[{"abstract":[{"lang":"eng","text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. "}],"type":"dissertation","month":"09","file_date_updated":"2022-09-12T11:24:21Z","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"corr_author":"1","acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"degree_awarded":"PhD","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","article_processing_charge":"No","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_created":"2022-09-08T21:53:03Z","doi":"10.15479/at:ista:12072","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"12076","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12077"}]},"_id":"12072","date_published":"2022-09-08T00:00:00Z","oa":1,"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"alternative_title":["ISTA Thesis"],"day":"08","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"has_accepted_license":"1","file":[{"file_id":"12073","relation":"main_file","file_name":"Thesis_final_draft.pdf","creator":"ashute","success":1,"date_created":"2022-09-08T21:50:34Z","date_updated":"2022-09-08T21:50:34Z","access_level":"open_access","file_size":1907386,"content_type":"application/pdf","checksum":"bf073344320e05d92c224786cec2e92d"},{"access_level":"closed","date_updated":"2022-09-12T11:24:21Z","date_created":"2022-09-08T21:50:42Z","checksum":"b054ac6baa09f70e8235403a4abbed80","file_size":495393,"content_type":"application/octet-stream","creator":"ashute","file_name":"athesis.tex","relation":"source_file","file_id":"12074"},{"file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","creator":"ashute","file_id":"12078","relation":"source_file","access_level":"closed","date_updated":"2022-09-12T11:24:21Z","date_created":"2022-09-09T12:05:00Z","file_size":944534,"checksum":"0a31e905f1cff5eb8110978cc90e1e79","content_type":"application/x-zip-compressed"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["512"],"citation":{"ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072.","mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022."},"page":"208","year":"2022","author":[{"id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810","first_name":"Alec L","last_name":"Shute","full_name":"Shute, Alec L"}],"date_updated":"2026-04-07T14:13:35Z"},{"page":"113","ddc":["570"],"citation":{"chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria.","mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022."},"status":"public","ec_funded":1,"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"file_size":14581024,"content_type":"application/pdf","checksum":"e54a3e69b83ebf166544164afd25608e","access_level":"open_access","date_updated":"2023-01-25T10:52:46Z","success":1,"date_created":"2023-01-25T10:52:46Z","creator":"cchlebak","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","relation":"main_file","file_id":"12369"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"date_updated":"2026-04-07T14:13:19Z","year":"2022","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan","first_name":"Feyza N"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","alternative_title":["ISTA Thesis"],"day":"29","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2022-09-29T00:00:00Z","related_material":{"record":[{"id":"9350","relation":"part_of_dissertation","status":"public"}]},"_id":"12368","corr_author":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-025-1 "]},"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"month":"09","file_date_updated":"2023-01-25T10:52:46Z","type":"dissertation","article_processing_charge":"No","date_created":"2023-01-25T10:43:24Z","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.15479/at:ista:12153","oa_version":"Published Version","title":"Remodeling of E-cadherin-mediated contacts via cortical flows","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"degree_awarded":"PhD"},{"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"type":"dissertation","file_date_updated":"2022-08-11T16:09:19Z","month":"08","abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"corr_author":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"date_created":"2022-08-10T15:51:19Z","oa_version":"Published Version","doi":"10.15479/at:ista:11777","article_processing_charge":"No","title":"High-dimensional expansion and crossing numbers of simplicial complexes","language":[{"iso":"eng"}],"publication_status":"published","_id":"11777","date_published":"2022-08-11T00:00:00Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","day":"11","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"publisher":"Institute of Science and Technology Austria","file":[{"checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","file_size":16828,"content_type":"text/x-python","date_created":"2022-08-10T15:34:04Z","date_updated":"2022-08-10T15:34:04Z","access_level":"open_access","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","relation":"supplementary_material","file_id":"11780","creator":"pwild","file_name":"flags.py"},{"file_id":"11781","relation":"supplementary_material","file_name":"lowerbound.cpp","creator":"pwild","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_size":12226,"content_type":"text/x-c++src","date_created":"2022-08-10T15:34:10Z","description":"Code for proof of Lemma 8.20 in Thesis","date_updated":"2022-08-10T15:34:10Z","access_level":"open_access"},{"file_size":3240,"checksum":"4cf81455c49e5dec3b9b2e3980137eeb","content_type":"text/x-python","date_created":"2022-08-10T15:34:17Z","description":"Code