":"Print Version","date_created":"2024-03-01T08:56:06Z","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","content_type":"application/pdf","description":"For printing purposes","access_level":"closed","relation":"other","file_id":"15044","checksum":"55c876b73d49db15228a7f571592ec77"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"file_date_updated":"2024-03-01T12:58:14Z","supervisor":[{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-01T15:25:17Z","ddc":["570","577"],"type":"dissertation","status":"public","_id":"13984","page":"89","date_published":"2023-08-08T00:00:00Z","doi":"10.15479/at:ista:13984","date_created":"2023-08-08T15:33:29Z","has_accepted_license":"1","year":"2023","day":"08","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Franschitz","full_name":"Franschitz, Anna","first_name":"Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Individual and social immunity against viral infections in ants","citation":{"ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"13","page":"151","date_created":"2023-09-13T10:07:18Z","doi":"10.15479/at:ista:14323","date_published":"2023-09-13T00:00:00Z","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14323.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323","apa":"Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323","mla":"Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna"}],"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-09-13T09:52:52Z","file_name":"PhDThesis_KK_final_pdfA.pdf","creator":"kkuzmicz","date_updated":"2023-09-13T10:08:25Z","file_size":10147911,"checksum":"bd83596869c814b24aeff7077d031c0e","file_id":"14324","embargo":"2025-03-13","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access"},{"file_name":"thesis_KK_final_corrections_092023.docx","date_created":"2023-09-13T09:53:29Z","file_size":103980668,"date_updated":"2023-09-13T09:53:29Z","creator":"kkuzmicz","file_id":"14325","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7883"}]},"_id":"14323","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","status":"public","date_updated":"2024-03-07T15:02:59Z","supervisor":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"file_date_updated":"2023-09-13T10:08:25Z"},{"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"ec_funded":1,"file":[{"date_created":"2023-12-06T13:13:26Z","file_name":"mike_thesis_v06-12-2023.odt","date_updated":"2023-12-06T13:13:26Z","file_size":46405919,"creator":"mhenness","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","file_id":"14648","content_type":"application/vnd.oasis.opendocument.text","access_level":"closed","relation":"source_file"},{"file_id":"14649","checksum":"f5203a61eddaf35235bbc51904d73982","embargo":"2024-11-30","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","date_created":"2023-12-06T13:14:15Z","file_name":"mike_thesis_v06-12-2023.pdf","creator":"mhenness","date_updated":"2023-12-06T13:14:15Z","file_size":21282155},{"creator":"cchlebak","date_updated":"2024-03-20T13:19:36Z","file_size":2930287,"date_created":"2024-03-20T13:19:36Z","file_name":"2023_Hennessey_Michael_Thesis_from_source.pdf","access_level":"closed","relation":"other","content_type":"application/pdf","file_id":"15145","checksum":"9f7b4d646f1cfb57e3b9106a8a9cdd9d"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"type":"dissertation","_id":"14641","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2024-03-20T13:19:36Z","ddc":["570"],"supervisor":[{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-22T13:21:17Z","publisher":"Institute of Science and Technology Austria","date_published":"2023-11-30T00:00:00Z","doi":"10.15479/at:ista:14641","date_created":"2023-12-04T13:17:37Z","page":"104","day":"30","has_accepted_license":"1","year":"2023","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Adaptive mutation in E. coli modulated by luxS","author":[{"first_name":"Mike","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike","last_name":"Hennessey-Wesen"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641","mla":"Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641."}},{"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","author":[{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice","last_name":"Marveggio"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587"},"project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"doi":"10.15479/at:ista:14587","date_published":"2023-11-21T00:00:00Z","date_created":"2023-11-21T11:41:05Z","page":"228","day":"21","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"file_date_updated":"2024-03-20T12:28:32Z","ddc":["515"],"supervisor":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"date_updated":"2024-03-22T13:21:28Z","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"14587","related_material":{"record":[{"status":"public","id":"11842","relation":"part_of_dissertation"},{"id":"14597","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","file_id":"14626","success":1,"creator":"amarvegg","date_updated":"2023-11-29T09:09:31Z","file_size":2881100,"date_created":"2023-11-29T09:09:31Z","file_name":"thesis_Marveggio.pdf"},{"date_created":"2023-11-29T09:10:19Z","file_name":"Thesis_Marveggio.zip","date_updated":"2024-03-20T12:28:32Z","file_size":10189696,"creator":"amarvegg","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","file_id":"14627","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero."}]},{"has_accepted_license":"1","year":"2023","day":"02","page":"187","doi":"10.15479/at:ista:12491","date_published":"2023-02-02T00:00:00Z","date_created":"2023-02-02T14:50:20Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina"}],"article_processing_charge":"No","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2024-02-07","file_id":"12527","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"date_updated":"2024-02-08T23:30:04Z","creator":"bzens","file_name":"PhDThesis_BettinaZens_2023_final.pdf","date_created":"2023-02-07T13:07:38Z"},{"creator":"bzens","date_updated":"2024-02-08T23:30:04Z","file_size":106169509,"date_created":"2023-02-07T13:09:05Z","file_name":"PhDThesis_BettinaZens_2023_final.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"12528","checksum":"8c66ed203495d6e078ed1002a866520c"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"8586","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"02","supervisor":[{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"date_updated":"2024-03-25T23:30:05Z","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"file_date_updated":"2024-02-08T23:30:04Z","_id":"12491","type":"dissertation","status":"public","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"]},{"citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","last_name":"Stephenson"}],"article_processing_charge":"No","title":"Generalizing medial axes with homology switches","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"24","page":"43","doi":"10.15479/at:ista:14226","date_published":"2023-08-24T00:00:00Z","date_created":"2023-08-24T13:01:18Z","_id":"14226","type":"dissertation","status":"public","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-26T23:30:04Z","ddc":["500"],"file_date_updated":"2024-02-26T23:30:03Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Master's Thesis"],"month":"08","publication_identifier":{"issn":["2791-4585"]},"publication_status":"published","degree_awarded":"MS","file":[{"creator":"cchlebak","file_size":15501411,"date_updated":"2024-02-26T23:30:03Z","file_name":"documents-export-2023-08-24.zip","date_created":"2023-08-24T13:02:49Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"14227","checksum":"453caf851d75c3478c10ed09bd242a91"},{"creator":"cchlebak","date_updated":"2024-02-26T23:30:03Z","file_size":6854783,"date_created":"2023-08-24T13:03:42Z","file_name":"thesis_pdf_a.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7349d29963d6695e555e171748648d9a","file_id":"14228","embargo":"2024-02-25"}],"language":[{"iso":"eng"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"12470","file_date_updated":"2023-07-27T22:30:54Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"date_updated":"2023-08-31T12:26:58Z","supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"ddc":["610"],"alternative_title":["ISTA Thesis"],"month":"01","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"id":"11943","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"11950","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":[" 978-3-99078-026-8"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2023-07-27T22:30:54Z","file_size":41771714,"date_created":"2023-01-31T15:11:42Z","file_name":"20230109_PhD_thesis_JM_final.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_id":"12471","embargo":"2023-07-09"},{"checksum":"0bebbdee0773443959e1f6ab8caf281f","file_id":"12472","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"20230109_PhD_thesis_JM_final.docx","date_created":"2023-01-31T15:11:51Z","file_size":66983464,"date_updated":"2023-07-10T22:30:04Z","creator":"cchlebak"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","author":[{"first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235"}],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","citation":{"chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"Institute of Science and Technology Austria","page":"201","date_created":"2023-01-31T15:10:53Z","date_published":"2023-01-09T00:00:00Z","doi":"10.15479/at:ista:12470","year":"2023","has_accepted_license":"1","day":"09"},{"abstract":[{"lang":"eng","text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics."}],"oa_version":"Published Version","alternative_title":["ISTA Master's Thesis"],"month":"02","publication_identifier":{"issn":["2791-4585"]},"degree_awarded":"MS","publication_status":"published","file":[{"embargo":"2024-02-08","checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_id":"12532","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","date_created":"2023-02-09T08:03:32Z","creator":"cchlebak","file_size":8369317,"date_updated":"2024-02-09T23:30:03Z"},{"file_size":11204408,"date_updated":"2024-02-09T23:30:03Z","creator":"cchlebak","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","date_created":"2023-02-10T09:32:06Z","embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_id":"12535"}],"language":[{"iso":"eng"}],"_id":"12531","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"date_updated":"2024-02-09T23:30:04Z","ddc":["570"],"file_date_updated":"2024-02-09T23:30:03Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"08","page":"46","date_published":"2023-02-08T00:00:00Z","doi":"10.15479/at:ista:12531","date_created":"2023-02-09T07:45:05Z","citation":{"mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Kirillova, Kseniia","last_name":"Kirillova","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","first_name":"Kseniia"}],"article_processing_charge":"No","title":"Panoramic functional gradients across the mouse retina"},{"citation":{"ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800.","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"last_name":"Julseth","full_name":"Julseth, Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara"}],"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","year":"2023","has_accepted_license":"1","day":"05","page":"21","date_created":"2023-04-04T18:57:11Z","doi":"10.15479/at:ista:12800","date_published":"2023-04-05T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2023-06-02T22:30:05Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"ddc":["576"],"file_date_updated":"2023-06-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"12800","type":"dissertation","status":"public","degree_awarded":"MS","publication_status":"published","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-04-06T06:09:40Z","file_name":"Dispersaldata.xlsx","date_updated":"2023-06-02T22:30:04Z","file_size":52795,"creator":"mjulseth","file_id":"12805","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","embargo_to":"open_access","access_level":"closed","relation":"supplementary_material"},{"file_id":"12806","checksum":"5a13b6d204371572e249f03795bc0d04","embargo":"2023-06-01","content_type":"application/vnd.wolfram.nb","access_level":"open_access","relation":"supplementary_material","date_created":"2023-04-06T06:11:27Z","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_updated":"2023-06-02T22:30:04Z","file_size":787239,"creator":"mjulseth"},{"checksum":"c3ec842839ed1e66bf2618ae33047df8","file_id":"12812","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2023-04-06T08:26:12Z","file_name":"ThesisMaraJulseth_04_23.docx","creator":"mjulseth","date_updated":"2023-06-02T22:30:04Z","file_size":1061763},{"file_size":1741364,"date_updated":"2023-06-02T22:30:04Z","creator":"mjulseth","file_name":"ThesisMaraJulseth_04_23.pdf","date_created":"2023-04-06T08:26:37Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2023-06-01","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_id":"12813"}],"abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Master's Thesis"],"month":"04"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"status":"public","_id":"14510","file_date_updated":"2023-11-23T13:10:55Z","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"date_updated":"2024-03-27T23:30:45Z","supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"11","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9887"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"language":[{"iso":"eng"}],"file":[{"file_id":"14567","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-11-20T09:18:51Z","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","creator":"ngnyliuk","date_updated":"2023-11-20T09:18:51Z","file_size":20824903},{"checksum":"bfc96d47fc4e7e857dd71656097214a4","file_id":"14568","embargo":"2024-11-23","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file","date_created":"2023-11-20T09:23:11Z","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_updated":"2023-11-23T13:10:55Z","file_size":24871844,"creator":"ngnyliuk"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_processing_charge":"No","author":[{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia"}],"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","citation":{"mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","page":"180","date_created":"2023-11-10T09:10:06Z","date_published":"2023-11-10T00:00:00Z","doi":"10.15479/at:ista:14510","year":"2023","has_accepted_license":"1","day":"10"},{"date_created":"2023-05-05T10:40:14Z","doi":"10.15479/at:ista:12897","date_published":"2023-05-05T00:00:00Z","page":"180","day":"05","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","article_processing_charge":"No","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897"},"project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"9817","status":"public"},{"id":"7117","status":"public","relation":"part_of_dissertation"},{"id":"13188","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-12-08T23:30:04Z","file_size":50714445,"creator":"chafner","date_created":"2023-05-11T10:43:20Z","file_name":"thesis-hafner-2023may11-a2b.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","file_id":"12942","embargo":"2023-12-07"},{"embargo_to":"open_access","content_type":"application/pdf","relation":"source_file","access_level":"closed","file_id":"12943","checksum":"a6b51334be2b81672357b1549afab40c","file_size":265319,"date_updated":"2023-12-08T23:30:04Z","creator":"chafner","file_name":"thesis-release-form.pdf","date_created":"2023-05-11T10:43:44Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-031-2"]},"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BeBi"}],"file_date_updated":"2023-12-08T23:30:04Z","ddc":["516","004","518","531"],"date_updated":"2024-01-29T10:47:51Z","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"status":"public","type":"dissertation","_id":"12897"},{"author":[{"first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","full_name":"Shute, Alec L","orcid":"0000-0002-1812-2810","last_name":"Shute"}],"article_processing_charge":"No","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","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.