[{"publisher":"Institute of Science and Technology Austria","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12076"},{"status":"public","relation":"part_of_dissertation","id":"12077"}]},"type":"dissertation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"degree_awarded":"PhD","doi":"10.15479/at:ista:12072","page":"208","has_accepted_license":"1","month":"09","author":[{"orcid":"0000-0002-1812-2810","id":"440EB050-F248-11E8-B48F-1D18A9856A87","first_name":"Alec L","full_name":"Shute, Alec L","last_name":"Shute"}],"article_processing_charge":"No","ddc":["512"],"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. "}],"date_published":"2022-09-08T00:00:00Z","file":[{"file_name":"Thesis_final_draft.pdf","date_updated":"2022-09-08T21:50:34Z","success":1,"content_type":"application/pdf","file_id":"12073","file_size":1907386,"access_level":"open_access","checksum":"bf073344320e05d92c224786cec2e92d","creator":"ashute","relation":"main_file","date_created":"2022-09-08T21:50:34Z"},{"access_level":"closed","file_size":495393,"file_id":"12074","content_type":"application/octet-stream","date_updated":"2022-09-12T11:24:21Z","file_name":"athesis.tex","date_created":"2022-09-08T21:50:42Z","relation":"source_file","creator":"ashute","checksum":"b054ac6baa09f70e8235403a4abbed80"},{"creator":"ashute","checksum":"0a31e905f1cff5eb8110978cc90e1e79","date_created":"2022-09-09T12:05:00Z","relation":"source_file","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip","date_updated":"2022-09-12T11:24:21Z","access_level":"closed","file_size":944534,"file_id":"12078","content_type":"application/x-zip-compressed"}],"status":"public","date_created":"2022-09-08T21:53:03Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"TiBr"}],"citation":{"short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072.","ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"file_date_updated":"2022-09-12T11:24:21Z","date_updated":"2023-02-21T16:37:35Z","_id":"12072","supervisor":[{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","full_name":"Browning, Timothy D","last_name":"Browning"}],"year":"2022","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.","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","day":"08"},{"oa_version":"Published Version","publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","language":[{"iso":"eng"}],"ec_funded":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772617"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","doi":"10.4230/LIPIcs.FSTTCS.2022.29","intvolume":" 250","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2022-12-14T00:00:00Z","abstract":[{"lang":"eng","text":"Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset."}],"ddc":["000"],"file":[{"success":1,"date_updated":"2023-01-20T10:39:44Z","file_name":"2022_LIPICs_Ahmadi.pdf","file_size":872534,"access_level":"open_access","content_type":"application/pdf","file_id":"12324","creator":"dernst","checksum":"6660c802489013f034c9e8bd57f4d46e","relation":"main_file","date_created":"2023-01-20T10:39:44Z"}],"quality_controlled":"1","status":"public","article_number":"29","has_accepted_license":"1","author":[{"first_name":"Ali","last_name":"Ahmadi","full_name":"Ahmadi, Ali"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"last_name":"Safavi Hemami","full_name":"Safavi Hemami, Roodabeh","first_name":"Roodabeh","id":"72ed2640-8972-11ed-ae7b-f9c81ec75154"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde"}],"month":"12","article_processing_charge":"No","scopus_import":"1","citation":{"short":"A. Ahmadi, K. Chatterjee, A.K. Goharshady, T. Meggendorfer, R. Safavi Hemami, D. Zikelic, in:, 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ista":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. 2022. Algorithms and hardness results for computing cores of Markov chains. 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTC: Foundations of Software Technology and Theoretical Computer Science vol. 250, 29.","apa":"Ahmadi, A., Chatterjee, K., Goharshady, A. K., Meggendorfer, T., Safavi Hemami, R., & Zikelic, D. (2022). Algorithms and hardness results for computing cores of Markov chains. In 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (Vol. 250). Madras, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29","chicago":"Ahmadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Tobias Meggendorfer, Roodabeh Safavi Hemami, and Dorde Zikelic. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” In 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Vol. 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29.","ama":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. Algorithms and hardness results for computing cores of Markov chains. In: 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.FSTTCS.2022.29","mla":"Ahmadi, Ali, et al. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, vol. 250, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:10.4230/LIPIcs.FSTTCS.2022.29.","ieee":"A. Ahmadi, K. Chatterjee, A. K. Goharshady, T. Meggendorfer, R. Safavi Hemami, and D. Zikelic, “Algorithms and hardness results for computing cores of Markov chains,” in 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Madras, India, 2022, vol. 250."},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"conference":{"location":"Madras, India","start_date":"2022-12-18","end_date":"2022-12-20","name":"FSTTC: Foundations of Software Technology and Theoretical Computer Science"},"file_date_updated":"2023-01-20T10:39:44Z","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"_id":"12102","date_updated":"2025-07-14T09:09:55Z","date_created":"2023-01-01T23:00:50Z","publication_status":"published","volume":250,"acknowledgement":"The research was partially supported by the Hong Kong Research Grants Council ECS\r\nProject No. 26208122, ERC CoG 863818 (FoRM-SMArt), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, HKUST– Kaisa Joint Research Institute Project Grant HKJRI3A-055 and HKUST Startup Grant R9272. Ali Ahmadi and Roodabeh Safavi were interns at HKUST.","day":"14","title":"Algorithms and hardness results for computing cores of Markov chains","year":"2022"},{"oa":1,"publisher":"Elsevier","intvolume":" 3","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"related_material":{"record":[{"relation":"other","id":"11478","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication":"STAR Protocols","oa_version":"Published