for proof of Proposition 7.9 in Thesis","date_updated":"2022-08-10T15:34:17Z","access_level":"open_access","file_id":"11782","relation":"supplementary_material","file_name":"upperbound.py","creator":"pwild"},{"checksum":"4e96575b10cbe4e0d0db2045b2847774","file_size":5086282,"content_type":"application/pdf","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","date_updated":"2022-08-11T16:08:33Z","access_level":"open_access","date_created":"2022-08-11T16:08:33Z","file_name":"finalthesisPascalWildPDFA.pdf","creator":"pwild","file_id":"11809","relation":"main_file"},{"checksum":"92d94842a1fb6dca5808448137573b2e","content_type":"application/zip","file_size":18150068,"date_created":"2022-08-11T16:09:19Z","access_level":"closed","date_updated":"2022-08-11T16:09:19Z","relation":"source_file","file_id":"11810","creator":"pwild","file_name":"ThesisSubmission.zip"}],"has_accepted_license":"1","ec_funded":1,"ddc":["500","516","514"],"page":"170","citation":{"apa":"Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11777","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology Austria, 2022.","mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11777.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology Austria, 2022.","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11777.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology Austria."},"status":"public","author":[{"full_name":"Wild, Pascal","first_name":"Pascal","last_name":"Wild","id":"4C20D868-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","date_updated":"2026-04-07T14:18:26Z"},{"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"degree_awarded":"PhD","title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","article_processing_charge":"No","doi":"10.15479/at:ista:11473","date_created":"2022-06-30T12:15:03Z","oa_version":"Published Version","abstract":[{"text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n","lang":"eng"}],"file_date_updated":"2022-07-05T08:17:12Z","type":"dissertation","month":"07","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","related_material":{"record":[{"id":"10564","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8705","relation":"part_of_dissertation"}]},"_id":"11473","date_published":"2022-07-01T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"year":"2022","author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof","first_name":"Krzysztof","last_name":"Mysliwy"}],"date_updated":"2026-04-07T14:14:52Z","acknowledged_ssus":[{"_id":"SSU"}],"ec_funded":1,"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","file_id":"11486","creator":"kmysliwy","file_name":"thes1_no_isbn_2_1b.pdf","checksum":"7970714a20a6052f75fb27a6c3e9976e","content_type":"application/pdf","file_size":1830973,"date_created":"2022-07-05T08:12:56Z","success":1,"date_updated":"2022-07-05T08:12:56Z","access_level":"open_access"},{"date_updated":"2022-07-05T08:17:12Z","access_level":"closed","date_created":"2022-07-05T08:15:52Z","checksum":"647a2011fdf56277096c9350fefe1097","file_size":5831060,"content_type":"application/zip","file_name":"thes_source.zip","creator":"kmysliwy","file_id":"11487","relation":"source_file"}],"status":"public","ddc":["515","539"],"page":"138","citation":{"chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473","mla":"Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473"}},{"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2022-08-23T00:00:00Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11995"}]},"_id":"11945","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"project":[{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level."}],"month":"08","type":"dissertation","file_date_updated":"2022-08-25T09:33:31Z","article_processing_charge":"No","oa_version":"Published Version","date_created":"2022-08-23T11:33:11Z","doi":"10.15479/at:ista:11945","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"degree_awarded":"PhD","ddc":["570"],"citation":{"short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria.","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945.","apa":"Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945","mla":"Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945.","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022."},"page":"133","status":"public","has_accepted_license":"1","file":[{"date_created":"2022-08-25T08:59:57Z","success":1,"access_level":"open_access","date_updated":"2022-08-25T08:59:57Z","checksum":"61b1b666a210ff7cdd0e95ea75207a13","content_type":"application/pdf","file_size":28079331,"relation":"main_file","file_id":"11970","creator":"rschulz","file_name":"Thesis_Rouven_Schulz_2022_final.pdf"},{"date_created":"2022-08-25T09:00:11Z","date_updated":"2022-08-25T09:33:31Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":27226963,"checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","relation":"source_file","file_id":"11971","creator":"rschulz","file_name":"Thesis_Rouven_Schulz_2022_final.docx"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"date_updated":"2026-04-07T14:17:59Z","year":"2022","author":[{"last_name":"Schulz","first_name":"Rouven","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"supervisor":[{"full_name":"Siegert, Sandra","last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","alternative_title":["ISTA