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","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.","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"page":"208","doi":"10.15479/at:ista:12072","date_published":"2022-09-08T00:00:00Z","date_created":"2022-09-08T21:53:03Z","has_accepted_license":"1","year":"2022","day":"08","publisher":"Institute of Science and Technology Austria","oa":1,"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.","file_date_updated":"2022-09-12T11:24:21Z","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"supervisor":[{"last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-02-21T16:37:35Z","ddc":["512"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","_id":"12072","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12076"},{"id":"12077","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"ashute","file_size":1907386,"date_updated":"2022-09-08T21:50:34Z","file_name":"Thesis_final_draft.pdf","date_created":"2022-09-08T21:50:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"bf073344320e05d92c224786cec2e92d","file_id":"12073"},{"file_id":"12074","checksum":"b054ac6baa09f70e8235403a4abbed80","relation":"source_file","access_level":"closed","content_type":"application/octet-stream","file_name":"athesis.tex","date_created":"2022-09-08T21:50:42Z","creator":"ashute","file_size":495393,"date_updated":"2022-09-12T11:24:21Z"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"0a31e905f1cff5eb8110978cc90e1e79","file_id":"12078","file_size":944534,"date_updated":"2022-09-12T11:24:21Z","creator":"ashute","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","date_created":"2022-09-09T12:05:00Z"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version"},{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"first_name":"Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","last_name":"Wild","full_name":"Wild, Pascal"}],"article_processing_charge":"No","title":"High-dimensional expansion and crossing numbers of simplicial complexes","citation":{"ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","apa":"Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777","mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology","oa":1,"page":"170","date_published":"2022-08-11T00:00:00Z","doi":"10.15479/at:ista:11777","date_created":"2022-08-10T15:51:19Z","has_accepted_license":"1","year":"2022","day":"11","type":"dissertation","status":"public","_id":"11777","file_date_updated":"2022-08-11T16:09:19Z","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"supervisor":[{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-06-22T09:56:36Z","ddc":["500","516","514"],"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"lang":"eng","text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise."}],"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"pwild","date_updated":"2022-08-10T15:34:04Z","file_size":16828,"date_created":"2022-08-10T15:34:04Z","file_name":"flags.py","access_level":"open_access","relation":"supplementary_material","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","content_type":"text/x-python","file_id":"11780","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4"},{"relation":"supplementary_material","access_level":"open_access","content_type":"text/x-c++src","description":"Code for proof of Lemma 8.20 in Thesis","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_id":"11781","creator":"pwild","file_size":12226,"date_updated":"2022-08-10T15:34:10Z","file_name":"lowerbound.cpp","date_created":"2022-08-10T15:34:10Z"},{"date_updated":"2022-08-10T15:34:17Z","file_size":3240,"creator":"pwild","date_created":"2022-08-10T15:34:17Z","file_name":"upperbound.py","content_type":"text/x-python","description":"Code for proof of Proposition 7.9 in Thesis","access_level":"open_access","relation":"supplementary_material","file_id":"11782","checksum":"4cf81455c49e5dec3b9b2e3980137eeb"},{"date_created":"2022-08-11T16:08:33Z","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","file_name":"finalthesisPascalWildPDFA.pdf","creator":"pwild","date_updated":"2022-08-11T16:08:33Z","file_size":5086282,"checksum":"4e96575b10cbe4e0d0db2045b2847774","file_id":"11809","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_id":"11810","checksum":"92d94842a1fb6dca5808448137573b2e","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"ThesisSubmission.zip","date_created":"2022-08-11T16:09:19Z","creator":"pwild","file_size":18150068,"date_updated":"2022-08-11T16:09:19Z"}],"language":[{"iso":"eng"}]},{"oa_version":"Published Version","abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"month":"04","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","file_size":11906472,"date_updated":"2022-04-07T08:11:34Z","file_name":"LenkaPhD_Official_PDFA.pdf","date_created":"2022-04-07T08:11:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"11129","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7"},{"date_created":"2022-04-07T08:11:51Z","file_name":"LenkaPhD Official_source.zip","date_updated":"2022-04-07T08:11:51Z","file_size":23036766,"creator":"cchlebak","checksum":"99d67040432fd07a225643a212ee8588","file_id":"11130","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"_id":"11128","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["576","582"],"date_updated":"2023-06-23T06:26:41Z","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"file_date_updated":"2022-04-07T08:11:51Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"06","year":"2022","has_accepted_license":"1","date_created":"2022-04-07T08:19:54Z","date_published":"2022-04-06T00:00:00Z","doi":"10.15479/at:ista:11128","page":"112","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128."},"title":"Genetic basis of flower colour as a model for adaptive evolution","article_processing_charge":"No","author":[{"first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","full_name":"Matejovicova, Lenka","last_name":"Matejovicova"}]},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11995"}]},"language":[{"iso":"eng"}],"file":[{"creator":"rschulz","date_updated":"2022-08-25T08:59:57Z","file_size":28079331,"date_created":"2022-08-25T08:59:57Z","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11970","checksum":"61b1b666a210ff7cdd0e95ea75207a13","success":1},{"date_created":"2022-08-25T09:00:11Z","file_name":"Thesis_Rouven_Schulz_2022_final.docx","date_updated":"2022-08-25T09:33:31Z","file_size":27226963,"creator":"rschulz","checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","file_id":"11971","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"08","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"file_date_updated":"2022-08-25T09:33:31Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"ddc":["570"],"date_updated":"2023-08-03T13:02:26Z","supervisor":[{"last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"11945","date_created":"2022-08-23T11:33:11Z","doi":"10.15479/at:ista:11945","date_published":"2022-08-23T00:00:00Z","page":"133","day":"23","year":"2022","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","article_processing_charge":"No","author":[{"id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven","last_name":"Schulz","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","mla":"Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945.","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","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022."},"project":[{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"15","year":"2022","has_accepted_license":"1","date_created":"2023-01-26T10:00:42Z","date_published":"2022-12-15T00:00:00Z","doi":"10.15479/at:ista:12390","page":"196","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 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","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria."},"title":"Translation-invariant quantum systems with effectively broken symmetry","article_processing_charge":"No","author":[{"first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928"}],"oa_version":"Published Version","abstract":[{"text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n","lang":"eng"}],"month":"12","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"b31460e937f33b557abb40ebef02b567","file_id":"12391","file_size":3095225,"date_updated":"2023-01-26T10:02:34Z","creator":"cchlebak","file_name":"Brooks_Thesis.pdf","date_created":"2023-01-26T10:02:34Z"},{"checksum":"9751869fa5e7981588ad4228f4fd4bd6","file_id":"12392","relation":"source_file","access_level":"closed","content_type":"application/octet-stream","file_name":"Brooks_Thesis.tex","date_created":"2023-01-26T10:02:42Z","creator":"cchlebak","file_size":809842,"date_updated":"2023-01-26T10:02:42Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9005"}]},"_id":"12390","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","ddc":["500"],"date_updated":"2023-08-07T13:32:09Z","supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-01-26T10:02:42Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}]},{"publisher":"Institute of Science and Technology Austria","oa":1,"page":"113","doi":"10.15479/at:ista:12153","date_published":"2022-09-29T00:00:00Z","date_created":"2023-01-25T10:43:24Z","has_accepted_license":"1","year":"2022","day":"29","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"author":[{"last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Remodeling of E-cadherin-mediated contacts via cortical flows","citation":{"chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria.","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.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\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."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"9350","status":"public"}]},"ec_funded":1,"publication_identifier":{"isbn":[" 978-3-99078-025-1 "],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"success":1,"checksum":"e54a3e69b83ebf166544164afd25608e","file_id":"12369","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","date_created":"2023-01-25T10:52:46Z","creator":"cchlebak","file_size":14581024,"date_updated":"2023-01-25T10:52:46Z"}],"language":[{"iso":"eng"}],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12368","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"file_date_updated":"2023-01-25T10:52:46Z","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"date_updated":"2023-08-08T13:14:10Z","ddc":["570"]},{"language":[{"iso":"eng"}],"file":[{"file_size":13210143,"date_updated":"2022-05-13T12:49:00Z","creator":"mlechner","file_name":"src.zip","date_created":"2022-05-13T12:33:26Z","content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","file_id":"11378"},{"file_name":"thesis_main-a2.pdf","date_created":"2022-05-16T08:02:28Z","creator":"mlechner","file_size":2732536,"date_updated":"2022-05-17T15:19:39Z","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","file_id":"11382","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-017-6"]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","related_material":{"record":[{"id":"10665","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10667"},{"id":"11366","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7808"},{"relation":"part_of_dissertation","id":"10666","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"month":"05","alternative_title":["ISTA Thesis"],"ddc":["004"],"date_updated":"2023-08-17T06:58:38Z","supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2022-05-17T15:19:39Z","_id":"11362","keyword":["neural networks","verification","machine learning"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"dissertation","day":"12","year":"2022","has_accepted_license":"1","date_created":"2022-05-12T07:14:01Z","doi":"10.15479/at:ista:11362","date_published":"2022-05-12T00:00:00Z","page":"124","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.","apa":"Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362","ama":"Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","mla":"Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362."},"title":"Learning verifiable representations","article_processing_charge":"No","author":[{"last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"}],"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}]},{"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"11486","checksum":"7970714a20a6052f75fb27a6c3e9976e","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-07-05T08:12:56Z","file_name":"thes1_no_isbn_2_1b.pdf","creator":"kmysliwy","date_updated":"2022-07-05T08:12:56Z","file_size":1830973},{"checksum":"647a2011fdf56277096c9350fefe1097","file_id":"11487","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2022-07-05T08:15:52Z","file_name":"thes_source.zip","date_updated":"2022-07-05T08:17:12Z","file_size":5831060,"creator":"kmysliwy"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10564"},{"status":"public","id":"8705","relation":"part_of_dissertation"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:43:52Z","ddc":["515","539"],"file_date_updated":"2022-07-05T08:17:12Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"_id":"11473","type":"dissertation","status":"public","has_accepted_license":"1","year":"2022","day":"01","page":"138","doi":"10.15479/at:ista:11473","date_published":"2022-07-01T00:00:00Z","date_created":"2022-06-30T12:15:03Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","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.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473","apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"}],"article_processing_charge":"No","title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting."}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"8724","status":"public"},{"id":"10803","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10802","relation":"part_of_dissertation"},{"status":"public","id":"6590","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"10823","checksum":"626bc523ae8822d20e635d0e2d95182e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"thesis.pdf","date_created":"2022-03-06T11:42:54Z","file_size":4204905,"date_updated":"2022-03-06T11:42:54Z","creator":"nkonstan"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"e2ca2b88350ac8ea1515b948885cbcb1","file_id":"10824","creator":"nkonstan","file_size":22841103,"date_updated":"2022-03-10T12:11:48Z","file_name":"thesis.zip","date_created":"2022-03-06T11:42:57Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-015-2"],"issn":["2663-337X"]},"keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"status":"public","type":"dissertation","_id":"10799","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file_date_updated":"2022-03-10T12:11:48Z","ddc":["000"],"date_updated":"2023-10-17T12:31:54Z","supervisor":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2022-02-28T13:03:49Z","date_published":"2022-03-08T00:00:00Z","doi":"10.15479/at:ista:10799","page":"176","day":"08","year":"2022","has_accepted_license":"1","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Robustness and fairness in machine learning","article_processing_charge":"No","author":[{"first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H","last_name":"Konstantinov"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799.","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","mla":"Konstantinov, Nikola H. Robustness and Fairness in Machine Learning. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.","apa":"Konstantinov, N. H. (2022). Robustness and fairness in machine learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022."}},{"ddc":["575"],"supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Eilon","full_name":"Shani, Eilon","last_name":"Shani"}],"date_updated":"2023-11-07T08:20:13Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2022-07-25T11:48:45Z","_id":"11626","status":"public","type":"dissertation","file":[{"creator":"mgallei","file_size":9730864,"date_updated":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf","date_created":"2022-07-25T09:08:47Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","file_id":"11645"},{"date_created":"2022-07-25T09:09:09Z","file_name":"Thesis_Gallei_source.docx","date_updated":"2022-07-25T09:39:58Z","file_size":19560720,"creator":"mgallei","file_id":"11646","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"file_id":"11647","checksum":"3994f7f20058941b5bb8a16886b21e71","access_level":"closed","relation":"source_file","content_type":"application/pdf","description":"This is the print version of the thesis including the full appendix","date_created":"2022-07-25T09:09:32Z","file_name":"Thesis_Gallei_to_print.pdf","creator":"mgallei","date_updated":"2022-07-25T09:39:58Z","file_size":24542837},{"date_created":"2022-07-25T11:48:45Z","file_name":"Thesis_Gallei_Appendix.pdf","creator":"mgallei","date_updated":"2022-07-25T11:48:45Z","file_size":15435966,"file_id":"11650","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"8931","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9287","status":"public"},{"id":"7142","status":"public","relation":"part_of_dissertation"},{"id":"7465","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8138"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"relation":"part_of_dissertation","id":"10411","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"month":"07","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","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.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","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."},"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","author":[{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"day":"20","has_accepted_license":"1","year":"2022","doi":"10.15479/at:ista:11626","date_published":"2022-07-20T00:00:00Z","date_created":"2022-07-20T11:21:53Z","page":"248","publisher":"Institute of Science and Technology Austria","oa":1},{"page":"138","date_created":"2023-01-24T10:49:46Z","date_published":"2022-09-22T00:00:00Z","doi":"10.15479/at:ista:12103","year":"2022","has_accepted_license":"1","day":"22","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"full_name":"Sperl, Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"}],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","citation":{"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.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","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","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11736"},{"status":"public","id":"9818","relation":"part_of_dissertation"},{"status":"public","id":"8385","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","description":"This is the main PDF file of the thesis. File size: 105 MB","content_type":"application/pdf","file_id":"12371","checksum":"083722acbb8115e52e3b0fdec6226769","creator":"cchlebak","date_updated":"2023-02-02T09:29:57Z","file_size":104497530,"title":"Thesis","date_created":"2023-01-25T12:04:41Z","file_name":"thesis_gsperl.pdf"},{"file_size":23183710,"date_updated":"2023-02-02T09:33:37Z","creator":"cchlebak","file_name":"thesis_gsperl_compressed.pdf","date_created":"2023-02-02T09:33:37Z","title":"Thesis (compressed 23MB)","content_type":"application/pdf","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","relation":"main_file","access_level":"open_access","checksum":"511f82025e5fcb70bff4731d6896ca07","file_id":"12483"},{"date_created":"2023-02-02T09:39:25Z","file_name":"thesis-source.zip","date_updated":"2023-02-02T09:39:25Z","file_size":98382247,"creator":"cchlebak","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_id":"12484","content_type":"application/x-zip-compressed","access_level":"open_access","relation":"source_file"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"file_date_updated":"2023-02-02T09:39:25Z","date_updated":"2024-02-28T12:57:46Z","supervisor":[{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000","620"],"type":"dissertation","status":"public","_id":"12358"},{"status":"public","type":"dissertation","_id":"10759","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"file_date_updated":"2022-02-22T07:20:12Z","ddc":["530"],"supervisor":[{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"date_updated":"2024-02-28T13:01:59Z","month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10762","status":"public"},{"status":"public","id":"8644","relation":"part_of_dissertation"},{"id":"7956","status":"public","relation":"part_of_dissertation"},{"id":"415","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"file_name":"Rzadkowski_thesis_final_source.zip","date_created":"2022-02-21T13:58:16Z","creator":"wrzadkow","file_size":17668233,"date_updated":"2022-02-22T07:20:12Z","file_id":"10785","checksum":"0fc54ad1eaede879c665ac9b53c93e22","relation":"source_file","access_level":"closed","content_type":"application/zip"},{"success":1,"checksum":"22d2d7af37ca31f6b1730c26cac7bced","file_id":"10786","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Rzadkowski_thesis_final.pdf","date_created":"2022-02-21T14:02:54Z","creator":"wrzadkow","file_size":13307331,"date_updated":"2022-02-21T14:02:54Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Analytic and machine learning approaches to composite quantum impurities","author":[{"first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759","apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759"},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2022-02-21T00:00:00Z","doi":"10.15479/at:ista:10759","date_created":"2022-02-16T13:27:37Z","page":"120","day":"21","has_accepted_license":"1","year":"2022"},{"_id":"11196","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","status":"public","date_updated":"2023-08-18T06:31:52Z","supervisor":[{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"ddc":["570"],"file_date_updated":"2023-04-20T22:30:03Z","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"abstract":[{"text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"04","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1616a8bf6f13a57c892dac873dcd0936","file_id":"11220","embargo":"2023-04-19","date_updated":"2023-04-20T22:30:03Z","file_size":21273537,"creator":"okim","date_created":"2022-04-20T14:21:56Z","file_name":"Olena_KIM_thesis_final.pdf"},{"date_created":"2022-04-20T14:22:56Z","file_name":"KIM_thesis_final.zip","creator":"okim","date_updated":"2023-04-20T22:30:03Z","file_size":59248569,"checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","file_id":"11221","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","embargo_to":"open_access"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"11222","status":"public"},{"relation":"part_of_dissertation","id":"7473","status":"public"}]},"project":[{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497","call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"citation":{"ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196.","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:10.15479/at:ista:11196","apa":"Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196","mla":"Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"full_name":"Kim, Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena"}],"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2022","has_accepted_license":"1","day":"20","page":"132","date_created":"2022-04-20T09:47:12Z","doi":"10.15479/at:ista:11196","date_published":"2022-04-20T00:00:00Z"},{"day":"07","year":"2022","has_accepted_license":"1","date_created":"2022-02-04T15:45:12Z","doi":"10.15479/AT:ISTA:10727","date_published":"2022-02-07T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.","apa":"Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria."},"title":"Pathogen-mediated sexual selection and immunization in ant colonies","article_processing_charge":"No","author":[{"last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina"}],"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"language":[{"iso":"eng"}],"file":[{"creator":"smetzler","file_size":6757886,"date_updated":"2023-02-03T23:30:03Z","file_name":"Thesis_Sina_Metzler.docx","date_created":"2022-02-04T15:36:12Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","file_id":"10728"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2023-02-02","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","file_id":"10730","file_size":6314921,"date_updated":"2023-02-03T23:30:03Z","creator":"smetzler","file_name":"Thesis_Sina_Metzler_A2.pdf","date_created":"2022-02-04T15:36:43Z"},{"date_created":"2022-02-07T10:35:02Z","file_name":"Thesis_Sina_Metzler_print.pdf","creator":"smetzler","date_updated":"2023-02-04T23:30:03Z","file_size":6882557,"checksum":"dedd14b7be7a75d63018dbfc68dd8113","file_id":"10742","embargo":"2023-02-02","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.","lang":"eng"}],"month":"02","alternative_title":["ISTA Thesis"],"ddc":["570"],"date_updated":"2023-09-07T13:43:23Z","supervisor":[{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"file_date_updated":"2023-02-04T23:30:03Z","_id":"10727","status":"public","type":"dissertation"},{"_id":"11879","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"status":"public","type":"dissertation","ddc":["580"],"date_updated":"2023-09-09T22:30:04Z","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"file_date_updated":"2023-09-09T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"month":"08","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"creator":"cartner","file_size":11113608,"date_updated":"2023-09-09T22:30:03Z","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","date_created":"2022-08-17T12:08:49Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2023-09-08","file_id":"11907","checksum":"a2c2fdc28002538840490bfa6a08b2cb"},{"file_name":"ChristinaArtner_PhD_Thesis_2022.7z","date_created":"2022-08-17T12:08:59Z","file_size":19097730,"date_updated":"2023-09-09T22:30:03Z","creator":"cartner","file_id":"11908","checksum":"66b461c074b815fbe63481b3f46a9f43","embargo_to":"open_access","content_type":"application/octet-stream","relation":"source_file","access_level":"closed"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","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","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.","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria."},"title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","article_processing_charge":"No","author":[{"last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina"}],"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).","oa":1,"publisher":"Institute of Science and Technology Austria","day":"17","year":"2022","has_accepted_license":"1","date_created":"2022-08-17T07:58:53Z","date_published":"2022-08-17T00:00:00Z","doi":"10.15479/at:ista:11879","page":"128"},{"status":"public","type":"dissertation","_id":"11393","file_date_updated":"2023-05-17T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"ddc":["570"],"date_updated":"2023-09-07T14:53:44Z","supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"7391","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"8fc695d88020d70d231dad0e9f10b138","file_id":"11395","creator":"cchlebak","file_size":56427603,"date_updated":"2023-05-17T22:30:03Z","file_name":"MJ thesis.docx","date_created":"2022-05-17T09:08:06Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"11397","checksum":"c1dd20a1aece521b3500607b00e463d6","embargo":"2023-05-16","date_updated":"2023-05-17T22:30:03Z","file_size":4351981,"creator":"cchlebak","date_created":"2022-05-17T12:09:25Z","file_name":"MJ_thesis_PDFA.pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","article_processing_charge":"No","author":[{"full_name":"Jevtic, Marijo","last_name":"Jevtic","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393","apa":"Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11393","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","mla":"Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11393."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2022-05-17T08:57:41Z","doi":"10.15479/at:ista:11393","date_published":"2022-05-16T00:00:00Z","page":"108","day":"16","year":"2022","has_accepted_license":"1"},{"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"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","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"ec_funded":1,"file":[{"file_id":"12367","checksum":"39eabb1e006b41335f17f3b29af09648","embargo":"2022-12-28","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-01-25T09:41:49Z","file_name":"Final_Thesis_ES_Redchenko.pdf","date_updated":"2023-01-26T23:30:44Z","file_size":56076868,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-024-4"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","_id":"12366","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"file_date_updated":"2023-01-26T23:30:44Z","ddc":["530"],"supervisor":[{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"date_updated":"2023-05-26T09:29:07Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2022-09-26T00:00:00Z","doi":"10.15479/at:ista:12132","date_created":"2023-01-25T09:17:02Z","page":"168","day":"26","has_accepted_license":"1","year":"2022","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"}],"title":"Controllable states of superconducting Qubit ensembles","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","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.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","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"}},{"day":"19","has_accepted_license":"1","year":"2022","date_published":"2022-08-19T00:00:00Z","doi":"10.15479/at:ista:11932","date_created":"2022-08-19T08:52:30Z","page":"136","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.","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","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.