[{"page":"152","date_created":"2023-01-24T13:09:57Z","doi":"10.15479/at:ista:12094","date_published":"2022-09-19T00:00:00Z","year":"2022","has_accepted_license":"1","day":"19","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"}],"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","citation":{"ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094","apa":"Dotter, C. (2022). Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12094","mla":"Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"},{"grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"3"},{"relation":"part_of_dissertation","status":"public","id":"11160"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"220923_Thesis_CDotter_Final.pdf","date_created":"2023-01-24T13:15:45Z","file_size":20457465,"date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","embargo":"2023-09-19","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","file_id":"12365","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"ad01bb20da163be6893b7af832e58419","file_id":"12482","file_size":22433512,"date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","file_name":"latex_source_CDotter_Thesis_2022.zip","date_created":"2023-02-02T09:15:35Z"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"file_date_updated":"2023-09-20T22:30:03Z","date_updated":"2023-11-16T13:10:22Z","supervisor":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"}],"ddc":["570"],"type":"dissertation","status":"public","_id":"12364"},{"date_updated":"2023-09-07T13:29:01Z","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"ddc":["006","514","516"],"file_date_updated":"2021-02-03T10:37:28Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"_id":"9056","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","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"9063","checksum":"bcf27986147cab0533b6abadd74e7629","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2021-02-02T14:09:25Z","file_name":"thesis_source.zip","creator":"patrickd","date_updated":"2021-02-03T10:37:28Z","file_size":13446994},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9064","checksum":"9cc8af266579a464385bbe2aff6af606","file_size":5210329,"date_updated":"2021-02-02T14:09:18Z","creator":"patrickd","file_name":"thesis_pdfA2b.pdf","date_created":"2021-02-02T14:09:18Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"187","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8703"}]},"abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"02","place":"Klosterneuburg","citation":{"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.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"}],"title":"Multi-cover persistence and Delaunay mosaics","year":"2021","has_accepted_license":"1","day":"01","page":"134","date_created":"2021-02-02T14:11:06Z","date_published":"2021-02-01T00:00:00Z","doi":"10.15479/AT:ISTA:9056","oa":1,"publisher":"Institute of Science and Technology Austria"},{"acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"25","year":"2021","has_accepted_license":"1","date_created":"2021-01-21T18:16:54Z","doi":"10.15479/AT:ISTA:9022","date_published":"2021-01-25T00:00:00Z","page":"380","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 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","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022.","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria."},"title":"Fluctuations in the spectrum of random matrices","article_processing_charge":"No","author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"}],"oa_version":"Published Version","abstract":[{"text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.","lang":"eng"}],"month":"01","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"5a93658a5f19478372523ee232887e2b","file_id":"9043","file_size":4127796,"date_updated":"2021-01-25T14:19:03Z","creator":"gcipollo","file_name":"thesis.pdf","date_created":"2021-01-25T14:19:03Z"},{"checksum":"e8270eddfe6a988e92a53c88d1d19b8c","file_id":"9044","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"Thesis_files.zip","date_created":"2021-01-25T14:19:10Z","file_size":12775206,"date_updated":"2021-01-25T14:19:10Z","creator":"gcipollo"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"_id":"9022","status":"public","type":"dissertation","ddc":["510"],"date_updated":"2023-09-07T13:29:32Z","supervisor":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"file_date_updated":"2021-01-25T14:19:10Z"},{"ddc":["515"],"date_updated":"2023-09-07T13:30:45Z","supervisor":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"file_date_updated":"2021-09-15T14:37:30Z","_id":"10007","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_name":"thesis_final_Hensel.zip","date_created":"2021-09-13T11:03:24Z","creator":"shensel","file_size":15022154,"date_updated":"2021-09-15T14:37:30Z","file_id":"10008","checksum":"c8475faaf0b680b4971f638f1db16347","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed"},{"creator":"shensel","date_updated":"2021-09-14T09:52:47Z","file_size":6583638,"date_created":"2021-09-13T14:18:56Z","file_name":"thesis_final_Hensel.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10014","checksum":"1a609937aa5275452822f45f2da17f07"}],"publication_status":"published","degree_awarded":"PhD","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"},{"relation":"part_of_dissertation","status":"public","id":"7489"}]},"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"],"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.