Thesis"],"day":"23"},{"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"open_access","date_updated":"2022-07-25T09:08:47Z","date_created":"2022-07-25T09:08:47Z","content_type":"application/pdf","file_size":9730864,"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","creator":"mgallei","file_name":"Thesis_Gallei.pdf","relation":"main_file","file_id":"11645"},{"date_updated":"2022-07-25T09:39:58Z","access_level":"closed","date_created":"2022-07-25T09:09:09Z","file_size":19560720,"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gallei_source.docx","creator":"mgallei","file_id":"11646","relation":"source_file"},{"file_name":"Thesis_Gallei_to_print.pdf","creator":"mgallei","file_id":"11647","relation":"source_file","description":"This is the print version of the thesis including the full appendix","access_level":"closed","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:32Z","content_type":"application/pdf","checksum":"3994f7f20058941b5bb8a16886b21e71","file_size":24542837},{"checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","content_type":"application/pdf","file_size":15435966,"date_created":"2022-07-25T11:48:45Z","access_level":"open_access","date_updated":"2022-07-25T11:48:45Z","file_id":"11650","relation":"main_file","file_name":"Thesis_Gallei_Appendix.pdf","creator":"mgallei"}],"has_accepted_license":"1","ec_funded":1,"status":"public","ddc":["575"],"citation":{"ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria."},"page":"248","author":[{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei"}],"year":"2022","date_updated":"2026-04-07T14:18:58Z","oa":1,"day":"20","alternative_title":["ISTA Thesis"],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Shani, Eilon","first_name":"Eilon","last_name":"Shani"}],"language":[{"iso":"eng"}],"publication_status":"published","_id":"11626","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8138"},{"status":"public","relation":"part_of_dissertation","id":"7142"},{"id":"6260","relation":"part_of_dissertation","status":"public"},{"id":"10411","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8931","relation":"part_of_dissertation"},{"id":"7465","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9287","relation":"part_of_dissertation"}]},"date_published":"2022-07-20T00:00:00Z","file_date_updated":"2022-07-25T11:48:45Z","type":"dissertation","month":"07","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"corr_author":"1","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","doi":"10.15479/at:ista:11626","date_created":"2022-07-20T11:21:53Z","oa_version":"Published Version","article_processing_charge":"No"},{"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.","lang":"eng"}],"type":"dissertation","month":"03","file_date_updated":"2022-03-10T12:11:48Z","corr_author":"1","publication_identifier":{"isbn":["978-3-99078-015-2"],"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"degree_awarded":"PhD","article_processing_charge":"No","doi":"10.15479/at:ista:10799","oa_version":"Published Version","date_created":"2022-02-28T13:03:49Z","title":"Robustness and fairness in machine learning","language":[{"iso":"eng"}],"publication_status":"published","keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10802"},{"status":"public","id":"10803","relation":"part_of_dissertation"},{"id":"6590","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8724"}]},"_id":"10799","date_published":"2022-03-08T00:00:00Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","alternative_title":["ISTA Thesis"],"day":"08","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","ec_funded":1,"file":[{"relation":"main_file","file_id":"10823","creator":"nkonstan","file_name":"thesis.pdf","date_created":"2022-03-06T11:42:54Z","success":1,"access_level":"open_access","date_updated":"2022-03-06T11:42:54Z","content_type":"application/pdf","file_size":4204905,"checksum":"626bc523ae8822d20e635d0e2d95182e"},{"creator":"nkonstan","file_name":"thesis.zip","relation":"source_file","file_id":"10824","file_size":22841103,"checksum":"e2ca2b88350ac8ea1515b948885cbcb1","content_type":"application/x-zip-compressed","date_updated":"2022-03-10T12:11:48Z","access_level":"closed","date_created":"2022-03-06T11:42:57Z"}],"publisher":"Institute of Science and Technology Austria","ddc":["000"],"citation":{"ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799.","short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022.","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799","mla":"Konstantinov, Nikola H. Robustness and Fairness in Machine Learning. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","apa":"Konstantinov, N. H. (2022). Robustness and fairness in machine learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799"},"page":"176","status":"public","year":"2022","author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0009-5204-7621","full_name":"Konstantinov, Nikola H","first_name":"Nikola H","last_name":"Konstantinov"}],"date_updated":"2026-04-07T14:19:48Z"},{"file_date_updated":"2022-02-22T07:20:12Z","month":"02","type":"dissertation","abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"title":"Analytic and machine learning approaches to composite quantum impurities","date_created":"2022-02-16T13:27:37Z","doi":"10.15479/at:ista:10759","oa_version":"Published Version","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published","_id":"10759","related_material":{"record":[{"status":"public","id":"10762","relation":"part_of_dissertation"},{"id":"415","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8644","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7956","status":"public"}]},"date_published":"2022-02-21T00:00:00Z","oa":1,"day":"21","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"closed","date_updated":"2022-02-22T07:20:12Z","date_created":"2022-02-21T13:58:16Z","content_type":"application/zip","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_size":17668233,"creator":"wrzadkow","file_name":"Rzadkowski_thesis_final_source.zip","relation":"source_file","file_id":"10785"},{"date_created":"2022-02-21T14:02:54Z","success":1,"access_level":"open_access","date_updated":"2022-02-21T14:02:54Z","file_size":13307331,"checksum":"22d2d7af37ca31f6b1730c26cac7bced","content_type":"application/pdf","file_id":"10786","relation":"main_file","file_name":"Rzadkowski_thesis_final.pdf","creator":"wrzadkow"}],"ec_funded":1,"has_accepted_license":"1","status":"public","citation":{"short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.","apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759"},"page":"120","ddc":["530"],"author":[{"full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski","orcid":"0000-0002-1106-4419","id":"48C55298-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","date_updated":"2026-04-07T14:20:12Z"},{"publisher":"Springer Nature","file":[{"creator":"dernst","file_name":"2022_BulletinMathBiology_Saona.pdf","relation":"main_file","file_id":"11455","file_size":463025,"content_type":"application/pdf","checksum":"05a1fe7d10914a00c2bca9b447993a65","date_updated":"2022-06-20T07:51:32Z","access_level":"open_access","success":1,"date_created":"2022-06-20T07:51:32Z"}],"ec_funded":1,"has_accepted_license":"1","scopus_import":"1","citation":{"ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z"},"ddc":["510","570"],"article_number":"74","publication":"Bulletin of Mathematical Biology","status":"public","author":[{"first_name":"Raimundo J","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova"}],"year":"2022","date_updated":"2026-04-15T08:51:10Z","oa":1,"article_type":"original","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","issue":"8","volume":84,"language":[{"iso":"eng"}],"pmid":1,"intvolume":" 84","publication_status":"published","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"isi":1,"_id":"11447","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}]},"date_published":"2022-06-17T00:00:00Z","external_id":{"isi":["000812509800001"],"pmid":["35713756"]},"project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181"}],"month":"06","type":"journal_article","file_date_updated":"2022-06-20T07:51:32Z","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","corr_author":"1","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"doi":"10.1007/s11538-022-01029-z","date_created":"2022-06-17T16:16:15Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions"},{"date_updated":"2026-04-16T08:20:52Z","year":"2022","author":[{"last_name":"Brooks","first_name":"Morris","full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"}],"ddc":["500"],"page":"196","citation":{"mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390","apa":"Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria."},"status":"public","has_accepted_license":"1","ec_funded":1,"file":[{"relation":"main_file","file_id":"12391","creator":"cchlebak","file_name":"Brooks_Thesis.pdf","file_size":3095225,"content_type":"application/pdf","checksum":"b31460e937f33b557abb40ebef02b567","date_created":"2023-01-26T10:02:34Z","success":1,"access_level":"open_access","date_updated":"2023-01-26T10:02:34Z"},{"date_updated":"2023-01-26T10:02:42Z","access_level":"closed","date_created":"2023-01-26T10:02:42Z","content_type":"application/octet-stream","checksum":"9751869fa5e7981588ad4228f4fd4bd6","file_size":809842,"file_name":"Brooks_Thesis.tex","creator":"cchlebak","file_id":"12392","relation":"source_file"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","alternative_title":["ISTA Thesis"],"day":"15","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa":1,"date_published":"2022-12-15T00:00:00Z","_id":"12390","related_material":{"record":[{"id":"9005","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.15479/at:ista:12390","oa_version":"Published Version","date_created":"2023-01-26T10:00:42Z","title":"Translation-invariant quantum systems with effectively broken symmetry","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"degree_awarded":"PhD","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"abstract":[{"text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n","lang":"eng"}],"file_date_updated":"2023-01-26T10:02:42Z","type":"dissertation","month":"12"},{"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"month":"09","type":"dissertation","file_date_updated":"2023-02-02T09:39:25Z","abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"corr_author":"1","publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"oa_version":"Published