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","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","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932"},"title":"On the encoding, transfer, and consolidation of spatial memories","author":[{"last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"creator":"mnardin","file_size":13515457,"date_updated":"2023-06-20T22:30:04Z","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","date_created":"2022-08-19T16:31:34Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","file_id":"11935","checksum":"2dbb70c74aaa3b64c1f463e943baf09c"},{"date_created":"2022-08-22T09:43:50Z","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","creator":"mnardin","date_updated":"2023-06-20T22:30:04Z","file_size":9906458,"file_id":"11941","checksum":"0ec94035ea35a47a9f589ed168e60b48","embargo":"2023-06-19","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"10077","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6194","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"month":"08","alternative_title":["ISTA Thesis"],"ddc":["573"],"supervisor":[{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-05T12:02:14Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"file_date_updated":"2023-06-20T22:30:04Z","_id":"11932","status":"public","type":"dissertation"},{"ddc":["570"],"date_updated":"2023-08-04T09:40:37Z","supervisor":[{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-04-12T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"_id":"12378","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_size":23890382,"date_updated":"2023-04-12T22:30:03Z","creator":"cchlebak","file_name":"Gloria_Colombo_Thesis.docx","date_created":"2023-01-25T14:31:32Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","file_id":"12379"},{"embargo":"2023-04-11","file_id":"12380","checksum":"8af4319c18b516e8758e9a6cb02b103b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Gloria_Colombo_Thesis.pdf","date_created":"2023-01-25T14:31:36Z","creator":"cchlebak","file_size":13802421,"date_updated":"2023-04-12T22:30:03Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"id":"12244","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"abstract":[{"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"}],"month":"11","alternative_title":["ISTA Thesis"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ieee":"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.","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."},"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","article_processing_charge":"No","author":[{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","last_name":"Colombo","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"day":"11","year":"2022","has_accepted_license":"1","date_created":"2023-01-25T14:27:43Z","date_published":"2022-11-11T00:00:00Z","doi":"10.15479/at:ista:12378","page":"142","oa":1,"publisher":"Institute of Science and Technology Austria"},{"_id":"11388","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-29T06:41:51Z","ddc":["576"],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2023-05-20T22:30:03Z","abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","publication_identifier":{"isbn":["978-3-99078-018-3"]},"publication_status":"published","degree_awarded":"PhD","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2023-05-19","file_id":"11398","checksum":"4d75e6a619df7e8a9d6e840aee182380","creator":"sbelohla","file_size":8247240,"date_updated":"2023-05-20T22:30:03Z","file_name":"thesis_sb_final_pdfa.pdf","date_created":"2022-05-19T13:03:13Z"},{"creator":"sbelohla","file_size":7094,"date_updated":"2023-05-20T22:30:03Z","file_name":"thesis_sb_final.zip","date_created":"2022-05-19T13:07:47Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"11399","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6713"}]},"citation":{"ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Belohlavy","full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2022","day":"18","page":"98","date_published":"2022-05-18T00:00:00Z","doi":"10.15479/at:ista:11388","date_created":"2022-05-16T16:49:18Z"},{"date_created":"2023-01-26T11:55:16Z","doi":"10.15479/at:ista:12401","date_published":"2022-12-22T00:00:00Z","page":"105","day":"22","year":"2022","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Role of microenvironment heterogeneity in cancer cell invasion","article_processing_charge":"No","author":[{"last_name":"Tasciyan","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401","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.","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria."},"related_material":{"record":[{"id":"679","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10703"},{"relation":"part_of_dissertation","status":"public","id":"9429"},{"relation":"part_of_dissertation","status":"public","id":"7885"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2023-12-20","file_id":"12402","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","file_size":42059787,"date_updated":"2023-12-21T23:30:03Z","creator":"cchlebak","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","date_created":"2023-01-26T11:58:14Z"},{"embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","file_id":"12403","file_size":261256696,"date_updated":"2023-12-21T23:30:03Z","creator":"cchlebak","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","date_created":"2023-01-26T12:00:10Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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."}],"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"file_date_updated":"2023-12-21T23:30:03Z","ddc":["610"],"date_updated":"2023-12-21T23:30:04Z","supervisor":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"status":"public","type":"dissertation","_id":"12401"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"10614","status":"public"},{"status":"public","id":"544","relation":"part_of_dissertation"}]},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11195","checksum":"999ab16884c4522486136ebc5ae8dbff","embargo":"2023-04-20","creator":"cchlebak","date_updated":"2023-04-21T22:30:03Z","file_size":8820951,"date_created":"2022-04-20T09:03:57Z","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf"},{"creator":"cchlebak","file_size":65864612,"date_updated":"2023-04-21T22:30:03Z","file_name":"Thesis_Stephanie_Wachner_20200414.zip","date_created":"2022-04-22T12:41:00Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"11329","checksum":"fd92b1e38d53bdf8b458213882d41383"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"04","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"file_date_updated":"2023-04-21T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"ddc":["570"],"supervisor":[{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"}],"date_updated":"2023-09-19T10:15:54Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"11193","doi":"10.15479/at:ista:11193","date_published":"2022-04-20T00:00:00Z","date_created":"2022-04-20T08:59:07Z","page":"170","day":"20","has_accepted_license":"1","year":"2022","publisher":"Institute of Science and Technology Austria","oa":1,"title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","author":[{"full_name":"Wachner, Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193","apa":"Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11193","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","mla":"Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11193.","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193."},"project":[{"name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}]},{"day":"19","has_accepted_license":"1","year":"2022","date_published":"2022-09-19T00:00:00Z","doi":"10.15479/at:ista:12094","date_created":"2023-01-24T13:09:57Z","page":"152","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","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","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","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.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria."},"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter"}],"article_processing_charge":"No","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"file":[{"embargo":"2023-09-19","file_id":"12365","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"220923_Thesis_CDotter_Final.pdf","date_created":"2023-01-24T13:15:45Z","creator":"cchlebak","file_size":20457465,"date_updated":"2023-09-20T22:30:03Z"},{"file_name":"latex_source_CDotter_Thesis_2022.zip","date_created":"2023-02-02T09:15:35Z","file_size":22433512,"date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","file_id":"12482","checksum":"ad01bb20da163be6893b7af832e58419","embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"3","status":"public"},{"id":"11160","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"oa_version":"Published Version","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"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-11-16T13:10:22Z","file_date_updated":"2023-09-20T22:30:03Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"_id":"12364","status":"public","type":"dissertation"},{"file_date_updated":"2021-02-03T10:37:28Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"ddc":["006","514","516"],"date_updated":"2023-09-07T13:29:01Z","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"9056","related_material":{"record":[{"id":"187","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"8703","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"file_size":13446994,"date_updated":"2021-02-03T10:37:28Z","creator":"patrickd","file_name":"thesis_source.zip","date_created":"2021-02-02T14:09:25Z","content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"bcf27986147cab0533b6abadd74e7629","file_id":"9063"},{"file_name":"thesis_pdfA2b.pdf","date_created":"2021-02-02T14:09:18Z","file_size":5210329,"date_updated":"2021-02-02T14:09:18Z","creator":"patrickd","success":1,"checksum":"9cc8af266579a464385bbe2aff6af606","file_id":"9064","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"02","place":"Klosterneuburg","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets."}],"title":"Multi-cover persistence and Delaunay mosaics","article_processing_charge":"No","author":[{"last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056."},"date_created":"2021-02-02T14:11:06Z","date_published":"2021-02-01T00:00:00Z","doi":"10.15479/AT:ISTA:9056","page":"134","day":"01","year":"2021","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"doi":"10.15479/AT:ISTA:9022","date_published":"2021-01-25T00:00:00Z","date_created":"2021-01-21T18:16:54Z","page":"380","day":"25","has_accepted_license":"1","year":"2021","publisher":"Institute of Science and Technology Austria","oa":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.","title":"Fluctuations in the spectrum of random matrices","author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","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","mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"ec_funded":1,"file":[{"file_size":4127796,"date_updated":"2021-01-25T14:19:03Z","creator":"gcipollo","file_name":"thesis.pdf","date_created":"2021-01-25T14:19:03Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9043","checksum":"5a93658a5f19478372523ee232887e2b"},{"date_created":"2021-01-25T14:19:10Z","file_name":"Thesis_files.zip","date_updated":"2021-01-25T14:19:10Z","file_size":12775206,"creator":"gcipollo","file_id":"9044","checksum":"e8270eddfe6a988e92a53c88d1d19b8c","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"file_date_updated":"2021-01-25T14:19:10Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"ddc":["510"],"supervisor":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"}],"date_updated":"2023-09-07T13:29:32Z","status":"public","type":"dissertation","_id":"9022"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-09-15T14:37:30Z","file_size":15022154,"creator":"shensel","date_created":"2021-09-13T11:03:24Z","file_name":"thesis_final_Hensel.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"c8475faaf0b680b4971f638f1db16347","file_id":"10008"},{"checksum":"1a609937aa5275452822f45f2da17f07","file_id":"10014","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"thesis_final_Hensel.pdf","date_created":"2021-09-13T14:18:56Z","file_size":6583638,"date_updated":"2021-09-14T09:52:47Z","creator":"shensel"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"10012","relation":"part_of_dissertation"},{"status":"public","id":"10013","relation":"part_of_dissertation"},{"id":"7489","status":"public","relation":"part_of_dissertation"}]},"_id":"10007","status":"public","type":"dissertation","ddc":["515"],"date_updated":"2023-09-07T13:30:45Z","supervisor":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"file_date_updated":"2021-09-15T14:37:30Z","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"14","year":"2021","has_accepted_license":"1","date_created":"2021-09-13T11:12:34Z","date_published":"2021-09-14T00:00:00Z","doi":"10.15479/at:ista:10007","page":"300","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021."},"title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","article_processing_charge":"No","author":[{"last_name":"Hensel","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}]},{"date_updated":"2023-09-07T13:31:06Z","supervisor":[{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"ddc":["515"],"file_date_updated":"2022-03-10T12:14:42Z","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"_id":"10030","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2022-03-10T12:14:42Z","file_size":3876668,"date_created":"2021-09-21T09:17:34Z","file_name":"tex_and_pictures.zip","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"8cd60dcb8762e8f21867e21e8001e183","file_id":"10032"},{"creator":"cchlebak","file_size":2532673,"date_updated":"2021-09-27T11:14:31Z","file_name":"thesis_portinale_Final (1).pdf","date_created":"2021-09-27T11:14:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9789e9d967c853c1503ec7f307170279","file_id":"10047"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10022","status":"public"},{"relation":"part_of_dissertation","id":"9792","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7573"}]},"abstract":[{"text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","citation":{"chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030","short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","project":[{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"year":"2021","has_accepted_license":"1","day":"22","date_created":"2021-09-21T09:14:15Z","date_published":"2021-09-22T00:00:00Z","doi":"10.15479/at:ista:10030","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","oa":1,"publisher":"Institute of Science and Technology Austria"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920.","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","mla":"Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920.","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920","apa":"Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021."},"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","author":[{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","day":"19","has_accepted_license":"1","year":"2021","date_published":"2021-08-19T00:00:00Z","doi":"10.15479/at:ista:9920","date_created":"2021-08-16T09:44:09Z","page":"149","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["539"],"supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"date_updated":"2023-09-07T13:31:22Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"file_date_updated":"2021-09-06T08:39:47Z","_id":"9920","status":"public","keyword":["quantum computing","superinductor","quantum metrology"],"type":"dissertation","file":[{"creator":"mperuzzo","date_updated":"2021-09-06T08:39:47Z","file_size":151387283,"date_created":"2021-08-16T09:33:21Z","file_name":"GeometricSuperinductorsForCQED.zip","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","file_id":"9924","checksum":"3cd1986efde5121d7581f6fcf9090da8"},{"file_id":"9939","checksum":"50928c621cdf0775d7a5906b9dc8602c","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-18T14:20:06Z","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","date_updated":"2021-09-06T08:39:47Z","file_size":17596344,"creator":"mperuzzo"},{"access_level":"closed","relation":"other","description":"Extra copy of the thesis as PDF/A-2b","content_type":"application/pdf","checksum":"37f486aa1b622fe44af00d627ec13f6c","file_id":"9940","creator":"mperuzzo","date_updated":"2021-09-06T08:39:47Z","file_size":17592425,"date_created":"2021-08-18T14:20:09Z","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-013-8"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"9928","status":"public"},{"relation":"part_of_dissertation","id":"8755","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"month":"08","alternative_title":["ISTA Thesis"]},{"date_updated":"2023-09-07T13:34:12Z","citation":{"ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422."