Version","doi":"10.1016/j.xpro.2022.101866","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"publication_identifier":{"issn":["2666-1667"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_number":"101866","scopus_import":"1","article_processing_charge":"No","month":"12","author":[{"first_name":"Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","last_name":"Hübschmann","full_name":"Hübschmann, Verena"},{"full_name":"Korkut, Medina","last_name":"Korkut","orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","first_name":"Medina"},{"full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"file":[{"creator":"dernst","checksum":"3c71b8a60633d42c2f77c49025d5559b","relation":"main_file","date_created":"2023-01-23T09:50:51Z","success":1,"file_name":"2022_STARProtocols_Huebschmann.pdf","date_updated":"2023-01-23T09:50:51Z","file_size":6251945,"access_level":"open_access","content_type":"application/pdf","file_id":"12340"}],"abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"ddc":["570"],"date_published":"2022-12-16T00:00:00Z","status":"public","article_type":"letter_note","quality_controlled":"1","date_created":"2023-01-12T11:56:38Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_status":"published","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"citation":{"ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” STAR Protocols, vol. 3, no. 4. Elsevier, 2022.","ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 2022;3(4). doi:10.1016/j.xpro.2022.101866","mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” STAR Protocols, vol. 3, no. 4, 101866, Elsevier, 2022, doi:10.1016/j.xpro.2022.101866.","chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” STAR Protocols. Elsevier, 2022. https://doi.org/10.1016/j.xpro.2022.101866.","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","apa":"Hübschmann, V., Korkut, M., & Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2022.101866","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022)."},"date_updated":"2023-11-02T12:21:32Z","_id":"12117","file_date_updated":"2023-01-23T09:50:51Z","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"},{"name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017"}],"year":"2022","issue":"4","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","volume":3,"title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","day":"16"},{"has_accepted_license":"1","scopus_import":"1","article_processing_charge":"No","author":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"full_name":"Gelová, Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"last_name":"Zou","full_name":"Zou, Minxia","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","full_name":"Giannini, Caterina"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"last_name":"Hrtyan","full_name":"Hrtyan, Mónika","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","full_name":"Randuch, Marek"},{"first_name":"Nikola","full_name":"Rýdza, Nikola","last_name":"Rýdza"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang"},{"id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia","full_name":"Teplova, Anastasiia","last_name":"Teplova"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"}],"month":"09","file":[{"date_updated":"2023-11-02T17:12:37Z","file_name":"Friml Nature 2022_merged.pdf","success":1,"content_type":"application/pdf","file_id":"14483","file_size":79774945,"access_level":"open_access","checksum":"a6055c606aefb900bf62ae3e7d15f921","creator":"amally","relation":"main_file","date_created":"2023-11-02T17:12:37Z"}],"date_published":"2022-09-15T00:00:00Z","ddc":["580"],"abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"article_type":"original","status":"public","quality_controlled":"1","oa":1,"publisher":"Springer Nature","isi":1,"intvolume":" 609","publication":"Nature","oa_version":"Submitted Version","language":[{"iso":"eng"}],"ec_funded":1,"doi":"10.1038/s41586-022-05187-x","page":"575-581","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"type":"journal_article","issue":"7927","year":"2022","volume":609,"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"day":"15","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","date_created":"2023-01-16T10:04:48Z","pmid":1,"publication_status":"published","citation":{"short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05187-x.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:10.1038/s41586-022-05187-x.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x","ieee":"J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022."},"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"_id":"12291","date_updated":"2023-11-07T08:16:09Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"file_date_updated":"2023-11-02T17:12:37Z"},{"title":"Tangible topology through the lens of limits","day":"28","volume":32,"year":"2022","issue":"5","date_updated":"2023-01-30T13:02:30Z","_id":"12307","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"citation":{"ieee":"B. A. Shipman and E. R. Stephenson, “Tangible topology through the lens of limits,” PRIMUS, vol. 32, no. 5. Taylor & Francis, pp. 593–609, 2022.","short":"B.A. Shipman, E.R. Stephenson, PRIMUS 32 (2022) 593–609.","ista":"Shipman BA, Stephenson ER. 2022. Tangible topology through the lens of limits. PRIMUS. 32(5), 593–609.","apa":"Shipman, B. A., & Stephenson, E. R. (2022). Tangible topology through the lens of limits. PRIMUS. Taylor & Francis. https://doi.org/10.1080/10511970.2021.1872750","chicago":"Shipman, Barbara A., and Elizabeth R Stephenson. “Tangible Topology through the Lens of Limits.” PRIMUS. Taylor & Francis, 2022. https://doi.org/10.1080/10511970.2021.1872750.","ama":"Shipman BA, Stephenson ER. Tangible topology through the lens of limits. PRIMUS. 2022;32(5):593-609. doi:10.1080/10511970.2021.1872750","mla":"Shipman, Barbara A., and Elizabeth R. Stephenson. “Tangible Topology through the Lens of Limits.” PRIMUS, vol. 32, no. 5, Taylor & Francis, 2022, pp. 593–609, doi:10.1080/10511970.2021.1872750."},"publication_status":"published","date_created":"2023-01-16T10:07:21Z","status":"public","article_type":"original","quality_controlled":"1","abstract":[{"text":"Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.","lang":"eng"}],"date_published":"2022-05-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","month":"05","author":[{"last_name":"Shipman","full_name":"Shipman, Barbara A.","first_name":"Barbara A."