Version","date_created":"2023-01-24T10:49:46Z","doi":"10.15479/at:ista:12103","article_processing_charge":"No","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","language":[{"iso":"eng"}],"publication_status":"published","_id":"12358","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11736"},{"id":"9818","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8385","relation":"part_of_dissertation"}]},"date_published":"2022-09-22T00:00:00Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","day":"22","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","file_id":"12371","creator":"cchlebak","file_name":"thesis_gsperl.pdf","date_created":"2023-01-25T12:04:41Z","date_updated":"2023-02-02T09:29:57Z","title":"Thesis","access_level":"open_access","description":"This is the main PDF file of the thesis. File size: 105 MB","content_type":"application/pdf","checksum":"083722acbb8115e52e3b0fdec6226769","file_size":104497530},{"creator":"cchlebak","file_name":"thesis_gsperl_compressed.pdf","relation":"main_file","file_id":"12483","title":"Thesis (compressed 23MB)","date_updated":"2023-02-02T09:33:37Z","access_level":"open_access","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","date_created":"2023-02-02T09:33:37Z","checksum":"511f82025e5fcb70bff4731d6896ca07","content_type":"application/pdf","file_size":23183710},{"date_updated":"2023-02-02T09:39:25Z","access_level":"open_access","date_created":"2023-02-02T09:39:25Z","content_type":"application/x-zip-compressed","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_size":98382247,"file_name":"thesis-source.zip","creator":"cchlebak","file_id":"12484","relation":"source_file"}],"has_accepted_license":"1","ec_funded":1,"ddc":["000","620"],"page":"138","citation":{"ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","apa":"Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103."},"status":"public","author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg","first_name":"Georg","last_name":"Sperl"}],"year":"2022","acknowledged_ssus":[{"_id":"SSU"}],"date_updated":"2026-04-16T08:31:54Z"},{"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2022-05-12T00:00:00Z","keyword":["neural networks","verification","machine learning"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11366"},{"relation":"part_of_dissertation","id":"10665","status":"public"},{"status":"public","id":"10667","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10666","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7808"}]},"_id":"11362","corr_author":"1","publication_identifier":{"isbn":["978-3-99078-017-6"]},"project":[{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"file_date_updated":"2022-05-17T15:19:39Z","type":"dissertation","month":"05","abstract":[{"lang":"eng","text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks."}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","date_created":"2022-05-12T07:14:01Z","oa_version":"Published Version","doi":"10.15479/at:ista:11362","article_processing_charge":"No","title":"Learning verifiable representations","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"ddc":["004"],"citation":{"short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.","mla":"Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.","apa":"Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362","ama":"Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022."},"page":"124","status":"public","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/zip","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","file_size":13210143,"access_level":"closed","date_updated":"2022-05-13T12:49:00Z","date_created":"2022-05-13T12:33:26Z","file_name":"src.zip","creator":"mlechner","file_id":"11378","relation":"source_file"},{"file_size":2732536,"content_type":"application/pdf","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","date_created":"2022-05-16T08:02:28Z","access_level":"open_access","date_updated":"2022-05-17T15:19:39Z","file_id":"11382","relation":"main_file","file_name":"thesis_main-a2.pdf","creator":"mlechner"}],"ec_funded":1,"has_accepted_license":"1","date_updated":"2026-04-16T09:46:06Z","author":[{"first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"oa":1,"supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"12","alternative_title":["ISTA Thesis"]},{"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","article_processing_charge":"No","doi":"10.15479/AT:ISTA:11653","date_created":"2022-07-26T11:01:47Z","oa_version":"Published Version","day":"05","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"file_date_updated":"2022-08-08T22:30:04Z","month":"08","type":"research_data","oa":1,"date_updated":"2025-04-15T08:34:17Z","date_published":"2022-08-05T00:00:00Z","_id":"11653","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12248"}]},"contributor":[{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"Hontoria ","first_name":"Francisco"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"year":"2022","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N"}],"status":"public","citation":{"ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","mla":"Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.","short":"M.N. Elkrewi, (2022).","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653."},"ddc":["570"],"has_accepted_license":"1","file":[{"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","content_type":"application/x-zip-compressed","file_size":2209382998,"date_created":"2022-07-26T12:37:52Z","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","date_updated":"2022-08-08T22:30:04Z","title":"Supplementary Datasets","access_level":"open_access","file_id":"11655","embargo":"2022-08-07","relation":"main_file","file_name":"Data.zip","creator":"melkrewi"}],"publisher":"Institute of Science and Technology Austria"},{"corr_author":"1","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","abstract":[{"text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. 