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","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"},"title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","article_processing_charge":"No","author":[{"orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"day":"14","year":"2021","has_accepted_license":"1","date_created":"2021-09-13T11:12:34Z","doi":"10.15479/at:ista:10007","date_published":"2021-09-14T00:00:00Z","page":"300","oa":1,"publisher":"Institute of Science and Technology Austria"},{"file":[{"date_created":"2021-09-21T09:17:34Z","file_name":"tex_and_pictures.zip","creator":"cchlebak","date_updated":"2022-03-10T12:14:42Z","file_size":3876668,"checksum":"8cd60dcb8762e8f21867e21e8001e183","file_id":"10032","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed"},{"file_id":"10047","checksum":"9789e9d967c853c1503ec7f307170279","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-09-27T11:14:31Z","file_name":"thesis_portinale_Final (1).pdf","date_updated":"2021-09-27T11:14:31Z","file_size":2532673,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10022"},{"id":"9792","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7573"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["515"],"supervisor":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"date_updated":"2023-09-07T13:31:06Z","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"file_date_updated":"2022-03-10T12:14:42Z","_id":"10030","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)"},"day":"22","has_accepted_license":"1","year":"2021","date_published":"2021-09-22T00:00:00Z","doi":"10.15479/at:ista:10030","date_created":"2021-09-21T09:14:15Z","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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."},"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","author":[{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"article_processing_charge":"No","project":[{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}]},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9928"},{"status":"public","id":"8755","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"3cd1986efde5121d7581f6fcf9090da8","file_id":"9924","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"GeometricSuperinductorsForCQED.zip","date_created":"2021-08-16T09:33:21Z","file_size":151387283,"date_updated":"2021-09-06T08:39:47Z","creator":"mperuzzo"},{"creator":"mperuzzo","date_updated":"2021-09-06T08:39:47Z","file_size":17596344,"date_created":"2021-08-18T14:20:06Z","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9939","checksum":"50928c621cdf0775d7a5906b9dc8602c"},{"checksum":"37f486aa1b622fe44af00d627ec13f6c","file_id":"9940","content_type":"application/pdf","description":"Extra copy of the thesis as PDF/A-2b","relation":"other","access_level":"closed","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","date_created":"2021-08-18T14:20:09Z","file_size":17592425,"date_updated":"2021-09-06T08:39:47Z","creator":"mperuzzo"}],"alternative_title":["ISTA Thesis"],"month":"08","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","file_date_updated":"2021-09-06T08:39:47Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"date_updated":"2023-09-07T13:31:22Z","supervisor":[{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["539"],"type":"dissertation","keyword":["quantum computing","superinductor","quantum metrology"],"status":"public","_id":"9920","page":"149","date_created":"2021-08-16T09:44:09Z","date_published":"2021-08-19T00:00:00Z","doi":"10.15479/at:ista:9920","year":"2021","has_accepted_license":"1","day":"19","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo"}],"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","citation":{"ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","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.","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","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi: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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"day":"07","file":[{"file_id":"10424","checksum":"114e8f4b2c002c6c352416c12de2c695","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2021-12-07T11:13:52Z","file_name":"Thesis.zip","creator":"cchlebak","date_updated":"2022-03-10T12:10:25Z","file_size":394018},{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"cd15ae991ced352a9959815f794e657c","file_id":"10425","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"},{"success":1,"file_id":"10426","checksum":"e6899c798b75ba42fab9822bce309050","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_Piankov_combined.pdf","date_created":"2021-12-07T11:20:35Z","file_size":484965,"date_updated":"2021-12-07T11:20:35Z","creator":"cchlebak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2791-4585"]},"has_accepted_license":"1","publication_status":"published","degree_awarded":"MS","year":"2021","doi":"10.15479/at:ista:10422","date_published":"2021-12-07T00:00:00Z","date_created":"2021-12-07T10:48:06Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"12","alternative_title":["ISTA Master's Thesis"],"publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["530"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"citation":{"mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 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","ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","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.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria."},"date_updated":"2023-09-07T13:34:12Z","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"title":"Towards designer materials using customizable particle shape","file_date_updated":"2022-03-10T12:10:25Z","author":[{"first_name":"Anton","id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","full_name":"Piankov, Anton","last_name":"Piankov"}],"article_processing_charge":"No","_id":"10422","status":"public","type":"dissertation"},{"article_processing_charge":"No","author":[{"first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong"}],"title":"Underspecification in deep learning","citation":{"chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"125","date_created":"2021-05-24T13:06:23Z","doi":"10.15479/AT:ISTA:9418","date_published":"2021-05-30T00:00:00Z","year":"2021","has_accepted_license":"1","day":"30","type":"dissertation","status":"public","_id":"9418","file_date_updated":"2021-05-24T11:56:02Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_updated":"2023-09-08T11:11:12Z","supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"ddc":["000"],"alternative_title":["ISTA Thesis"],"month":"05","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"oa_version":"Published Version","related_material":{"record":[{"id":"7435","status":"deleted","relation":"part_of_dissertation"},{"status":"public","id":"7481","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9416","status":"public"},{"status":"public","id":"7479","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":2673905,"date_updated":"2021-05-24T11:22:29Z","creator":"bphuong","file_name":"mph-thesis-v519-pdfimages.pdf","date_created":"2021-05-24T11:22:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4f0abe64114cfed264f9d36e8d1197e3","file_id":"9419"},{"date_created":"2021-05-24T11:56:02Z","file_name":"thesis.zip","creator":"bphuong","date_updated":"2021-05-24T11:56:02Z","file_size":92995100,"checksum":"f5699e876bc770a9b0df8345a77720a2","file_id":"9420","access_level":"closed","relation":"source_file","content_type":"application/zip"}]},{"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4f412a1ee60952221b499a4b1268df35","file_id":"10225","file_size":2915234,"date_updated":"2021-11-08T14:12:22Z","creator":"vtoman","file_name":"toman_th_final.pdf","date_created":"2021-11-08T14:12:22Z"},{"checksum":"9584943f99127be2dd2963f6784c37d4","file_id":"10226","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"toman_thesis.zip","date_created":"2021-11-08T14:12:46Z","creator":"vtoman","file_size":8616056,"date_updated":"2021-11-09T09:00:50Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10190"},{"status":"public","id":"10191","relation":"part_of_dissertation"},{"status":"public","id":"9987","relation":"part_of_dissertation"},{"status":"public","id":"141","relation":"part_of_dissertation"}]},"ec_funded":1,"_id":"10199","type":"dissertation","status":"public","keyword":["concurrency","verification","model checking"],"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"date_updated":"2023-09-19T09:59:54Z","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"file_date_updated":"2021-11-09T09:00:50Z","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","day":"31","page":"166","doi":"10.15479/at:ista:10199","date_published":"2021-10-31T00:00:00Z","date_created":"2021-10-29T20:09:01Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","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"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"citation":{"chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. 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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Toman","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Improved verification techniques for concurrent systems"},{"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10044","status":"public"},{"id":"10049","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"637","relation":"part_of_dissertation"},{"id":"10041","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6430","status":"public"},{"id":"10048","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10082","checksum":"73a44345c683e81f3e765efbf86fdcc5","creator":"cchlebak","file_size":2104726,"date_updated":"2021-10-04T12:22:33Z","file_name":"thesis_pdfa.pdf","date_created":"2021-10-04T12:22:33Z"},{"checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","file_id":"10085","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"thesis_final (1).zip","date_created":"2021-10-05T07:04:37Z","creator":"cchlebak","file_size":9538359,"date_updated":"2022-03-10T12:15:18Z"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","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])."}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"file_date_updated":"2022-03-10T12:15:18Z","date_updated":"2023-10-17T09:24:07Z","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["519"],"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":"10035","page":"276","date_created":"2021-09-23T07:31:44Z","doi":"10.15479/at:ista:10035","date_published":"2021-09-23T00:00:00Z","year":"2021","has_accepted_license":"1","day":"23","oa":1,"publisher":"Institute of Science and Technology