},"supervisor":[{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["530"],"article_processing_charge":"No","author":[{"last_name":"Piankov","full_name":"Piankov, Anton","id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","first_name":"Anton"}],"file_date_updated":"2022-03-10T12:10:25Z","title":"Towards designer materials using customizable particle shape","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"_id":"10422","type":"dissertation","status":"public","publication_status":"published","degree_awarded":"MS","year":"2021","publication_identifier":{"issn":["2791-4585"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"file_size":394018,"date_updated":"2022-03-10T12:10:25Z","creator":"cchlebak","file_name":"Thesis.zip","date_created":"2021-12-07T11:13:52Z","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"10424","checksum":"114e8f4b2c002c6c352416c12de2c695"},{"creator":"cchlebak","date_updated":"2022-03-10T12:10:25Z","file_size":47638,"date_created":"2021-12-07T11:14:01Z","file_name":"Preliminary_pages_Piankov.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"cd15ae991ced352a9959815f794e657c","file_id":"10425"},{"success":1,"checksum":"e6899c798b75ba42fab9822bce309050","file_id":"10426","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_Piankov_combined.pdf","date_created":"2021-12-07T11:20:35Z","creator":"cchlebak","file_size":484965,"date_updated":"2021-12-07T11:20:35Z"}],"day":"07","date_created":"2021-12-07T10:48:06Z","date_published":"2021-12-07T00:00:00Z","doi":"10.15479/at:ista:10422","abstract":[{"text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Master's Thesis"],"month":"12"},{"file":[{"file_name":"mph-thesis-v519-pdfimages.pdf","date_created":"2021-05-24T11:22:29Z","creator":"bphuong","file_size":2673905,"date_updated":"2021-05-24T11:22:29Z","success":1,"file_id":"9419","checksum":"4f0abe64114cfed264f9d36e8d1197e3","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"checksum":"f5699e876bc770a9b0df8345a77720a2","file_id":"9420","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2021-05-24T11:56:02Z","file_name":"thesis.zip","date_updated":"2021-05-24T11:56:02Z","file_size":92995100,"creator":"bphuong"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"7435","status":"deleted"},{"relation":"part_of_dissertation","status":"public","id":"7481"},{"relation":"part_of_dissertation","id":"9416","status":"public"},{"relation":"part_of_dissertation","id":"7479","status":"public"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"abstract":[{"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.","lang":"eng"}],"month":"05","alternative_title":["ISTA Thesis"],"ddc":["000"],"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"date_updated":"2023-09-08T11:11:12Z","file_date_updated":"2021-05-24T11:56:02Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"_id":"9418","status":"public","type":"dissertation","day":"30","has_accepted_license":"1","year":"2021","doi":"10.15479/AT:ISTA:9418","date_published":"2021-05-30T00:00:00Z","date_created":"2021-05-24T13:06:23Z","page":"125","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418."},"title":"Underspecification in deep learning","author":[{"full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"title":"Improved verification techniques for concurrent systems","article_processing_charge":"No","author":[{"orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","first_name":"Viktor"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199","mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2021-10-29T20:09:01Z","doi":"10.15479/at:ista:10199","date_published":"2021-10-31T00:00:00Z","page":"166","day":"31","year":"2021","has_accepted_license":"1","keyword":["concurrency","verification","model checking"],"status":"public","type":"dissertation","_id":"10199","file_date_updated":"2021-11-09T09:00:50Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-09-19T09:59:54Z","supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"10190","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10191"},{"status":"public","id":"9987","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"141","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"4f412a1ee60952221b499a4b1268df35","file_id":"10225","creator":"vtoman","file_size":2915234,"date_updated":"2021-11-08T14:12:22Z","file_name":"toman_th_final.pdf","date_created":"2021-11-08T14:12:22Z"},{"file_id":"10226","checksum":"9584943f99127be2dd2963f6784c37d4","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2021-11-08T14:12:46Z","file_name":"toman_thesis.zip","creator":"vtoman","date_updated":"2021-11-09T09:00:50Z","file_size":8616056}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]}},{"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"file_date_updated":"2022-03-10T12:15:18Z","supervisor":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"date_updated":"2023-10-17T09:24:07Z","ddc":["519"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10035","related_material":{"record":[{"status":"public","id":"10044","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10049"},{"id":"637","status":"public","relation":"part_of_dissertation"},{"id":"10041","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6430","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10048","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"73a44345c683e81f3e765efbf86fdcc5","file_id":"10082","success":1,"date_updated":"2021-10-04T12:22:33Z","file_size":2104726,"creator":"cchlebak","date_created":"2021-10-04T12:22:33Z","file_name":"thesis_pdfa.pdf"},{"checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","file_id":"10085","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2021-10-05T07:04:37Z","file_name":"thesis_final (1).zip","creator":"cchlebak","date_updated":"2022-03-10T12:15:18Z","file_size":9538359}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","full_name":"Klein, Karen"}],"article_processing_charge":"No","title":"On the adaptive security of graph-based games","citation":{"ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"page":"276","date_published":"2021-09-23T00:00:00Z","doi":"10.15479/at:ista:10035","date_created":"2021-09-23T07:31:44Z","has_accepted_license":"1","year":"2021","day":"23","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n"},{"ddc":["000"],"date_updated":"2023-10-17T11:48:55Z","supervisor":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-03-28T12:55:12Z","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"_id":"10429","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6bf14e9a523387328f016c0689f5e10e","file_id":"10436","success":1,"date_updated":"2021-12-09T17:47:49Z","file_size":2370859,"creator":"gnadirad","date_created":"2021-12-09T17:47:49Z","file_name":"Thesis_Final_09_12_2021.pdf"},{"checksum":"914d6c5ca86bd0add471971a8f4c4341","file_id":"10437","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2021-12-09T17:47:49Z","file_name":"Thesis_Final_09_12_2021.zip","creator":"gnadirad","date_updated":"2022-03-28T12:55:12Z","file_size":2596924}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10432","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6673"},{"status":"public","id":"5965","relation":"part_of_dissertation"},{"id":"10435","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same."}],"month":"12","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429."},"title":"On achieving scalability through relaxation","article_processing_charge":"No","author":[{"orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"day":"09","year":"2021","has_accepted_license":"1","date_created":"2021-12-08T21:52:28Z","date_published":"2021-12-09T00:00:00Z","doi":"10.15479/at:ista:10429","page":"132","oa":1,"publisher":"Institute of Science and Technology Austria"},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"20","has_accepted_license":"1","year":"2021","date_published":"2021-08-20T00:00:00Z","doi":"10.15479/at:ista:9733","date_created":"2021-07-27T15:48:30Z","page":"180","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733."},"title":"The polaron at strong coupling","author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario","last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"month":"08","alternative_title":["ISTA Thesis"],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9944","checksum":"e88bb8ca43948abe060eb2d2fa719881","creator":"dfelicia","file_size":1958710,"date_updated":"2021-09-06T09:28:56Z","file_name":"Thesis_FeliciangeliA.pdf","date_created":"2021-08-19T14:03:48Z"},{"checksum":"72810843abee83705853505b3f8348aa","file_id":"9945","content_type":"application/octet-stream","relation":"source_file","access_level":"closed","file_name":"thesis.7z","date_created":"2021-08-19T14:06:35Z","file_size":3771669,"date_updated":"2022-03-10T12:13:57Z","creator":"dfelicia"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9787"},{"id":"9792","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9225"},{"relation":"part_of_dissertation","id":"9781","status":"public"},{"id":"9791","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"_id":"9733","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"ddc":["515","519","539"],"supervisor":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"date_updated":"2024-03-06T12:30:44Z","file_date_updated":"2022-03-10T12:13:57Z","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}]},{"_id":"9992","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"date_updated":"2023-09-07T13:38:33Z","ddc":["575"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2021-09-15T22:30:26Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"lhoermaye","date_updated":"2021-09-15T22:30:26Z","file_size":25179004,"date_created":"2021-09-09T07:29:48Z","file_name":"Thesis_vupload.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb"},{"checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_id":"9996","embargo":"2021-09-09","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-09-09T14:25:08Z","file_name":"Thesis_vfinal_pdfa.pdf","date_updated":"2021-09-15T22:30:26Z","file_size":6246900,"creator":"lhoermaye"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"6351","relation":"part_of_dissertation"},{"id":"6943","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8002","status":"public"}]},"ec_funded":1,"project":[{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926"}],"article_processing_charge":"No","title":"Wound healing in the Arabidopsis root meristem","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","day":"13","page":"168","doi":"10.15479/at:ista:9992","date_published":"2021-09-13T00:00:00Z","date_created":"2021-09-09T07:37:20Z"},{"month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"related_material":{"record":[{"id":"9750","status":"public","relation":"part_of_dissertation"},{"id":"9006","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"e039225a47ef32666d59bf35ddd30ecf","file_id":"9624","creator":"scaballe","date_updated":"2022-07-02T22:30:06Z","file_size":131946790,"date_created":"2021-07-01T14:48:54Z","file_name":"PhDThesis_SCM.docx"},{"creator":"scaballe","file_size":17094958,"date_updated":"2022-07-02T22:30:06Z","file_name":"PhDThesis_SCM.pdf","date_created":"2021-07-01T14:46:25Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-07-01","file_id":"9625","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","_id":"9623","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"file_date_updated":"2022-07-02T22:30:06Z","ddc":["570"],"date_updated":"2023-09-07T13:33:27Z","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2021-07-01T14:50:17Z","doi":"10.15479/at:ista:9623","date_published":"2021-07-01T00:00:00Z","page":"111","year":"2021","has_accepted_license":"1","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","article_processing_charge":"No","author":[{"full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria."}},{"_id":"10058","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","keyword":["qubits","quantum computing","holes"],"status":"public","date_updated":"2023-09-08T11:41:08Z","supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"ddc":["621","539"],"file_date_updated":"2022-12-20T23:30:07Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"abstract":[{"lang":"eng","text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","file_id":"10061","content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2021-09-30T14:29:14Z","file_name":"PHD_Thesis_Jirovec_Source.zip","date_updated":"2022-12-20T23:30:07Z","file_size":32397600,"creator":"djirovec"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-10-06","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_id":"10087","file_size":26910829,"date_updated":"2022-12-20T23:30:07Z","creator":"djirovec","file_name":"PHD_Thesis_pdfa2b_1.pdf","date_created":"2021-10-05T07:56:49Z"}],"related_material":{"record":[{"status":"public","id":"8831","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10065"},{"relation":"part_of_dissertation","status":"public","id":"10066"},{"status":"public","id":"8909","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5816"}]},"project":[{"grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"}],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","day":"05","page":"151","date_created":"2021-09-30T07:53:49Z","doi":"10.15479/at:ista:10058","date_published":"2021-10-05T00:00:00Z"},{"alternative_title":["ISTA Thesis"],"month":"05","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"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2021-05-17T12:29:12Z","file_name":"KHuljev_Thesis_corrections.docx","creator":"khuljev","date_updated":"2022-05-21T22:30:04Z","file_size":47799741},{"creator":"khuljev","file_size":16542131,"date_updated":"2022-05-21T22:30:04Z","file_name":"new_KHuljev_Thesis_corrections.pdf","date_created":"2021-05-18T14:50:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-05-20","file_id":"9401","checksum":"bf512f8a1e572a543778fc4b227c01ba"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","_id":"9397","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"file_date_updated":"2022-05-21T22:30:04Z","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2023-09-07T13:32:32Z","ddc":["571"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"101","date_published":"2021-05-18T00:00:00Z","doi":"10.15479/at:ista:9397","date_created":"2021-05-17T12:31:30Z","has_accepted_license":"1","year":"2021","day":"18","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla"}],"article_processing_charge":"No","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","citation":{"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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-11T12:55:53Z","supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"file_date_updated":"2022-07-02T22:30:04Z","_id":"9562","type":"dissertation","status":"public","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"embargo":"2022-07-01","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z","creator":"dkleindienst"},{"embargo_to":"open_access","content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"9564","checksum":"3bcf63a2b19e5b6663be051bea332748","file_size":369804895,"date_updated":"2022-07-02T22:30:04Z","creator":"dkleindienst","file_name":"Thesis_source.zip","date_created":"2021-06-17T14:04:30Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9756"},{"status":"public","id":"9437","relation":"part_of_dissertation"},{"id":"8532","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"612","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","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.","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.","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","last_name":"Kleindienst"}],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","year":"2021","has_accepted_license":"1","day":"01","page":"124","date_created":"2021-06-17T14:10:47Z","date_published":"2021-06-01T00:00:00Z","doi":"10.15479/at:ista:9562","oa":1,"publisher":"Institute of Science and Technology Austria"},{"oa":1,"publisher":"Institute of Science and Technology Austria","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).","page":"278","date_created":"2020-12-10T12:17:07Z","doi":"10.15479/AT:ISTA:8934","date_published":"2021-01-01T00:00:00Z","year":"2021","has_accepted_license":"1","day":"01","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"article_processing_charge":"No","author":[{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"}],"title":"Parameterized and algebro-geometric advances in static program analysis","citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","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","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","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.