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The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n"}],"month":"04","file_date_updated":"2023-04-20T22:30:03Z","type":"dissertation","project":[{"call_identifier":"H2020","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"}],"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","related_material":{"record":[{"status":"public","id":"7473","relation":"part_of_dissertation"},{"id":"11222","relation":"part_of_dissertation","status":"public"}]},"_id":"11196","date_published":"2022-04-20T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published"},{"oa":1,"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"day":"07","supervisor":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer"}],"ec_funded":1,"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2023-02-03T23:30:03Z","access_level":"closed","date_created":"2022-02-04T15:36:12Z","embargo_to":"open_access","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":6757886,"creator":"smetzler","file_name":"Thesis_Sina_Metzler.docx","relation":"source_file","file_id":"10728"},{"checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","file_size":6314921,"content_type":"application/pdf","date_updated":"2023-02-03T23:30:03Z","access_level":"open_access","date_created":"2022-02-04T15:36:43Z","file_name":"Thesis_Sina_Metzler_A2.pdf","creator":"smetzler","file_id":"10730","embargo":"2023-02-02","relation":"main_file"},{"file_size":6882557,"checksum":"dedd14b7be7a75d63018dbfc68dd8113","content_type":"application/pdf","date_updated":"2023-02-04T23:30:03Z","access_level":"open_access","date_created":"2022-02-07T10:35:02Z","creator":"smetzler","file_name":"Thesis_Sina_Metzler_print.pdf","relation":"main_file","embargo":"2023-02-02","file_id":"10742"}],"citation":{"chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","apa":"Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727","mla":"Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022."},"ddc":["570"],"status":"public","year":"2022","author":[{"first_name":"Sina","last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"date_updated":"2026-04-07T14:30:18Z","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history."}],"file_date_updated":"2023-02-04T23:30:03Z","type":"dissertation","month":"02","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"degree_awarded":"PhD","article_processing_charge":"No","oa_version":"Published Version","date_created":"2022-02-04T15:45:12Z","doi":"10.15479/AT:ISTA:10727","title":"Pathogen-mediated sexual selection and immunization in ant colonies","language":[{"iso":"eng"}],"publication_status":"published","_id":"10727","date_published":"2022-02-07T00:00:00Z"},{"page":"128","citation":{"ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11879.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:10.15479/at:ista:11879","mla":"Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11879.","apa":"Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11879","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022."},"ddc":["580"],"status":"public","file":[{"file_size":11113608,"checksum":"a2c2fdc28002538840490bfa6a08b2cb","content_type":"application/pdf","date_created":"2022-08-17T12:08:49Z","date_updated":"2023-09-09T22:30:03Z","access_level":"open_access","embargo":"2023-09-08","relation":"main_file","file_id":"11907","creator":"cartner","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf"},{"date_updated":"2023-09-09T22:30:03Z","access_level":"closed","date_created":"2022-08-17T12:08:59Z","embargo_to":"open_access","checksum":"66b461c074b815fbe63481b3f46a9f43","file_size":19097730,"content_type":"application/octet-stream","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","creator":"cartner","file_id":"11908","relation":"source_file"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"date_updated":"2026-04-07T14:30:39Z","author":[{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina"}],"year":"2022","oa":1,"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","day":"17","alternative_title":["ISTA Thesis"],"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2022-08-17T00:00:00Z","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"_id":"11879","acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","corr_author":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-022-0"]},"project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"type":"dissertation","month":"08","file_date_updated":"2023-09-09T22:30:03Z","abstract":[{"text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT.","lang":"eng"}],"doi":"10.15479/at:ista:11879","oa_version":"Published Version","date_created":"2022-08-17T07:58:53Z","article_processing_charge":"No","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"EvBe"}]},{"author":[{"last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","date_updated":"2026-04-07T14:30:57Z","publisher":"Institute of Science and Technology