Austria","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","article_processing_charge":"No","author":[{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"}],"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","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}]},{"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"file_date_updated":"2022-03-28T12:55:12Z","date_updated":"2023-10-17T11:48:55Z","supervisor":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"ddc":["000"],"type":"dissertation","status":"public","_id":"10429","ec_funded":1,"related_material":{"record":[{"status":"public","id":"10432","relation":"part_of_dissertation"},{"id":"6673","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5965"},{"status":"public","id":"10435","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10436","checksum":"6bf14e9a523387328f016c0689f5e10e","file_size":2370859,"date_updated":"2021-12-09T17:47:49Z","creator":"gnadirad","file_name":"Thesis_Final_09_12_2021.pdf","date_created":"2021-12-09T17:47:49Z"},{"date_created":"2021-12-09T17:47:49Z","file_name":"Thesis_Final_09_12_2021.zip","date_updated":"2022-03-28T12:55:12Z","file_size":2596924,"creator":"gnadirad","file_id":"10437","checksum":"914d6c5ca86bd0add471971a8f4c4341","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"alternative_title":["ISTA Thesis"],"month":"12","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."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","last_name":"Nadiradze"}],"title":"On achieving scalability through relaxation","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.","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. 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.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"page":"132","date_created":"2021-12-08T21:52:28Z","date_published":"2021-12-09T00:00:00Z","doi":"10.15479/at:ista:10429","year":"2021","has_accepted_license":"1","day":"09","oa":1,"publisher":"Institute of Science and Technology Austria"},{"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)"},"status":"public","_id":"9733","file_date_updated":"2022-03-10T12:13:57Z","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"supervisor":[{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"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","ddc":["515","519","539"],"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9787"},{"relation":"part_of_dissertation","id":"9792","status":"public"},{"id":"9225","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9781","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9791"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"dfelicia","file_size":1958710,"date_updated":"2021-09-06T09:28:56Z","file_name":"Thesis_FeliciangeliA.pdf","date_created":"2021-08-19T14:03:48Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9944","checksum":"e88bb8ca43948abe060eb2d2fa719881"},{"relation":"source_file","access_level":"closed","content_type":"application/octet-stream","checksum":"72810843abee83705853505b3f8348aa","file_id":"9945","creator":"dfelicia","file_size":3771669,"date_updated":"2022-03-10T12:13:57Z","file_name":"thesis.7z","date_created":"2021-08-19T14:06:35Z"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"author":[{"last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario"}],"article_processing_charge":"No","title":"The polaron at strong coupling","citation":{"chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi: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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa":1,"page":"180","doi":"10.15479/at:ista:9733","date_published":"2021-08-20T00:00:00Z","date_created":"2021-07-27T15:48:30Z","has_accepted_license":"1","year":"2021","day":"20"},{"day":"13","year":"2021","has_accepted_license":"1","date_created":"2021-09-09T07:37:20Z","doi":"10.15479/at:ista:9992","date_published":"2021-09-13T00:00:00Z","page":"168","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","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","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."},"title":"Wound healing in the Arabidopsis root meristem","article_processing_charge":"No","author":[{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-09-15T22:30:26Z","file_size":25179004,"creator":"lhoermaye","date_created":"2021-09-09T07:29:48Z","file_name":"Thesis_vupload.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"c763064adaa720e16066c1a4f9682bbb","file_id":"9993"},{"embargo":"2021-09-09","file_id":"9996","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_vfinal_pdfa.pdf","date_created":"2021-09-09T14:25:08Z","file_size":6246900,"date_updated":"2021-09-15T22:30:26Z","creator":"lhoermaye"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"6351","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6943","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8002"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","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. "}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["575"],"date_updated":"2023-09-07T13:38:33Z","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"file_date_updated":"2021-09-15T22:30:26Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"_id":"9992","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"},{"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-07-02T22:30:06Z","file_size":131946790,"creator":"scaballe","date_created":"2021-07-01T14:48:54Z","file_name":"PhDThesis_SCM.