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"01","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","related_material":{"record":[{"status":"public","id":"1386","relation":"part_of_dissertation"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"311","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6056"},{"status":"public","id":"6380","relation":"part_of_dissertation"},{"status":"public","id":"639","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"66","status":"public"},{"status":"public","id":"6780","relation":"part_of_dissertation"},{"id":"6918","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7810"},{"relation":"part_of_dissertation","status":"public","id":"6175"},{"relation":"part_of_dissertation","id":"6378","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6490"},{"relation":"part_of_dissertation","status":"public","id":"7014"},{"status":"public","id":"8089","relation":"part_of_dissertation"},{"id":"8728","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"7158","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5977"},{"relation":"part_of_dissertation","status":"public","id":"6009"},{"id":"6340","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"949","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"embargo":"2021-12-22","file_id":"8969","checksum":"d1b9db3725aed34dadd81274aeb9426c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis-pdfa.pdf","date_created":"2020-12-22T20:08:44Z","creator":"akafshda","file_size":5251507,"date_updated":"2021-12-23T23:30:04Z"},{"file_name":"source.zip","date_created":"2020-12-22T20:08:50Z","creator":"akafshda","file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","checksum":"1661df7b393e6866d2460eba3c905130","file_id":"8970","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"dissertation","status":"public","_id":"8934","file_date_updated":"2021-12-23T23:30:04Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_updated":"2023-09-22T10:03:21Z","supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"ddc":["005"]},{"has_accepted_license":"1","year":"2021","day":"18","page":"73","date_published":"2021-11-18T00:00:00Z","doi":"10.15479/at:ista:10307","date_created":"2021-11-18T15:05:06Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek"}],"article_processing_charge":"No","title":"Pathogenic Escherichia coli hijack the host immune response","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_updated":"2022-12-20T23:30:05Z","file_size":13266088,"creator":"ktomasek","date_created":"2021-11-18T15:07:31Z","file_name":"ThesisTomasekKathrin.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b39c9e0ef18d0484d537a67551effd02","file_id":"10308","embargo":"2022-11-18"},{"file_id":"10309","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2021-11-18T15:07:46Z","file_name":"ThesisTomasekKathrin.docx","date_updated":"2022-12-20T23:30:05Z","file_size":7539509,"creator":"ktomasek"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"abstract":[{"text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"date_updated":"2023-09-07T13:34:38Z","ddc":["570"],"file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"_id":"10307","type":"dissertation","status":"public"},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"22","has_accepted_license":"1","year":"2021","doi":"10.15479/at:ista:10303","date_published":"2021-11-22T00:00:00Z","date_created":"2021-11-18T11:20:59Z","page":"139","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303."},"title":"Role of hormones in nitrate regulated growth","author":[{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"month":"11","alternative_title":["ISTA Thesis"],"file":[{"creator":"rabualia","file_size":28005730,"date_updated":"2022-12-20T23:30:06Z","file_name":"AbualiaPhDthesisfinalv3.pdf","date_created":"2021-11-22T14:48:21Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-11-23","file_id":"10331","checksum":"dea38b98aa4da1cea03dcd0f10862818"},{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_id":"10332","creator":"rabualia","date_updated":"2022-12-20T23:30:06Z","file_size":62841883,"date_created":"2021-11-22T14:48:34Z","file_name":"AbualiaPhDthesisfinalv3.docx"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"status":"public","id":"9913","relation":"part_of_dissertation"},{"status":"public","id":"47","relation":"part_of_dissertation"}]},"_id":"10303","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580","581"],"supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"date_updated":"2023-09-19T14:42:45Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:06Z"},{"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"file_date_updated":"2022-09-03T22:30:04Z","date_updated":"2023-09-22T09:58:30Z","supervisor":[{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"status":"public","_id":"9962","related_material":{"record":[{"id":"8569","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"960"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-09-03T22:30:04Z","file_size":10629190,"creator":"ahansen","date_created":"2021-08-30T09:17:39Z","file_name":"Thesis_Hansen.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","file_id":"9971"},{"date_created":"2021-08-30T09:29:44Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","creator":"ahansen","date_updated":"2022-09-03T22:30:04Z","file_size":13457469,"file_id":"9972","checksum":"204fa40321a1c6289b68c473634c4bf3","embargo":"2022-09-02","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"}],"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","citation":{"ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"}],"page":"182","date_created":"2021-08-29T12:36:50Z","doi":"10.15479/at:ista:9962","date_published":"2021-09-02T00:00:00Z","year":"2021","has_accepted_license":"1","day":"02","oa":1,"publisher":"Institute of Science and Technology Austria"},{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"citation":{"chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"title":"Rapid cell growth regulation in Arabidopsis","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","day":"06","date_created":"2021-10-04T13:33:10Z","doi":"10.15479/at:ista:10083","date_published":"2021-10-06T00:00:00Z","_id":"10083","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"dissertation","status":"public","date_updated":"2023-10-31T19:30:02Z","supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"ddc":["575"],"file_date_updated":"2022-12-20T23:30:03Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"abstract":[{"text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-10-14T08:00:07Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","creator":"cchlebak","date_updated":"2022-12-20T23:30:03Z","file_size":8616142,"checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","file_id":"10138","embargo":"2022-10-14","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"f23ed258ca894f6aabf58b0c128bf242","file_id":"10139","creator":"cchlebak","file_size":15058499,"date_updated":"2022-12-20T23:30:03Z","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","date_created":"2021-10-14T08:00:13Z"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"442"},{"id":"8931","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9287"},{"relation":"part_of_dissertation","id":"8283","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8986"},{"id":"6627","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10095","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10015"}]}},{"status":"public","type":"dissertation","_id":"10293","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"file_date_updated":"2022-12-20T23:30:08Z","ddc":["519","576"],"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"date_updated":"2023-11-07T08:28:29Z","month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9997"},{"relation":"part_of_dissertation","status":"public","id":"2"},{"relation":"part_of_dissertation","status":"public","id":"9402"}]},"ec_funded":1,"file":[{"embargo_to":"open_access","content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"86a05b430756ca12ae8107b6e6f3c1e5","file_id":"10305","file_size":29703124,"date_updated":"2022-12-20T23:30:08Z","creator":"lschmid","file_name":"submission_new.zip","date_created":"2021-11-18T12:41:46Z"},{"file_id":"10306","checksum":"d940af042e94660c6b6a7b4f0b184d47","embargo":"2022-10-18","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-11-18T12:59:15Z","file_name":"thesis_new_upload.pdf","date_updated":"2022-12-20T23:30:08Z","file_size":8320985,"creator":"lschmid"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","author":[{"first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293"},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2021-11-17T00:00:00Z","doi":"10.15479/at:ista:10293","date_created":"2021-11-15T17:12:57Z","page":"171","day":"17","has_accepted_license":"1","year":"2021"},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9160"}]},"publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"cziletti","file_size":28508629,"date_updated":"2022-12-20T23:30:05Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","date_created":"2021-10-27T07:45:37Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"ce7108853e6cec6224f17cd6429b51fe","file_id":"10186"},{"checksum":"0d7afb846e8e31ec794de47bf44e12ef","file_id":"10187","embargo":"2022-10-28","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-27T07:45:57Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","creator":"cziletti","date_updated":"2022-12-20T23:30:05Z","file_size":10623525}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"supervisor":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-01-25T10:53:29Z","ddc":["570"],"type":"dissertation","status":"public","_id":"10135","doi":"10.15479/at:ista:10135","date_published":"2021-10-13T00:00:00Z","date_created":"2021-10-13T13:42:48Z","has_accepted_license":"1","year":"2021","day":"13","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"full_name":"Semerádová, Hana","last_name":"Semerádová","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","citation":{"ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746"}]},{"citation":{"ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728","apa":"Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728","mla":"Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal","last_name":"Agrawal"}],"article_processing_charge":"No","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","day":"29","page":"118","date_published":"2021-07-29T00:00:00Z","doi":"10.15479/at:ista:9728","date_created":"2021-07-27T13:40:30Z","_id":"9728","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-28T13:14:39Z","ddc":["532"],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2022-07-29T22:30:05Z","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","date_created":"2021-07-28T13:32:02Z","file_size":22859658,"date_updated":"2022-07-29T22:30:05Z","creator":"nagrawal","checksum":"77436be3563a90435024307b1b5ee7e8","file_id":"9744","embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"},{"embargo":"2022-07-28","file_id":"9745","checksum":"72a891d7daba85445c29b868c22575ed","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","date_created":"2021-07-28T13:32:05Z","creator":"nagrawal","file_size":18658048,"date_updated":"2022-07-29T22:30:05Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"6189","status":"public"}]}},{"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_Forkert_PDFA.pdf","date_created":"2020-04-14T10:47:59Z","file_size":3297129,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"7658","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","date_updated":"2020-07-14T12:48:01Z","file_size":1063908,"creator":"dernst","date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_source.zip"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","date_updated":"2023-09-07T13:03:12Z","supervisor":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:48:01Z","_id":"7629","type":"dissertation","status":"public","year":"2020","has_accepted_license":"1","day":"31","page":"154","date_created":"2020-04-02T06:40:23Z","doi":"10.15479/AT:ISTA:7629","date_published":"2020-03-31T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L","last_name":"Forkert"}],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}]},{"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"oa_version":"Published Version","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","success":1,"creator":"dernst","date_updated":"2020-09-28T07:25:35Z","file_size":6354833,"date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf"},{"checksum":"a8de2c14a1bb4e53c857787efbb289e1","file_id":"8576","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-09-28T07:25:37Z","file_name":"thesisFiles_EnikoSzep.zip","date_updated":"2020-09-28T07:25:37Z","file_size":23020401,"creator":"dernst"}],"type":"dissertation","status":"public","_id":"8574","department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-28T07:25:37Z","date_updated":"2023-09-07T13:11:39Z","supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"158","date_created":"2020-09-28T07:33:38Z","date_published":"2020-09-20T00:00:00Z","doi":"10.15479/AT:ISTA:8574","year":"2020","has_accepted_license":"1","day":"20","article_processing_charge":"No","author":[{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","last_name":"Szep"}],"title":"Local adaptation in metapopulations","citation":{"mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"ddc":["510"],"date_updated":"2023-09-07T13:12:42Z","supervisor":[{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"_id":"7514","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_name":"thesis.pdf","date_created":"2020-02-24T09:15:06Z","file_size":1563429,"date_updated":"2020-07-14T12:47:59Z","creator":"dernst","file_id":"7515","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_id":"7516","creator":"dernst","file_size":2028038,"date_updated":"2020-07-14T12:47:59Z","file_name":"thesis_source.zip","date_created":"2020-02-24T09:15:16Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7524","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.","lang":"eng"}],"month":"02","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514."