},{"full_name":"Stephenson, Elizabeth R","last_name":"Stephenson","orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R"}],"doi":"10.1080/10511970.2021.1872750","page":"593-609","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Education","General Mathematics"],"publication_identifier":{"eissn":["1935-4053"],"issn":["1051-1970"]},"language":[{"iso":"eng"}],"oa_version":"None","publication":"PRIMUS","publisher":"Taylor & Francis","intvolume":" 32"},{"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-01-24T10:49:46Z","date_updated":"2024-02-28T12:57:46Z","_id":"12358","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"}],"file_date_updated":"2023-02-02T09:39:25Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"citation":{"ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","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.","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","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103"},"year":"2022","supervisor":[{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","day":"22","oa":1,"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","page":"138","doi":"10.15479/at:ista:12103","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"SSU"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"11736","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9818"},{"status":"public","id":"8385","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","article_processing_charge":"No","month":"09","author":[{"first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","full_name":"Sperl, Georg"}],"has_accepted_license":"1","status":"public","file":[{"relation":"main_file","date_created":"2023-01-25T12:04:41Z","creator":"cchlebak","checksum":"083722acbb8115e52e3b0fdec6226769","file_size":104497530,"access_level":"open_access","description":"This is the main PDF file of the thesis. File size: 105 MB","content_type":"application/pdf","file_id":"12371","title":"Thesis","date_updated":"2023-02-02T09:29:57Z","file_name":"thesis_gsperl.pdf"},{"title":"Thesis (compressed 23MB)","date_updated":"2023-02-02T09:33:37Z","file_name":"thesis_gsperl_compressed.pdf","access_level":"open_access","file_size":23183710,"file_id":"12483","content_type":"application/pdf","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","creator":"cchlebak","checksum":"511f82025e5fcb70bff4731d6896ca07","date_created":"2023-02-02T09:33:37Z","relation":"main_file"},{"checksum":"ed4cb85225eedff761c25bddfc37a2ed","creator":"cchlebak","relation":"source_file","date_created":"2023-02-02T09:39:25Z","file_name":"thesis-source.zip","date_updated":"2023-02-02T09:39:25Z","content_type":"application/x-zip-compressed","file_id":"12484","file_size":98382247,"access_level":"open_access"}],"ddc":["000","620"],"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"}],"date_published":"2022-09-22T00:00:00Z"},{"date_created":"2023-01-24T13:09:57Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"citation":{"ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094","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.","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","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."},"project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205"}],"file_date_updated":"2023-09-20T22:30:03Z","date_updated":"2023-11-16T13:10:22Z","_id":"12364","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino"}],"year":"2022","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","day":"19","publisher":"Institute of Science and Technology Austria","oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"3","status":"public"},{"relation":"part_of_dissertation","id":"11160","status":"public"}]},"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"152","doi":"10.15479/at:ista:12094","degree_awarded":"PhD","has_accepted_license":"1","month":"09","author":[{"first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph"}],"article_processing_charge":"No","ddc":["570"],"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."}],"date_published":"2022-09-19T00:00:00Z","file":[{"creator":"cchlebak","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","embargo":"2023-09-19","date_created":"2023-01-24T13:15:45Z","relation":"main_file","date_updated":"2023-09-20T22:30:03Z","file_name":"220923_Thesis_CDotter_Final.pdf","access_level":"open_access","file_size":20457465,"file_id":"12365","content_type":"application/pdf"},{"date_created":"2023-02-02T09:15:35Z","relation":"source_file","checksum":"ad01bb20da163be6893b7af832e58419","creator":"cchlebak","file_id":"12482","content_type":"application/x-zip-compressed","access_level":"closed","file_size":22433512,"embargo_to":"open_access","date_updated":"2023-09-20T22:30:03Z","file_name":"latex_source_CDotter_Thesis_2022.zip"}],"status":"public"},{"ddc":["530"],"abstract":[{"text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n","lang":"eng"}],"date_published":"2022-09-26T00:00:00Z","file":[{"date_created":"2023-01-25T09:41:49Z","relation":"main_file","embargo":"2022-12-28","checksum":"39eabb1e006b41335f17f3b29af09648","creator":"cchlebak","file_id":"12367","content_type":"application/pdf","access_level":"open_access","file_size":56076868,"date_updated":"2023-01-26T23:30:44Z","file_name":"Final_Thesis_ES_Redchenko.pdf"}],"status":"public","has_accepted_license":"1","month":"09","author":[{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"degree_awarded":"PhD","page":"168","doi":"10.15479/at:ista:12132","publisher":"Institute of Science and Technology Austria","oa":1,"title":"Controllable states of superconducting Qubit ensembles","day":"26","supervisor":[{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"year":"2022","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"citation":{"ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:10.15479/at:ista:12132","mla":"Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","apa":"Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022."},"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"grant_number":"862644","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"file_date_updated":"2023-01-26T23:30:44Z","date_updated":"2024-08-07T07:11:56Z","_id":"12366","date_created":"2023-01-25T09:17:02Z","publication_status":"published","alternative_title":["ISTA Thesis"]},{"has_accepted_license":"1","month":"09","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","first_name":"Feyza N","full_name":"Arslan, Feyza N","last_name":"Arslan"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts."}],"ddc":["570"],"date_published":"2022-09-29T00:00:00Z","file":[{"file_id":"12369","content_type":"application/pdf","access_level":"open_access","file_size":14581024,"file_name":"THESIS_FINAL_FArslan_pdfa.pdf","date_updated":"2023-01-25T10:52:46Z","success":1,"date_created":"2023-01-25T10:52:46Z","relation":"main_file","checksum":"e54a3e69b83ebf166544164afd25608e","creator":"cchlebak"}],"status":"public","oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"9350","relation":"part_of_dissertation"}]},"type":"dissertation","publication_identifier":{"isbn":[" 978-3-99078-025-1 "],"issn":["2663-337X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"degree_awarded":"PhD","page":"113","doi":"10.15479/at:ista:12153","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"year":"2022","title":"Remodeling of E-cadherin-mediated contacts via cortical flows","day":"29","date_created":"2023-01-25T10:43:24Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"citation":{"ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","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","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.","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"},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573"}],"file_date_updated":"2023-01-25T10:52:46Z","date_updated":"2023-08-08T13:14:10Z","_id":"12368"},{"publisher":"Institute of Science and Technology Austria","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"12244","relation":"part_of_dissertation"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"degree_awarded":"PhD","page":"142","doi":"10.15479/at:ista:12378","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"dissertation","has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Colombo","full_name":"Colombo, Gloria","first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"}],"month":"11","file":[{"date_updated":"2023-04-12T22:30:03Z","file_name":"Gloria_Colombo_Thesis.docx","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12379","file_size":23890382,"access_level":"closed","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","creator":"cchlebak","relation":"source_file","date_created":"2023-01-25T14:31:32Z"},{"checksum":"8af4319c18b516e8758e9a6cb02b103b","creator":"cchlebak","relation":"main_file","date_created":"2023-01-25T14:31:36Z","embargo":"2023-04-11","file_name":"Gloria_Colombo_Thesis.pdf","date_updated":"2023-04-12T22:30:03Z","content_type":"application/pdf","file_id":"12380","file_size":13802421,"access_level":"open_access"}],"date_published":"2022-11-11T00:00:00Z","abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia.","lang":"eng"}],"ddc":["570"],"status":"public","date_created":"2023-01-25T14:27:43Z","alternative_title":["ISTA Thesis"],"publication_status":"published","citation":{"ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","apa":"Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378","mla":"Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378.","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022."},"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"_id":"12378","date_updated":"2023-08-04T09:40:37Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file_date_updated":"2023-04-12T22:30:03Z","year":"2022","supervisor":[{"full_name":"Siegert, Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"day":"11","title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes"},{"status":"public","date_published":"2022-12-15T00:00:00Z","abstract":[{"lang":"eng","text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n"}],"ddc":["500"],"file":[{"file_id":"12391","content_type":"application/pdf","access_level":"open_access","file_size":3095225,"file_name":"Brooks_Thesis.pdf","date_updated":"2023-01-26T10:02:34Z","success":1,"date_created":"2023-01-26T10:02:34Z","relation":"main_file","checksum":"b31460e937f33b557abb40ebef02b567","creator":"cchlebak"},{"content_type":"application/octet-stream","file_id":"12392","file_size":809842,"access_level":"closed","date_updated":"2023-01-26T10:02:42Z","file_name":"Brooks_Thesis.tex","relation":"source_file","date_created":"2023-01-26T10:02:42Z","checksum":"9751869fa5e7981588ad4228f4fd4bd6","creator":"cchlebak"}],"author":[{"orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris","full_name":"Brooks, Morris","last_name":"Brooks"}],"month":"12","article_processing_charge":"No","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/at:ista:12390","page":"196","degree_awarded":"PhD","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"9005","relation":"part_of_dissertation"}]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"oa":1,"publisher":"Institute of Science and Technology Austria","day":"15","title":"Translation-invariant quantum systems with effectively broken symmetry","supervisor":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"year":"2022","file_date_updated":"2023-01-26T10:02:42Z","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"}],"_id":"12390","date_updated":"2023-08-07T13:32:09Z","citation":{"ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390","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.","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","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022."},"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-01-26T10:00:42Z"},{"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-01-26T11:55:16Z","_id":"12401","date_updated":"2024-09-10T12:04:26Z","file_date_updated":"2023-12-21T23:30:03Z","citation":{"ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401.","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022."},"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"year":"2022","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"day":"22","title":"Role of microenvironment heterogeneity in cancer cell invasion","oa":1,"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","page":"105","doi":"10.15479/at:ista:12401","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","id":"679","status":"public"},{"status":"public","id":"10703","relation":"part_of_dissertation"},{"id":"7885","relation":"part_of_dissertation","status":"public"},{"id":"9429","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"}],"month":"12","has_accepted_license":"1","status":"public","file":[{"checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","creator":"cchlebak","relation":"main_file","date_created":"2023-01-26T11:58:14Z","embargo":"2023-12-20","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","date_updated":"2023-12-21T23:30:03Z","content_type":"application/pdf","file_id":"12402","file_size":42059787,"access_level":"open_access"},{"checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","creator":"cchlebak","date_created":"2023-01-26T12:00:10Z","relation":"source_file","embargo_to":"open_access","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","date_updated":"2023-12-21T23:30:03Z","file_id":"12403","content_type":"application/x-zip-compressed","access_level":"closed","file_size":261256696}],"date_published":"2022-12-22T00:00:00Z","ddc":["610"],"abstract":[{"lang":"eng","text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening."}]},{"day":"28","title":"Repeated prophet inequality with near-optimal bounds","status":"public","external_id":{"arxiv":["2209.14368"]},"date_published":"2022-09-28T00:00:00Z","abstract":[{"lang":"eng","text":"In modern sample-driven Prophet Inequality, an adversary chooses a sequence of n items with values v1,v2,…,vn to be presented to a decision maker (DM). The process follows in two phases. In the first phase (sampling phase), some items, possibly selected at random, are revealed to the DM, but she can never accept them. In the second phase, the DM is presented with the other items in a random order and online fashion. For each item, she must make an irrevocable decision to either accept the item and stop the process or reject the item forever and proceed to the next item. The goal of the DM is to maximize the expected value as compared to a Prophet (or offline algorithm) that has access to all information. In this setting, the sampling phase has no cost and is not part of the optimization process. However, in many scenarios, the samples are obtained as part of the decision-making process.\r\nWe model this aspect as a two-phase Prophet Inequality where an adversary chooses a sequence of 2n items with values v1,v2,…,v2n and the items are randomly ordered. Finally, there are two phases of the Prophet Inequality problem with the first n-items and the rest of the items, respectively. We show that some basic algorithms achieve a ratio of at most 0.450. We present an algorithm that achieves a ratio of at least 0.495. Finally, we show that for every algorithm the ratio it can achieve is at most 0.502. Hence our algorithm is near-optimal."}],"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Mohammadi, Mona","last_name":"Mohammadi","id":"4363614d-b686-11ed-a7d5-ac9e4a24bc2e","first_name":"Mona"},{"last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X"}],"month":"09","article_processing_charge":"No","article_number":"2209.14368","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"type":"preprint","doi":"10.48550/ARXIV.2209.14368","_id":"12677","date_updated":"2025-07-14T09:09:51Z","citation":{"apa":"Chatterjee, K., Mohammadi, M., & Saona Urmeneta, R. J. (n.d.). Repeated prophet inequality with near-optimal bounds. arXiv. https://doi.org/10.48550/ARXIV.2209.14368","ista":"Chatterjee K, Mohammadi M, Saona Urmeneta RJ. Repeated prophet inequality with near-optimal bounds. arXiv, 2209.14368.","short":"K. Chatterjee, M. Mohammadi, R.J. Saona Urmeneta, ArXiv (n.d.).","ama":"Chatterjee K, Mohammadi M, Saona Urmeneta RJ. Repeated prophet inequality with near-optimal bounds. arXiv. doi:10.48550/ARXIV.2209.14368","mla":"Chatterjee, Krishnendu, et al. “Repeated Prophet Inequality with Near-Optimal Bounds.” ArXiv, 2209.14368, doi:10.48550/ARXIV.2209.14368.","chicago":"Chatterjee, Krishnendu, Mona Mohammadi, and Raimundo J Saona Urmeneta. “Repeated Prophet Inequality with Near-Optimal Bounds.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2209.14368.","ieee":"K. Chatterjee, M. Mohammadi, and R. J. Saona Urmeneta, “Repeated prophet inequality with near-optimal bounds,” arXiv. ."},"arxiv":1,"oa_version":"Preprint","publication":"arXiv","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"language":[{"iso":"eng"}],"ec_funded":1,"publication_status":"submitted","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.14368"}],"date_created":"2023-02-24T12:21:40Z","oa":1},{"date_created":"2023-03-23T14:33:13Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.15607","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publication_status":"submitted","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"language":[{"iso":"eng"}],"publication":"arXiv","arxiv":1,"citation":{"ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” arXiv. .","ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. arXiv. doi:10.48550/arXiv.2210.15607","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” ArXiv, 2210.15607, doi:10.48550/arXiv.2210.15607.","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2210.15607.","apa":"Brighi, P., Ljubotina, M., & Serbyn, M. (n.d.). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. arXiv. https://doi.org/10.48550/arXiv.2210.15607","ista":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. arXiv, 2210.15607.","short":"P. Brighi, M. Ljubotina, M. Serbyn, ArXiv (n.d.)."},"oa_version":"Preprint","related_material":{"record":[{"relation":"dissertation_contains","id":"12732","status":"public"},{"id":"14334","relation":"later_version","status":"public"}]},"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-20T10:46:29Z","_id":"12750","doi":"10.48550/arXiv.2210.15607","article_number":"2210.15607","year":"2022","month":"11","author":[{"first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","full_name":"Brighi, Pietro"},{"first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","orcid":"0000-0003-0038-7068","last_name":"Ljubotina","full_name":"Ljubotina, Marko"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"article_processing_charge":"No","abstract":[{"text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring a conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored universality classes of dynamics and invite their further theoretical and experimental studies.","lang":"eng"}],"date_published":"2022-11-07T00:00:00Z","title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","day":"07","status":"public","external_id":{"arxiv":["2210.15607"]}},{"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-04-25T07:34:49Z","_id":"12860","doi":"10.48550/arXiv.2203.16701","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"language":[{"iso":"eng"}],"publication":"arXiv","citation":{"short":"S. Bombari, A. Achille, Z. Wang, Y.-X. Wang, Y. Xie, K.Y. Singh, S. Appalaraju, V. Mahadevan, S. Soatto, ArXiv (n.d.).","apa":"Bombari, S., Achille, A., Wang, Z., Wang, Y.