[{"supervisor":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"supplementarymaterial":"not applicable","file":[{"file_size":11917734,"creator":"gpascual","content_type":"application/x-zip-compressed","file_id":"18099","date_updated":"2024-09-19T12:35:38Z","relation":"source_file","checksum":"ce0dca715b3df48e52e2e891b6ac1bc5","date_created":"2024-09-19T12:35:38Z","access_level":"closed","file_name":"thesis_bundle.zip"},{"file_id":"18100","content_type":"application/pdf","creator":"gpascual","file_size":2729427,"file_name":"thesis_gpasper.pdf","date_created":"2024-09-19T12:36:08Z","access_level":"open_access","relation":"main_file","date_updated":"2024-09-19T12:36:08Z","checksum":"4a2c72e90f1a0ef2a13cff800f8d1265"}],"day":"18","author":[{"full_name":"Pascual Perez, Guillermo","first_name":"Guillermo","orcid":"0000-0001-8630-415X","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez"}],"doi_confirm":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","das_tickbox":"1","page":"239","ec_funded":1,"OA_place":"publisher","oa":1,"date_published":"2024-09-18T00:00:00Z","date_created":"2024-09-18T12:59:49Z","type":"dissertation","related_material":{"record":[{"id":"10408","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11476"},{"status":"public","id":"10049","relation":"part_of_dissertation"},{"status":"public","id":"18086","relation":"part_of_dissertation"}]},"researchdata_availability":"yes","year":"2024","status":"public","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18088","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","title":"On the efficiency and security of secure group messaging","degree_awarded":"PhD","_id":"18088","publisher":"Institute of Science and Technology Austria","ddc":["000"],"date_updated":"2026-10-16T08:11:08Z","has_accepted_license":"1","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:18088","file_date_updated":"2024-09-19T12:36:08Z","citation":{"ama":"Pascual Perez G. On the efficiency and security of secure group messaging. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18088\">10.15479/at:ista:18088</a>","short":"G. Pascual Perez, On the Efficiency and Security of Secure Group Messaging, Institute of Science and Technology Austria, 2024.","chicago":"Pascual Perez, Guillermo. “On the Efficiency and Security of Secure Group Messaging.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18088\">https://doi.org/10.15479/at:ista:18088</a>.","ista":"Pascual Perez G. 2024. On the efficiency and security of secure group messaging. Institute of Science and Technology Austria.","ieee":"G. Pascual Perez, “On the efficiency and security of secure group messaging,” Institute of Science and Technology Austria, 2024.","apa":"Pascual Perez, G. (2024). <i>On the efficiency and security of secure group messaging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18088\">https://doi.org/10.15479/at:ista:18088</a>","mla":"Pascual Perez, Guillermo. <i>On the Efficiency and Security of Secure Group Messaging</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18088\">10.15479/at:ista:18088</a>."},"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Instant messaging applications like Whatsapp, Signal or Telegram have become ubiquitous in today's society.\r\nMany of them provide not only end-to-end encryption, but also security guarantees even when the key material gets compromised.\r\nThese are achieved through frequent key update performed by users.\r\nIn particular, the compromise of a group key should preserve confidentiality of previously exchanged messages (forward secrecy), and a subsequent key update will ensure security for future ones (post-compromise security).\r\nThough great protocols for one-on-one communication have been known for some time, the design of ones that scale efficiently for larger groups while achieving akin security guarantees is a hard problem.\r\nA great deal of research has been aimed at this topic, much of it under the umbrella of the Messaging Layer Security (MLS) working group at the IETF. \r\nStarted in 2018, this joint effort by academics and industry culminated in 2023 with the publication of the first standard for secure group messaging [IETF, RFC9420].\r\n\r\nAt the core of secure group messaging is a cryptographic primitive termed Continuous Group Key Agreement, or CGKA [Alwen et al. 2021], that essentially allows a changing group of users to agree on a common key with the added functionality security against compromises is achieved by users asynchronously issuing a key update. In this thesis we contribute to the understanding of CGKA across different angles.\r\nFirst, we present a new technique to effect dynamic operations in groups, i.e., add or remove members, that can be more efficient that the one employed by MLS in certain settings.\r\nConsidering the setting of users belonging to multiple overlapping groups, we then show lowerbounds on the communication cost of constructions that leverage said overlap, at the same time showing protocols that are asymptotically optimal and efficient for practical settings, respectively. Along the way, we show that the communication cost of key updates in MLS is average-cost optimal.\r\nAn important feature in CGKA protocols, particularly for big groups, is the possibility of executing several group operations concurrently. While later versions of MLS support this, they do at the cost of worsening the communication efficiency of future group operations.