},"title":"The free energy of a dilute two-dimensional Bose gas","article_processing_charge":"No","author":[{"full_name":"Mayer, Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"24","year":"2020","has_accepted_license":"1","date_created":"2020-02-24T09:17:27Z","date_published":"2020-02-24T00:00:00Z","doi":"10.15479/AT:ISTA:7514","page":"148","oa":1,"publisher":"Institute of Science and Technology Austria"},{"has_accepted_license":"1","year":"2020","day":"09","page":"191","doi":"10.15479/AT:ISTA:8353","date_published":"2020-09-09T00:00:00Z","date_created":"2020-09-09T14:27:01Z","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Steiner","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"}],"article_processing_charge":"No","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_size":117547589,"date_updated":"2021-09-16T12:40:56Z","creator":"jsteiner","file_name":"Thesis_Julia_Steiner_pdfA.pdf","date_created":"2020-09-09T14:22:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_id":"8354"},{"creator":"jsteiner","file_size":223328668,"date_updated":"2020-09-15T08:48:37Z","file_name":"Thesis_Julia_Steiner.docx","date_created":"2020-09-09T14:23:25Z","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8355","checksum":"ba112f957b7145462d0ab79044873ee9"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"8284","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"09","supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:14:09Z","ddc":["572"],"file_date_updated":"2021-09-16T12:40:56Z","department":[{"_id":"LeSa"}],"_id":"8353","type":"dissertation","status":"public"},{"publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","doi":"10.15479/AT:ISTA:8589","date_published":"2020-09-30T00:00:00Z","date_created":"2020-09-30T14:50:51Z","page":"164","day":"30","has_accepted_license":"1","year":"2020","title":"Novel insights into PIN polarity regulation during Arabidopsis development","author":[{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"status":"public","id":"7643","relation":"part_of_dissertation"}]},"file":[{"file_name":"2020_Han_Thesis.docx","date_created":"2020-09-30T14:50:20Z","file_size":49198118,"date_updated":"2020-09-30T14:50:20Z","creator":"dernst","checksum":"c4bda1947d4c09c428ac9ce667b02327","file_id":"8590","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"date_updated":"2021-10-01T13:33:02Z","file_size":15513963,"creator":"dernst","date_created":"2020-09-30T14:49:59Z","file_name":"2020_Han_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8591","checksum":"3f4f5d1718c2230adf30639ecaf8a00b"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","_id":"8589","file_date_updated":"2021-10-01T13:33:02Z","department":[{"_id":"JiFr"}],"ddc":["580"],"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:13:05Z"},{"_id":"8155","type":"dissertation","status":"public","date_updated":"2023-09-07T13:13:27Z","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"ddc":["530","570"],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z","abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8176","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","date_created":"2020-07-27T12:00:07Z","creator":"rgrah","file_size":16638998,"date_updated":"2020-07-27T12:00:07Z"},{"date_updated":"2020-07-30T13:04:55Z","file_size":347459978,"creator":"rgrah","date_created":"2020-07-27T12:02:23Z","file_name":"Thesis_new.zip","content_type":"application/zip","access_level":"closed","relation":"main_file","file_id":"8177"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7675"},{"status":"public","id":"7569","relation":"part_of_dissertation"},{"status":"public","id":"7652","relation":"part_of_dissertation"}]},"project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"title":"Gene regulation across scales – how biophysical constraints shape evolution","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"24","page":"310","date_created":"2020-07-23T09:51:28Z","date_published":"2020-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:8155"},{"_id":"7460","status":"public","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"ddc":["514"],"supervisor":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"date_updated":"2023-09-07T13:15:30Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:58Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"month":"02","alternative_title":["ISTA Thesis"],"file":[{"file_id":"7461","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"thesis_ist-final_noack.pdf","date_created":"2020-02-06T14:43:54Z","file_size":76195184,"date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe"},{"date_created":"2020-02-06T14:52:45Z","file_name":"latex-files.zip","date_updated":"2020-07-14T12:47:58Z","file_size":122103715,"creator":"koelsboe","file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4","description":"latex source files, figures","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"6608","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020."},"title":"The hole system of triangulated shapes","author":[{"first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck","full_name":"Ölsböck, Katharina","orcid":"0000-0002-4672-8297"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"10","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:7460","date_published":"2020-02-10T00:00:00Z","date_created":"2020-02-06T14:56:53Z","page":"155"},{"day":"25","has_accepted_license":"1","year":"2020","date_published":"2020-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:7896","date_created":"2020-05-26T14:08:55Z","page":"126","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896."},"title":"On the average-case hardness of total search problems","author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"}],"article_processing_charge":"No","project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"file":[{"file_id":"7897","checksum":"b39e2e1c376f5819b823fb7077491c64","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-26T14:08:13Z","file_name":"2020_Thesis_Kamath.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":1622742},{"date_created":"2020-05-26T14:08:23Z","file_name":"Thesis_Kamath.zip","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":15301529,"file_id":"7898","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6677"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. "}],"month":"05","alternative_title":["ISTA Thesis"],"ddc":["000"],"supervisor":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:15:55Z","file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"KrPi"}],"_id":"7896","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2020-06-09T00:00:00Z","doi":"10.15479/AT:ISTA:7944","date_created":"2020-06-08T00:49:46Z","page":"160","day":"09","has_accepted_license":"1","year":"2020","title":"Reconfiguration problems","author":[{"last_name":"Masárová","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944."},"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"7950","relation":"part_of_dissertation"},{"id":"5986","status":"public","relation":"part_of_dissertation"}]},"license":"https://creativecommons.org/licenses/by-sa/4.0/","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_id":"7945","file_size":13661779,"date_updated":"2020-07-14T12:48:05Z","creator":"zmasarov","file_name":"THESIS_Zuzka_Masarova.pdf","date_created":"2020-06-08T00:34:00Z"},{"creator":"zmasarov","date_updated":"2020-07-14T12:48:05Z","file_size":32184006,"date_created":"2020-06-08T00:35:30Z","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"7946","checksum":"45341a35b8f5529c74010b7af43ac188"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"type":"dissertation","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"_id":"7944","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:05Z","ddc":["516","514"],"supervisor":[{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"date_updated":"2023-09-07T13:17:37Z"},{"abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","date_created":"2020-09-08T09:00:29Z","creator":"dernst","file_size":65246782,"date_updated":"2021-09-16T12:49:12Z","checksum":"70871b335a595252a66c6bbf0824fb02","file_id":"8342","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"59a62275088b00b7241e6ff4136434c7","file_id":"8343","creator":"dernst","date_updated":"2021-09-16T12:49:12Z","file_size":31259058,"date_created":"2020-09-08T09:00:27Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"7580","relation":"part_of_dissertation"}]},"_id":"8341","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","supervisor":[{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:17:06Z","ddc":["570"],"file_date_updated":"2021-09-16T12:49:12Z","department":[{"_id":"MaLo"}],"acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2020","day":"08","page":"215","date_published":"2020-09-08T00:00:00Z","doi":"10.15479/AT:ISTA:8341","date_created":"2020-09-08T08:53:53Z","citation":{"apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","last_name":"Bezeljak","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631"}],"article_processing_charge":"No","title":"In vitro reconstitution of a Rab activation switch"},{"doi":"10.15479/AT:ISTA:8032","date_published":"2020-06-26T00:00:00Z","date_created":"2020-06-26T10:00:36Z","page":"xviii+120","day":"26","has_accepted_license":"1","year":"2020","publisher":"Institute of Science and Technology Austria","oa":1,"title":"Combinatorial width parameters for 3-dimensional manifolds","author":[{"id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf","last_name":"Huszár","full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032.","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032."},"related_material":{"record":[{"status":"public","id":"6556","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"7093","status":"public"}]},"file":[{"file_id":"8034","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-06-26T10:03:58Z","file_name":"Kristof_Huszar-Thesis.pdf","date_updated":"2020-07-14T12:48:08Z","file_size":2637562,"creator":"khuszar"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"d5f8456202b32f4a77552ef47a2837d1","file_id":"8035","creator":"khuszar","file_size":7163491,"date_updated":"2020-07-14T12:48:08Z","file_name":"Kristof_Huszar-Thesis-source.zip","date_created":"2020-06-26T10:10:06Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-006-0"]},"publication_status":"published","degree_awarded":"PhD","month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:08Z","department":[{"_id":"UlWa"}],"ddc":["514"],"supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"date_updated":"2023-09-07T13:18:27Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8032"},{"article_processing_charge":"No","author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R"}],"title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","citation":{"ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"135","date_created":"2020-09-10T09:26:49Z","doi":"10.15479/AT:ISTA:8358","date_published":"2020-09-10T00:00:00Z","year":"2020","has_accepted_license":"1","day":"10","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","department":[{"_id":"MaLo"}],"file_date_updated":"2020-09-11T07:48:10Z","date_updated":"2023-09-07T13:18:51Z","supervisor":[{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"ddc":["572"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"8358","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7572"},{"id":"7197","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":141602462,"date_updated":"2020-09-10T12:11:29Z","creator":"pcaldas","file_name":"phd_thesis_pcaldas.pdf","date_created":"2020-09-10T12:11:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"882f93fe9c351962120e2669b84bf088","file_id":"8364"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"8365","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","creator":"pcaldas","file_size":450437458,"date_updated":"2020-09-11T07:48:10Z","file_name":"phd_thesis_latex_pcaldas.zip","date_created":"2020-09-10T12:18:17Z"}],"alternative_title":["ISTA Thesis"],"month":"09","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n","lang":"eng"}],"oa_version":"Published Version"},{"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/AT:ISTA:8332","date_published":"2020-09-03T00:00:00Z","date_created":"2020-09-04T12:24:12Z","page":"120","day":"03","has_accepted_license":"1","year":"2020","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","author":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"133"},{"status":"public","id":"8012","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8195"},{"relation":"part_of_dissertation","status":"public","id":"160"}]},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"26fe261550f691280bda4c454bf015c7","file_id":"8333","creator":"bkragl","date_updated":"2020-09-04T12:17:47Z","file_size":1348815,"date_created":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf"},{"file_size":372312,"date_updated":"2020-09-04T13:00:17Z","creator":"bkragl","file_name":"kragl-thesis.zip","date_created":"2020-09-04T13:00:17Z","content_type":"application/zip","relation":"source_file","access_level":"closed","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","_id":"8332","file_date_updated":"2020-09-04T13:00:17Z","department":[{"_id":"ToHe"}],"ddc":["000"],"supervisor":[{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-13T08:45:08Z"},{"page":"125","doi":"10.15479/AT:ISTA:8958","date_published":"2020-12-21T00:00:00Z","date_created":"2020-12-21T09:44:30Z","has_accepted_license":"1","year":"2020","day":"21","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang","last_name":"Li","full_name":"Li, Xiang"}],"article_processing_charge":"No","title":"Rotation of coupled cold molecules in the presence of a many-body environment","citation":{"mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5886"},{"id":"8587","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1120"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_updated":"2020-12-22T10:55:56Z","file_size":3622305,"creator":"xli","date_created":"2020-12-22T10:55:56Z","file_name":"THESIS_Xiang_Li.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8967","checksum":"3994c54a1241451d561db1d4f43bad30","success":1},{"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"0954ecfc5554c05615c14de803341f00","file_id":"8968","date_updated":"2020-12-30T07:18:03Z","file_size":4018859,"creator":"xli","date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"12","abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"oa_version":"Published Version","department":[{"_id":"MiLe"}],"file_date_updated":"2020-12-30T07:18:03Z","supervisor":[{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-20T11:30:58Z","ddc":["539"],"type":"dissertation","status":"public","_id":"8958"},{"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"486"},{"relation":"part_of_dissertation","id":"1002","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","file_id":"8388","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-09-14T01:02:59Z","file_name":"Thesis_Ran.zip","date_updated":"2020-09-14T12:18:43Z","file_size":1245800191,"creator":"rzhang"},{"date_updated":"2020-09-15T12:51:53Z","file_size":161385316,"creator":"rzhang","date_created":"2020-09-15T12:51:53Z","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"817e20c33be9247f906925517c56a40d","file_id":"8396","success":1}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.","lang":"eng"}],"file_date_updated":"2020-09-15T12:51:53Z","department":[{"_id":"BeBi"}],"ddc":["003"],"date_updated":"2023-09-22T09:49:31Z","supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"status":"public","type":"dissertation","_id":"8386","date_created":"2020-09-14T01:04:53Z","date_published":"2020-09-14T00:00:00Z","doi":"10.15479/AT:ISTA:8386","page":"148","day":"14","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","article_processing_charge":"No","author":[{"orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386."