-X., Xie, Y., Singh, K. Y., … Soatto, S. (n.d.). Towards differential relational privacy and its use in question answering. arXiv. https://doi.org/10.48550/arXiv.2203.16701","ista":"Bombari S, Achille A, Wang Z, Wang Y-X, Xie Y, Singh KY, Appalaraju S, Mahadevan V, Soatto S. Towards differential relational privacy and its use in question answering. arXiv, 2203.16701.","chicago":"Bombari, Simone, Alessandro Achille, Zijian Wang, Yu-Xiang Wang, Yusheng Xie, Kunwar Yashraj Singh, Srikar Appalaraju, Vijay Mahadevan, and Stefano Soatto. “Towards Differential Relational Privacy and Its Use in Question Answering.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2203.16701.","mla":"Bombari, Simone, et al. “Towards Differential Relational Privacy and Its Use in Question Answering.” ArXiv, 2203.16701, doi:10.48550/arXiv.2203.16701.","ama":"Bombari S, Achille A, Wang Z, et al. Towards differential relational privacy and its use in question answering. arXiv. doi:10.48550/arXiv.2203.16701","ieee":"S. Bombari et al., “Towards differential relational privacy and its use in question answering,” arXiv. ."},"arxiv":1,"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.16701","open_access":"1"}],"publication_status":"submitted","date_created":"2023-04-23T16:11:48Z","oa":1,"title":"Towards differential relational privacy and its use in question answering","day":"30","status":"public","external_id":{"arxiv":["2203.16701"]},"abstract":[{"lang":"eng","text":"Memorization of the relation between entities in a dataset can lead to privacy issues when using a trained model for question answering. We introduce Relational Memorization (RM) to understand, quantify and control this phenomenon. While bounding general memorization can have detrimental effects on the performance of a trained model, bounding RM does not prevent effective learning. The difference is most pronounced when the data distribution is long-tailed, with many queries having only few training examples: Impeding general memorization prevents effective learning, while impeding only relational memorization still allows learning general properties of the underlying concepts. We formalize the notion of Relational Privacy (RP) and, inspired by Differential Privacy (DP), we provide a possible definition of Differential Relational Privacy (DrP). These notions can be used to describe and compute bounds on the amount of RM in a trained model. We illustrate Relational Privacy concepts in experiments with large-scale models for Question Answering."}],"date_published":"2022-03-30T00:00:00Z","month":"03","author":[{"last_name":"Bombari","full_name":"Bombari, Simone","first_name":"Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa"},{"full_name":"Achille, Alessandro","last_name":"Achille","first_name":"Alessandro"},{"first_name":"Zijian","last_name":"Wang","full_name":"Wang, Zijian"},{"last_name":"Wang","full_name":"Wang, Yu-Xiang","first_name":"Yu-Xiang"},{"last_name":"Xie","full_name":"Xie, Yusheng","first_name":"Yusheng"},{"first_name":"Kunwar Yashraj","last_name":"Singh","full_name":"Singh, Kunwar Yashraj"},{"last_name":"Appalaraju","full_name":"Appalaraju, Srikar","first_name":"Srikar"},{"full_name":"Mahadevan, Vijay","last_name":"Mahadevan","first_name":"Vijay"},{"first_name":"Stefano","last_name":"Soatto","full_name":"Soatto, Stefano"}],"article_processing_charge":"No","article_number":"2203.16701","year":"2022"},{"extern":"1","oa_version":"Published Version","publication":"Genetics in Medicine","language":[{"iso":"eng"}],"page":"2194-2203","doi":"10.1016/j.gim.2022.07.013","keyword":["Human mediator complex","MED11","MEDopathies"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1098-3600"]},"type":"journal_article","publisher":"Elsevier","oa":1,"intvolume":" 24","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","file_size":1434037,"file_id":"14371","content_type":"application/pdf","success":1,"date_updated":"2023-09-25T08:56:06Z","file_name":"2022_GeneticsMedicine_Calin.pdf","date_created":"2023-09-25T08:56:06Z","relation":"main_file","creator":"dernst","checksum":"8117175a89129eb5022d81ffe7625f9f"}],"date_published":"2022-10-01T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Purpose: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. Methods: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. Results: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. Conclusion: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics."}],"article_type":"original","status":"public","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Elisa","last_name":"Cali","full_name":"Cali, Elisa"},{"first_name":"Sheng-Jia","last_name":"Lin","full_name":"Lin, Sheng-Jia"},{"full_name":"Rocca, Clarissa","last_name":"Rocca","first_name":"Clarissa"},{"full_name":"Sahin, Yavuz","last_name":"Sahin","first_name":"Yavuz"},{"full_name":"Al Shamsi, Aisha","last_name":"Al Shamsi","first_name":"Aisha"},{"last_name":"El Chehadeh","full_name":"El Chehadeh, Salima","first_name":"Salima"},{"first_name":"Myriam","last_name":"Chaabouni","full_name":"Chaabouni, Myriam"},{"first_name":"Kshitij","last_name":"Mankad","full_name":"Mankad, Kshitij"},{"first_name":"Evangelia","full_name":"Galanaki, Evangelia","last_name":"Galanaki"},{"first_name":"Stephanie","full_name":"Efthymiou, Stephanie","last_name":"Efthymiou"},{"last_name":"Sudhakar","full_name":"Sudhakar, Sniya","first_name":"Sniya"},{"first_name":"Alkyoni","full_name":"Athanasiou-Fragkouli, Alkyoni","last_name":"Athanasiou-Fragkouli"},{"last_name":"Celik","full_name":"Celik, Tamer","first_name":"Tamer"},{"first_name":"Nejat","last_name":"Narli","full_name":"Narli, Nejat"},{"last_name":"Bianca","full_name":"Bianca, Sebastiano","first_name":"Sebastiano"},{"last_name":"Murphy","full_name":"Murphy, David","first_name":"David"},{"full_name":"Moreira, Francisco Martins De Carvalho","last_name":"Moreira","first_name":"Francisco Martins De Carvalho"},{"full_name":"Accogli, Andrea","last_name":"Accogli","first_name":"Andrea"},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","first_name":"Kevin","full_name":"Huang, Kevin","last_name":"Huang"},{"first_name":"Kamel","full_name":"Monastiri, Kamel","last_name":"Monastiri"},{"first_name":"Masoud","last_name":"Edizadeh","full_name":"Edizadeh, Masoud"},{"first_name":"Rosaria","full_name":"Nardello, Rosaria","last_name":"Nardello"},{"full_name":"Ognibene, Marzia","last_name":"Ognibene","first_name":"Marzia"},{"last_name":"De Marco","full_name":"De