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"e039225a47ef32666d59bf35ddd30ecf","file_id":"9624"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9625","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","embargo":"2022-07-01","date_updated":"2022-07-02T22:30:06Z","file_size":17094958,"creator":"scaballe","date_created":"2021-07-01T14:46:25Z","file_name":"PhDThesis_SCM.pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"related_material":{"record":[{"status":"public","id":"9750","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9006","status":"public"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"month":"07","alternative_title":["ISTA Thesis"],"ddc":["570"],"date_updated":"2023-09-07T13:33:27Z","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"file_date_updated":"2022-07-02T22:30:06Z","_id":"9623","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","year":"2021","has_accepted_license":"1","date_created":"2021-07-01T14:50:17Z","doi":"10.15479/at:ista:9623","date_published":"2021-07-01T00:00:00Z","page":"111","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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.","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."},"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","article_processing_charge":"No","author":[{"orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"}]},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/x-zip-compressed","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"10061","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","date_updated":"2022-12-20T23:30:07Z","file_size":32397600,"creator":"djirovec","date_created":"2021-09-30T14:29:14Z","file_name":"PHD_Thesis_Jirovec_Source.zip"},{"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","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-10-06","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_id":"10087"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8831"},{"relation":"part_of_dissertation","id":"10065","status":"public"},{"status":"public","id":"10066","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8909"},{"relation":"part_of_dissertation","status":"public","id":"5816"}]},"_id":"10058","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":["qubits","quantum computing","holes"],"supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"date_updated":"2023-09-08T11:41:08Z","ddc":["621","539"],"file_date_updated":"2022-12-20T23:30:07Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","day":"05","page":"151","date_published":"2021-10-05T00:00:00Z","doi":"10.15479/at:ista:10058","date_created":"2021-09-30T07:53:49Z","project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"citation":{"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","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 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.","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.","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"article_processing_charge":"No","title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases"},{"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","creator":"khuljev","file_size":47799741,"date_updated":"2022-05-21T22:30:04Z","file_name":"KHuljev_Thesis_corrections.docx","date_created":"2021-05-17T12:29:12Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9401","checksum":"bf512f8a1e572a543778fc4b227c01ba","embargo":"2022-05-20","creator":"khuljev","date_updated":"2022-05-21T22:30:04Z","file_size":16542131,"date_created":"2021-05-18T14:50:28Z","file_name":"new_KHuljev_Thesis_corrections.pdf"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","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"}],"date_updated":"2023-09-07T13:32:32Z","ddc":["571"],"department":[{"_id":"CaHe"},{"_id":"GradSch"}],"file_date_updated":"2022-05-21T22:30:04Z","_id":"9397","type":"dissertation","status":"public","has_accepted_license":"1","year":"2021","day":"18","page":"101","doi":"10.15479/at:ista:9397","date_published":"2021-05-18T00:00:00Z","date_created":"2021-05-17T12:31:30Z","publisher":"Institute of Science and Technology Austria","oa":1,"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.","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.","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.","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","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"},{"article_processing_charge":"No","author":[{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","full_name":"Kleindienst, David"}],"title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","citation":{"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.","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.","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.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"124","date_created":"2021-06-17T14:10:47Z","doi":"10.15479/at:ista:9562","date_published":"2021-06-01T00:00:00Z","year":"2021","has_accepted_license":"1","day":"01","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"date_updated":"2023-09-11T12:55:53Z","supervisor":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"type":"dissertation","status":"public","_id":"9562","related_material":{"record":[{"relation":"part_of_dissertation","id":"9756","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9437"},{"relation":"part_of_dissertation","status":"public","id":"8532"},{"id":"612","status":"public","relation":"part_of_dissertation"}]},"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","embargo":"2022-07-01","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z","creator":"dkleindienst","file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z"},{"creator":"dkleindienst","file_size":369804895,"date_updated":"2022-07-02T22:30:04Z","file_name":"Thesis_source.zip","date_created":"2021-06-17T14:04:30Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","checksum":"3bcf63a2b19e5b6663be051bea332748","file_id":"9564"}],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version"},{"related_material":{"record":[{"id":"1386","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"311"},{"relation":"part_of_dissertation","status":"public","id":"6056"},{"id":"6380","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"639","status":"public"},{"relation":"part_of_dissertation","id":"66","status":"public"},{"status":"public","id":"6780","relation":"part_of_dissertation"},{"status":"public","id":"6918","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7810","status":"public"},{"relation":"part_of_dissertation","id":"6175","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6378"},{"id":"6490","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"7014","relation":"part_of_dissertation"},{"status":"public","id":"8089","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8728","status":"public"},{"status":"public","id":"7158","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5977","status":"public"},{"status":"public","id":"6009","relation":"part_of_dissertation"},{"id":"6340","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"949","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"embargo":"2021-12-22","file_id":"8969","checksum":"d1b9db3725aed34dadd81274aeb9426c","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis-pdfa.pdf","date_created":"2020-12-22T20:08:44Z","file_size":5251507,"date_updated":"2021-12-23T23:30:04Z","creator":"akafshda"},{"file_name":"source.zip","date_created":"2020-12-22T20:08:50Z","creator":"akafshda","file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","file_id":"8970","checksum":"1661df7b393e6866d2460eba3c905130","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2021-12-23T23:30:04Z","ddc":["005"],"date_updated":"2023-09-22T10:03:21Z","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"status":"public","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","_id":"8934","date_created":"2020-12-10T12:17:07Z","doi":"10.15479/AT:ISTA:8934","date_published":"2021-01-01T00:00:00Z","page":"278","day":"01","year":"2021","has_accepted_license":"1","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).","title":"Parameterized and algebro-geometric advances in static program analysis","article_processing_charge":"No","author":[{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","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.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","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."},"project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2021-11-18T15:05:06Z","doi":"10.15479/at:ista:10307","date_published":"2021-11-18T00:00:00Z","page":"73","day":"18","year":"2021","has_accepted_license":"1","title":"Pathogenic Escherichia coli hijack the host immune response","article_processing_charge":"No","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","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","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.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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"}],"related_material":{"record":[{"id":"10316","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-11-18T15:07:31Z","file_name":"ThesisTomasekKathrin.pdf","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","file_size":13266088,"file_id":"10308","checksum":"b39c9e0ef18d0484d537a67551effd02","embargo":"2022-11-18","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_size":7539509,"date_updated":"2022-12-20T23:30:05Z","creator":"ktomasek","file_name":"ThesisTomasekKathrin.docx","date_created":"2021-11-18T15:07:46Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","file_id":"10309"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"status":"public","type":"dissertation","_id":"10307","file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"ddc":["570"],"date_updated":"2023-09-07T13:34:38Z","supervisor":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}]},{"date_updated":"2023-09-19T14:42:45Z","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"ddc":["580","581"],"file_date_updated":"2022-12-20T23:30:06Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"_id":"10303","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":[{"file_size":28005730,"date_updated":"2022-12-20T23:30:06Z","creator":"rabualia","file_name":"AbualiaPhDthesisfinalv3.pdf","date_created":"2021-11-22T14:48:21Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-11-23","file_id":"10331","checksum":"dea38b98aa4da1cea03dcd0f10862818"},{"checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_id":"10332","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2021-11-22T14:48:34Z","file_name":"AbualiaPhDthesisfinalv3.docx","date_updated":"2022-12-20T23:30:06Z","file_size":62841883,"creator":"rabualia"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"id":"9913","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"47","status":"public"}]},"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","citation":{"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.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"}],"title":"Role of hormones in nitrate regulated growth","year":"2021","has_accepted_license":"1","day":"22","page":"139","date_created":"2021-11-18T11:20:59Z","doi":"10.15479/at:ista:10303","date_published":"2021-11-22T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria"}]