Austria","file":[{"file_name":"220923_Thesis_CDotter_Final.pdf","creator":"cchlebak","file_id":"12365","relation":"main_file","embargo":"2023-09-19","access_level":"open_access","date_updated":"2023-09-20T22:30:03Z","date_created":"2023-01-24T13:15:45Z","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","file_size":20457465,"content_type":"application/pdf"},{"creator":"cchlebak","file_name":"latex_source_CDotter_Thesis_2022.zip","relation":"source_file","file_id":"12482","content_type":"application/x-zip-compressed","file_size":22433512,"checksum":"ad01bb20da163be6893b7af832e58419","date_updated":"2023-09-20T22:30:03Z","access_level":"closed","date_created":"2023-02-02T09:15:35Z","embargo_to":"open_access"}],"ec_funded":1,"has_accepted_license":"1","page":"152","citation":{"chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","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","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi: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.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022."},"ddc":["570"],"status":"public","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"19","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia"}],"oa":1,"_id":"12364","related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"id":"3","relation":"part_of_dissertation","status":"public"}]},"date_published":"2022-09-19T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"date_created":"2023-01-24T13:09:57Z","oa_version":"Published Version","doi":"10.15479/at:ista:12094","article_processing_charge":"No","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"I04205","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-09-20T22:30:03Z","type":"dissertation","month":"09","abstract":[{"lang":"eng","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."}],"corr_author":"1","publication_identifier":{"issn":["2663-337X"]}},{"supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"16","alternative_title":["ISTA Thesis"],"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"date_updated":"2026-04-07T14:31:19Z","author":[{"first_name":"Marijo","last_name":"Jevtic","full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","ddc":["570"],"page":"108","citation":{"chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393","apa":"Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11393","mla":"Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11393.","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022."},"status":"public","publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2023-05-17T22:30:03Z","access_level":"closed","date_created":"2022-05-17T09:08:06Z","embargo_to":"open_access","file_size":56427603,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"8fc695d88020d70d231dad0e9f10b138","creator":"cchlebak","file_name":"MJ thesis.docx","relation":"source_file","file_id":"11395"},{"content_type":"application/pdf","file_size":4351981,"checksum":"c1dd20a1aece521b3500607b00e463d6","date_updated":"2023-05-17T22:30:03Z","access_level":"open_access","date_created":"2022-05-17T12:09:25Z","file_name":"MJ_thesis_PDFA.pdf","creator":"cchlebak","file_id":"11397","embargo":"2023-05-16","relation":"main_file"}],"has_accepted_license":"1","doi":"10.15479/at:ista:11393","oa_version":"Published Version","date_created":"2022-05-17T08:57:41Z","article_processing_charge":"No","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"RySh"}],"corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"month":"05","file_date_updated":"2023-05-17T22:30:03Z","type":"dissertation","abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"date_published":"2022-05-16T00:00:00Z","_id":"11393","related_material":{"record":[{"relation":"part_of_dissertation","id":"7391","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}]},{"date_updated":"2026-04-07T14:22:39Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"author":[{"last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"}],"year":"2022","status":"public","page":"168","ddc":["530"],"citation":{"ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:10.15479/at:ista:12132","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","apa":"Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132","mla":"Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132."},"file":[{"file_size":56076868,"checksum":"39eabb1e006b41335f17f3b29af09648","content_type":"application/pdf","date_updated":"2023-01-26T23:30:44Z","access_level":"open_access","date_created":"2023-01-25T09:41:49Z","file_name":"Final_Thesis_ES_Redchenko.pdf","creator":"cchlebak","file_id":"12367","embargo":"2022-12-28","relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"has_accepted_license":"1","supervisor":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"day":"26","alternative_title":["ISTA Thesis"],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_published":"2022-09-26T00:00:00Z","_id":"12366","publication_status":"published","language":[{"iso":"eng"}],"title":"Controllable states of superconducting Qubit ensembles","doi":"10.15479/at:ista:12132","oa_version":"Published Version","date_created":"2023-01-25T09:17:02Z","article_processing_charge":"No","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]},"corr_author":"1","file_date_updated":"2023-01-26T23:30:44Z","month":"09","type":"dissertation","abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","grant_number":"862644","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"}]}]