},"project":[{"grant_number":"642841","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria."},"title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","author":[{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka"}],"article_processing_charge":"No","day":"22","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:7996","date_published":"2020-06-22T00:00:00Z","date_created":"2020-06-22T09:22:23Z","page":"178","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["530"],"supervisor":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"date_updated":"2023-09-26T15:50:22Z","file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"GeKa"}],"_id":"7996","status":"public","type":"dissertation","file":[{"checksum":"467e52feb3e361ce8cf5fe8d5c254ece","file_id":"7997","access_level":"closed","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2020-06-22T09:22:04Z","file_name":"JK_thesis_latex_source_files.zip","creator":"dernst","date_updated":"2020-07-14T12:48:07Z","file_size":392794743},{"checksum":"1de716bf110dbd77d383e479232bf496","file_id":"7998","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-06-22T09:21:29Z","file_name":"PhD_thesis_JK_pdfa.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:07Z","file_size":28453247}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"1328","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7541"},{"id":"77","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"23"},{"id":"840","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity."}],"month":"06","alternative_title":["ISTA Thesis"]},{"status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"8390","department":[{"_id":"ChLa"}],"file_date_updated":"2020-09-14T13:39:17Z","ddc":["000"],"supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"date_updated":"2023-10-16T10:04:02Z","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"related_material":{"record":[{"id":"7936","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"7937","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8193","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"id":"911","status":"public","relation":"part_of_dissertation"}]},"file":[{"checksum":"c914d2f88846032f3d8507734861b6ee","file_id":"8391","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-14T13:39:14Z","file_name":"2020_Thesis_Royer.pdf","creator":"dernst","date_updated":"2020-09-14T13:39:14Z","file_size":30224591},{"relation":"main_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"8392","checksum":"ae98fb35d912cff84a89035ae5794d3c","creator":"dernst","file_size":74227627,"date_updated":"2020-09-14T13:39:17Z","file_name":"thesis_sources.zip","date_created":"2020-09-14T13:39:17Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390."},"publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","doi":"10.15479/AT:ISTA:8390","date_published":"2020-09-14T00:00:00Z","date_created":"2020-09-14T13:42:09Z","page":"197","day":"14","has_accepted_license":"1","year":"2020"},{"type":"dissertation","status":"public","_id":"7196","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:52Z","date_updated":"2023-10-17T12:29:46Z","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"ddc":["519"],"alternative_title":["ISTA Thesis"],"month":"01","abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"oa_version":"Published Version","related_material":{"record":[{"id":"7210","status":"public","relation":"dissertation_contains"},{"status":"public","id":"5751","relation":"dissertation_contains"},{"id":"7212","status":"public","relation":"dissertation_contains"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7255","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2020-01-12T11:49:49Z","file_name":"thesis.zip","creator":"jtkadlec","date_updated":"2020-07-14T12:47:52Z","file_size":21100497},{"file_name":"2020_Tkadlec_Thesis.pdf","date_created":"2020-01-28T07:32:42Z","file_size":11670983,"date_updated":"2020-07-14T12:47:52Z","creator":"dernst","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","file_id":"7367","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"article_processing_charge":"No","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"}],"title":"A role of graphs in evolutionary processes","citation":{"ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"144","date_created":"2019-12-20T12:26:36Z","date_published":"2020-01-12T00:00:00Z","doi":"10.15479/AT:ISTA:7196","year":"2020","has_accepted_license":"1","day":"12"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria."},"title":"Topological methods in geometry and discrete mathematics","article_processing_charge":"No","author":[{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","last_name":"Avvakumov"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"24","year":"2020","has_accepted_license":"1","date_created":"2020-07-23T09:51:29Z","date_published":"2020-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:8156","page":"119","_id":"8156","status":"public","type":"dissertation","ddc":["514"],"date_updated":"2023-12-18T10:51:01Z","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-27T12:46:53Z","oa_version":"Published Version","abstract":[{"text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.","lang":"eng"}],"month":"07","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_created":"2020-07-27T12:44:51Z","file_name":"source.zip","creator":"savvakum","date_updated":"2020-07-27T12:44:51Z","file_size":1061740,"file_id":"8178","access_level":"closed","relation":"source_file","content_type":"application/zip"},{"file_name":"thesis_pdfa.pdf","date_created":"2020-07-27T12:46:53Z","creator":"savvakum","file_size":1336501,"date_updated":"2020-07-27T12:46:53Z","success":1,"file_id":"8179","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"8182","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8183","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8185"},{"relation":"part_of_dissertation","status":"public","id":"8184"},{"id":"6355","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"75","relation":"part_of_dissertation"}]}},{"citation":{"mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Guseinov","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Computational design of curved thin shells: From glass façades to programmable matter","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"has_accepted_license":"1","year":"2020","day":"21","page":"118","date_published":"2020-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:8366","date_created":"2020-09-10T16:19:55Z","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"date_updated":"2024-02-21T12:44:29Z","ddc":["000"],"file_date_updated":"2020-09-16T15:11:01Z","department":[{"_id":"BeBi"}],"_id":"8366","type":"dissertation","status":"public","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-010-7"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"rguseino","date_updated":"2020-09-10T16:11:49Z","file_size":70950442,"date_created":"2020-09-10T16:11:49Z","file_name":"thesis_rguseinov.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8367","checksum":"f8da89553da36037296b0a80f14ebf50","success":1},{"date_updated":"2020-09-16T15:11:01Z","file_size":76207597,"creator":"rguseino","date_created":"2020-09-11T09:39:48Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"e8fd944c960c20e0e27e6548af69121d","file_id":"8374"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"7151","status":"deleted"},{"status":"public","id":"7262","relation":"part_of_dissertation"},{"id":"8562","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"1001","relation":"part_of_dissertation"},{"relation":"research_data","id":"8375","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09"},{"publisher":"Institute of Science and Technology Austria","oa":1,"page":"79","date_published":"2020-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:7525","date_created":"2020-02-26T10:56:37Z","has_accepted_license":"1","year":"2020","day":"28","author":[{"full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","citation":{"chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","mla":"Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525.","apa":"Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"02","abstract":[{"lang":"eng","text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"embargo":"2021-02-28","file_id":"7538","checksum":"4589234fdb12b4ad72273b311723a7b4","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Pradeep Bhandari Thesis.pdf","date_created":"2020-02-28T08:37:53Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","creator":"pbhandari","file_size":9646346,"date_updated":"2021-03-01T23:30:04Z"},{"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","date_created":"2020-02-28T08:47:14Z","file_name":"Pradeep Bhandari Thesis.docx","date_updated":"2021-03-01T23:30:04Z","file_size":35252164,"creator":"pbhandari","file_id":"7539","checksum":"aa79490553ca0a5c9b6fbcd152e93928","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"_id":"7525","department":[{"_id":"RySh"}],"file_date_updated":"2021-03-01T23:30:04Z","supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:20:03Z","ddc":["570"]},{"supervisor":[{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:20:48Z","ddc":["571","530","570"],"file_date_updated":"2021-10-07T22:30:03Z","department":[{"_id":"GaTk"}],"_id":"8657","type":"dissertation","status":"public","publication_identifier":{"isbn":["978-3-99078-011-4"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","file_id":"8663","embargo":"2021-10-06","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-15T06:41:20Z","file_name":"kavcicB_thesis202009.pdf","creator":"bkavcic","date_updated":"2021-10-07T22:30:03Z","file_size":52636162},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","checksum":"bb35f2352a04db19164da609f00501f3","file_id":"8664","creator":"bkavcic","file_size":321681247,"date_updated":"2021-10-07T22:30:03Z","file_name":"2020b.zip","date_created":"2020-10-15T06:41:53Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7673"},{"relation":"part_of_dissertation","status":"public","id":"8250"}]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","citation":{"ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic"}],"article_processing_charge":"No","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","has_accepted_license":"1","year":"2020","day":"14","page":"271","date_published":"2020-10-14T00:00:00Z","doi":"10.15479/AT:ISTA:8657","date_created":"2020-10-13T16:46:14Z","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","publisher":"Institute of Science and Technology Austria","oa":1},{"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_without-signatures_PDFA.pdf","date_created":"2020-04-28T11:19:21Z","creator":"stgingl","file_size":3268017,"date_updated":"2021-10-31T23:30:05Z","embargo":"2021-10-30","file_id":"7692","checksum":"fb9a4468eb27be92690728e35c823796","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_size":5167703,"date_updated":"2021-10-31T23:30:05Z","creator":"stgingl","file_name":"Thesis_without signatures.docx","date_created":"2020-04-28T11:19:24Z","embargo_to":"open_access","content_type":"application/octet-stream","relation":"source_file","access_level":"closed","file_id":"7693","checksum":"f6c80ca97104a631a328cb79a2c53493"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"1028","relation":"dissertation_contains"}]},"oa_version":"None","abstract":[{"text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo.","lang":"eng"}],"month":"04","alternative_title":["ISTA Thesis"],"ddc":["570"],"date_updated":"2023-09-22T09:20:10Z","supervisor":[{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"file_date_updated":"2021-10-31T23:30:05Z","department":[{"_id":"CaGu"}],"_id":"7680","status":"public","type":"dissertation","day":"24","year":"2020","has_accepted_license":"1","date_created":"2020-04-24T16:00:51Z","doi":"10.15479/AT:ISTA:7680","date_published":"2020-04-24T00:00:00Z","page":"98","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria."},"title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","article_processing_charge":"No","author":[{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"}]},{"language":[{"iso":"eng"}],"file":[{"file_id":"8621","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","embargo":"2021-10-15","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-07T14:41:49Z","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","creator":"jmorande","date_updated":"2021-10-16T22:30:04Z","file_size":16155786},{"date_updated":"2021-10-16T22:30:04Z","file_size":24344152,"creator":"jmorande","date_created":"2020-10-07T14:45:07Z","file_name":"Jasmin_Morandell_Thesis-2020_final.zip","content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"5e0464af453734210ce7aab7b4a92e3a","file_id":"8622"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7800"},{"relation":"part_of_dissertation","status":"public","id":"8131"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages."}],"month":"10","alternative_title":["ISTA Thesis"],"ddc":["610"],"date_updated":"2023-09-07T13:22:14Z","supervisor":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"}],"file_date_updated":"2021-10-16T22:30:04Z","department":[{"_id":"GaNo"}],"_id":"8620","status":"public","type":"dissertation","day":"12","year":"2020","has_accepted_license":"1","date_created":"2020-10-07T14:53:13Z","date_published":"2020-10-12T00:00:00Z","doi":"10.15479/AT:ISTA:8620","page":"138","acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","mla":"Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:10.15479/AT:ISTA:8620","apa":"Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620"},"title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","article_processing_charge":"No","author":[{"full_name":"Morandell, Jasmin","last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"grant_number":"F07807","name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}]},{"oa_version":"None","abstract":[{"lang":"eng","text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"checksum":"dd270baf82121eb4472ad19d77bf227c","file_id":"8345","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2020-09-08T13:32:06Z","file_name":"ThesisFull20200908.docx","creator":"dkampjut","date_updated":"2021-09-11T22:30:04Z","file_size":166146359},{"creator":"dernst","file_size":13873769,"date_updated":"2021-09-11T22:30:04Z","file_name":"2020_Thesis_Kampjut.pdf","date_created":"2020-09-14T15:02:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-09-10","file_id":"8393","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-008-4"]},"ec_funded":1,"related_material":{"record":[{"id":"6848","status":"public","relation":"part_of_dissertation"}]},"_id":"8340","status":"public","type":"dissertation","ddc":["572"],"date_updated":"2023-09-07T13:26:17Z","supervisor":[{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"file_date_updated":"2021-09-11T22:30:04Z","department":[{"_id":"LeSa"}],"acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"09","year":"2020","has_accepted_license":"1","date_created":"2020-09-07T18:42:23Z","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8340","page":"242","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","mla":"Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340","apa":"Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340"},"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","article_processing_charge":"No","author":[{"last_name":"Kampjut","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen"}]}]