Marco, Patrizia","first_name":"Patrizia"},{"last_name":"Ruggieri","full_name":"Ruggieri, Martino","first_name":"Martino"},{"first_name":"Federico","last_name":"Zara","full_name":"Zara, Federico"},{"last_name":"Striano","full_name":"Striano, Pasquale","first_name":"Pasquale"},{"first_name":"Yavuz","last_name":"Sahin","full_name":"Sahin, Yavuz"},{"first_name":"Lihadh","full_name":"Al-Gazali, Lihadh","last_name":"Al-Gazali"},{"first_name":"Marie Therese Abi","last_name":"Warde","full_name":"Warde, Marie Therese Abi"},{"full_name":"Gerard, Benedicte","last_name":"Gerard","first_name":"Benedicte"},{"first_name":"Giovanni","last_name":"Zifarelli","full_name":"Zifarelli, Giovanni"},{"full_name":"Beetz, Christian","last_name":"Beetz","first_name":"Christian"},{"first_name":"Sara","full_name":"Fortuna, Sara","last_name":"Fortuna"},{"first_name":"Miguel","last_name":"Soler","full_name":"Soler, Miguel"},{"last_name":"Valente","full_name":"Valente, Enza Maria","first_name":"Enza Maria"},{"full_name":"Varshney, Gaurav","last_name":"Varshney","first_name":"Gaurav"},{"first_name":"Reza","last_name":"Maroofian","full_name":"Maroofian, Reza"},{"full_name":"Salpietro, Vincenzo","last_name":"Salpietro","first_name":"Vincenzo"},{"first_name":"Henry","last_name":"Houlden","full_name":"Houlden, Henry"},{"first_name":"SYNaPS Study","full_name":"Grp, SYNaPS Study","last_name":"Grp"}],"month":"10","citation":{"apa":"Cali, E., Lin, S.-J., Rocca, C., Sahin, Y., Al Shamsi, A., El Chehadeh, S., … Grp, Syn. S. (2022). A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. Elsevier. https://doi.org/10.1016/j.gim.2022.07.013","ista":"Cali E, Lin S-J, Rocca C, Sahin Y, Al Shamsi A, El Chehadeh S, Chaabouni M, Mankad K, Galanaki E, Efthymiou S, Sudhakar S, Athanasiou-Fragkouli A, Celik T, Narli N, Bianca S, Murphy D, Moreira FMDC, Accogli A, Petree C, Huang K, Monastiri K, Edizadeh M, Nardello R, Ognibene M, De Marco P, Ruggieri M, Zara F, Striano P, Sahin Y, Al-Gazali L, Warde MTA, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H, Grp SynS. 2022. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 24(10), 2194–2203.","short":"E. Cali, S.-J. Lin, C. Rocca, Y. Sahin, A. Al Shamsi, S. El Chehadeh, M. Chaabouni, K. Mankad, E. Galanaki, S. Efthymiou, S. Sudhakar, A. Athanasiou-Fragkouli, T. Celik, N. Narli, S. Bianca, D. Murphy, F.M.D.C. Moreira, A. Accogli, C. Petree, K. Huang, K. Monastiri, M. Edizadeh, R. Nardello, M. Ognibene, P. De Marco, M. Ruggieri, F. Zara, P. Striano, Y. Sahin, L. Al-Gazali, M.T.A. Warde, B. Gerard, G. Zifarelli, C. Beetz, S. Fortuna, M. Soler, E.M. Valente, G. Varshney, R. Maroofian, V. Salpietro, H. Houlden, Syn.S. Grp, Genetics in Medicine 24 (2022) 2194–2203.","mla":"Cali, Elisa, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” Genetics in Medicine, vol. 24, no. 10, Elsevier, 2022, pp. 2194–203, doi:10.1016/j.gim.2022.07.013.","ama":"Cali E, Lin S-J, Rocca C, et al. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 2022;24(10):2194-2203. doi:10.1016/j.gim.2022.07.013","chicago":"Cali, Elisa, Sheng-Jia Lin, Clarissa Rocca, Yavuz Sahin, Aisha Al Shamsi, Salima El Chehadeh, Myriam Chaabouni, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” Genetics in Medicine. Elsevier, 2022. https://doi.org/10.1016/j.gim.2022.07.013.","ieee":"E. Cali et al., “A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease,” Genetics in Medicine, vol. 24, no. 10. Elsevier, pp. 2194–2203, 2022."},"department":[{"_id":"GradSch"}],"_id":"14355","date_updated":"2023-09-25T08:57:07Z","file_date_updated":"2023-09-25T08:56:06Z","date_created":"2023-09-20T20:57:18Z","publication_status":"published","volume":24,"day":"01","title":"A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease","issue":"10","year":"2022"},{"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"citation":{"short":"K. Chatterjee, R.J. Saona Urmeneta, B. Ziliotto, Mathematics of Operations Research 47 (2022) 100–119.","apa":"Chatterjee, K., Saona Urmeneta, R. J., & Ziliotto, B. (2022). Finite-memory strategies in POMDPs with long-run average objectives. Mathematics of Operations Research. Institute for Operations Research and the Management Sciences. https://doi.org/10.1287/moor.2020.1116","ista":"Chatterjee K, Saona Urmeneta RJ, Ziliotto B. 2022. Finite-memory strategies in POMDPs with long-run average objectives. Mathematics of Operations Research. 47(1), 100–119.","chicago":"Chatterjee, Krishnendu, Raimundo J Saona Urmeneta, and Bruno Ziliotto. “Finite-Memory Strategies in POMDPs with Long-Run Average Objectives.” Mathematics of Operations Research. Institute for Operations Research and the Management Sciences, 2022. https://doi.org/10.1287/moor.2020.1116.","ama":"Chatterjee K, Saona Urmeneta RJ, Ziliotto B. Finite-memory strategies in POMDPs with long-run average objectives. Mathematics of Operations Research. 2022;47(1):100-119. doi:10.1287/moor.2020.1116","mla":"Chatterjee, Krishnendu, et al. “Finite-Memory Strategies in POMDPs with Long-Run Average Objectives.” Mathematics of Operations Research, vol. 47, no. 1, Institute for Operations Research and the Management Sciences, 2022, pp. 100–19, doi:10.1287/moor.2020.1116.","ieee":"K. Chatterjee, R. J. Saona Urmeneta, and B. Ziliotto, “Finite-memory strategies in POMDPs with long-run average objectives,” Mathematics of Operations Research, vol. 47, no. 1. Institute for Operations Research and the Management Sciences, pp. 100–119, 2022."},"project":[{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"}],"date_updated":"2023-09-05T13:16:11Z","_id":"9311","date_created":"2021-04-08T09:33:31Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.13360"}],"publication_status":"published","acknowledgement":"Partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407, by CONICYT Chile through grant PII 20150140, and by ECOS-CONICYT through grant C15E03.\r\n","volume":47,"title":"Finite-memory strategies in POMDPs with long-run average objectives","day":"01","external_id":{"isi":["000731918100001"],"arxiv":["1904.13360"]},"year":"2022","issue":"1","language":[{"iso":"eng"}],"publication":"Mathematics of Operations Research","arxiv":1,"oa_version":"Preprint","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1526-5471"],"issn":["0364-765X"]},"keyword":["Management Science and Operations Research","General Mathematics","Computer Science Applications"],"page":"100-119","doi":"10.1287/moor.2020.1116","intvolume":" 47","isi":1,"publisher":"Institute for Operations Research and the Management Sciences","oa":1,"abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are standard models for dynamic systems with probabilistic and nondeterministic behaviour in uncertain environments. We prove that in POMDPs with long-run average objective, the decision maker has approximately optimal strategies with finite memory. This implies notably that approximating the long-run value is recursively enumerable, as well as a weak continuity property of the value with respect to the transition function. ","lang":"eng"}],"date_published":"2022-02-01T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original","month":"02","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J"},{"last_name":"Ziliotto","full_name":"Ziliotto, Bruno","first_name":"Bruno"}],"scopus_import":"1","article_processing_charge":"No"},{"date_created":"2021-09-13T11:12:34Z","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021."},"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"948819","name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"file_date_updated":"2021-09-15T14:37:30Z","_id":"10007","date_updated":"2023-09-07T13:30:45Z","supervisor":[{"last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"}],"year":"2021","day":"14","title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"id":"10012","relation":"part_of_dissertation","status":"public"},{"id":"10013","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7489","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","doi":"10.15479/at:ista:10007","page":"300","degree_awarded":"PhD","has_accepted_license":"1","author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","full_name":"Hensel, Sebastian","last_name":"Hensel"}],"month":"09","article_processing_charge":"No","date_published":"2021-09-14T00:00:00Z","ddc":["515"],"abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"file":[{"relation":"source_file","date_created":"2021-09-13T11:03:24Z","checksum":"c8475faaf0b680b4971f638f1db16347","creator":"shensel","content_type":"application/x-zip-compressed","file_id":"10008","file_size":15022154,"access_level":"closed","file_name":"thesis_final_Hensel.zip","date_updated":"2021-09-15T14:37:30Z"},{"checksum":"1a609937aa5275452822f45f2da17f07","creator":"shensel","date_created":"2021-09-13T14:18:56Z","relation":"main_file","date_updated":"2021-09-14T09:52:47Z","file_name":"thesis_final_Hensel.pdf","file_id":"10014","content_type":"application/pdf","access_level":"open_access","file_size":6583638}],"status":"public"},{"has_accepted_license":"1","article_processing_charge":"No","month":"09","author":[{"last_name":"Portinale","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"cchlebak","checksum":"8cd60dcb8762e8f21867e21e8001e183","date_created":"2021-09-21T09:17:34Z","relation":"source_file","date_updated":"2022-03-10T12:14:42Z","file_name":"tex_and_pictures.zip","access_level":"closed","file_size":3876668,"file_id":"10032","content_type":"application/x-zip-compressed"},{"file_id":"10047","content_type":"application/pdf","access_level":"open_access","file_size":2532673,"file_name":"thesis_portinale_Final (1).pdf","date_updated":"2021-09-27T11:14:31Z","date_created":"2021-09-27T11:14:31Z","relation":"main_file","checksum":"9789e9d967c853c1503ec7f307170279","creator":"cchlebak"}],"ddc":["515"],"abstract":[{"lang":"eng","text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces."}],"date_published":"2021-09-22T00:00:00Z","status":"public","publisher":"Institute of Science and Technology Austria","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10022"},{"relation":"part_of_dissertation","id":"9792","status":"public"},{"status":"public","id":"7573","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"oa_version":"Published Version","degree_awarded":"PhD","doi":"10.15479/at:ista:10030","type":"dissertation","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2021","supervisor":[{"first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan"}],"acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","day":"22","date_created":"2021-09-21T09:14:15Z","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"citation":{"short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030","mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030.","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021."},"date_updated":"2023-09-07T13:31:06Z","_id":"10030","project":[{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"file_date_updated":"2022-03-10T12:14:42Z"},{"citation":{"ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035.","ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035."},"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"_id":"10035","date_updated":"2023-10-17T09:24:07Z","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"file_date_updated":"2022-03-10T12:15:18Z","date_created":"2021-09-23T07:31:44Z","alternative_title":["ISTA Thesis"],"publication_status":"published","acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","day":"23","title":"On the adaptive security of graph-based games","year":"2021","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10044","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10049"},{"relation":"part_of_dissertation","id":"637","status":"public"},{"relation":"part_of_dissertation","id":"10041","status":"public"},{"relation":"part_of_dissertation","id":"6430","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10048"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"page":"276","doi":"10.15479/at:ista:10035","degree_awarded":"PhD","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","publisher":"Institute of Science and Technology Austria","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_id":"10082","content_type":"application/pdf","access_level":"open_access","file_size":2104726,"date_updated":"2021-10-04T12:22:33Z","file_name":"thesis_pdfa.pdf","success":1,"date_created":"2021-10-04T12:22:33Z","relation":"main_file","checksum":"73a44345c683e81f3e765efbf86fdcc5","creator":"cchlebak"},{"date_created":"2021-10-05T07:04:37Z","relation":"source_file","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","creator":"cchlebak","file_id":"10085","content_type":"application/x-zip-compressed","access_level":"closed","file_size":9538359,"file_name":"thesis_final (1).zip","date_updated":"2022-03-10T12:15:18Z"}],"date_published":"2021-09-23T00:00:00Z","ddc":["519"],"abstract":[{"text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).","lang":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"No","author":[{"full_name":"Klein, Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"}],"month":"09"}]