\r\nIn this thesis we introduce two new protocols that permit concurrency without any negative effect on efficiency. Our protocols circumvent previously existing lower bounds by satisfying a new notion of post-compromise security that only asks for security to be re-established after a certain number of key updates have taken place. While this can be slower than MLS in terms of rounds of communication, we show that it leads to more efficient overall communication. \r\nAdditionally, we introduce a new technique that allows group members to decrease the information they need to store and download, which makes one of our protocols enjoy much lower download cost than any other existing CGKA constructions. "}],"article_processing_charge":"No"},{"page":"294–313","das_tickbox":"0","day":"10","isi":1,"author":[{"first_name":"Joel F","full_name":"Alwen, Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","first_name":"Benedikt","full_name":"Auerbach, Benedikt"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","last_name":"Cueto Noval","orcid":"0000-0002-2505-4246","first_name":"Miguel","full_name":"Cueto Noval, Miguel"},{"full_name":"Klein, Karen","first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","full_name":"Pascual Perez, Guillermo","first_name":"Guillermo"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"quality_controlled":"1","editor":[{"full_name":"Galdi, Clemente","first_name":"Clemente","last_name":"Galdi"},{"first_name":"Duong Hieu","full_name":"Phan, Duong Hieu","last_name":"Phan"}],"supplementarymaterial":"no","volume":14974,"publication":"Security and Cryptography for Networks: 14th International Conference","fulldoi":"https://doi.org/10.1007/978-3-031-71073-5_14","publication_status":"published","conference":{"start_date":"2024-09-11","end_date":"2024-09-13","name":"SCN: Security and Cryptography for Networks","location":"Amalfi, Italy"},"type":"conference","status":"public","year":"2024","researchdata_availability":"no","intvolume":"     14974","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18088"}]},"date_published":"2024-09-10T00:00:00Z","date_created":"2024-09-18T11:35:14Z","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"09","abstract":[{"lang":"eng","text":"Abstract. Continuous group key agreement (CGKA) allows a group of\r\nusers to maintain a continuously updated shared key in an asynchronous\r\nsetting where parties only come online sporadically and their messages\r\nare relayed by an untrusted server. CGKA captures the basic primitive\r\nunderlying group messaging schemes.\r\nCurrent solutions including TreeKEM (“Messaging Layer Security”\r\n(MLS) IETF RFC 9420) cannot handle concurrent requests while retaining low communication complexity. The exception being CoCoA, which\r\nis concurrent while having extremely low communication complexity (in\r\ngroups of size n and for m concurrent updates the communication per\r\nuser is log(n), i.e., independent of m). The main downside of CoCoA\r\nis that in groups of size n, users might have to do up to log(n) update\r\nrequests to the server to ensure their (potentially corrupted) key material has been refreshed.\r\nIn this work we present a “fast healing” concurrent CGKA protocol,\r\nnamed DeCAF, where users will heal after at most log(t) requests, with\r\nt being the number of corrupted users. While also suitable for the standard central-server setting, our protocol is particularly interesting for\r\nrealizing decentralized group messaging, where protocol messages (add,\r\nremove, update) are being posted on some append-only data structure\r\nrather than sent to a server. In this setting, concurrency is crucial once\r\nthe rate of requests exceeds, say, the rate at which new blocks are added\r\nto a blockchain.\r\nIn the central-server setting, CoCoA (the only alternative with concurrency, sub-linear communication and basic post-compromise security)\r\nenjoys much lower download communication. However, in the decentralized setting – where there is no server which can craft specific messages\r\nfor different users to reduce their download communication – our protocol\r\nsignificantly outperforms CoCoA. DeCAF heals in fewer epochs (log(t)\r\nvs. log(n)) while incurring a similar per epoch per user communication\r\ncost."}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031710735"],"isbn":["9783031710728"],"eissn":["1611-3349"]},"doi":"10.1007/978-3-031-71073-5_14","citation":{"mla":"Alwen, Joel F., et al. “DeCAF: Decentralizable CGKA with Fast Healing.” <i>Security and Cryptography for Networks: 14th International Conference</i>, edited by Clemente Galdi and Duong Hieu Phan, vol. 14974, Springer Nature, 2024, pp. 294–313, doi:<a href=\"https://doi.org/10.1007/978-3-031-71073-5_14\">10.1007/978-3-031-71073-5_14</a>.","apa":"Alwen, J. F., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., &#38; Pietrzak, K. Z. (2024). DeCAF: Decentralizable CGKA with fast healing. In C. Galdi &#38; D. H. Phan (Eds.), <i>Security and Cryptography for Networks: 14th International Conference</i> (Vol. 14974, pp. 294–313). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-71073-5_14\">https://doi.org/10.1007/978-3-031-71073-5_14</a>","ieee":"J. F. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, and K. Z. Pietrzak, “DeCAF: Decentralizable CGKA with fast healing,” in <i>Security and Cryptography for Networks: 14th International Conference</i>, Amalfi, Italy, 2024, vol. 14974, pp. 294–313.","ista":"Alwen JF, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ. 2024. DeCAF: Decentralizable CGKA with fast healing. Security and Cryptography for Networks: 14th International Conference. SCN: Security and Cryptography for Networks, LNCS, vol. 14974, 294–313.","chicago":"Alwen, Joel F, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “DeCAF: Decentralizable CGKA with Fast Healing.” In <i>Security and Cryptography for Networks: 14th International Conference</i>, edited by Clemente Galdi and Duong Hieu Phan, 14974:294–313. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-71073-5_14\">https://doi.org/10.1007/978-3-031-71073-5_14</a>.","short":"J.F. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, in:, C. Galdi, D.H. Phan (Eds.), Security and Cryptography for Networks: 14th International Conference, Springer Nature, Cham, 2024, pp. 294–313.","ama":"Alwen JF, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ. DeCAF: Decentralizable CGKA with fast healing. In: Galdi C, Phan DH, eds. <i>Security and Cryptography for Networks: 14th International Conference</i>. Vol 14974. Cham: Springer Nature; 2024:294–313. doi:<a href=\"https://doi.org/10.1007/978-3-031-71073-5_14\">10.1007/978-3-031-71073-5_14</a>"},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"alternative_title":["LNCS"],"corr_author":"1","place":"Cham","external_id":{"isi":["001330408000014"]},"date_updated":"2026-10-16T08:11:07Z","publisher":"Springer Nature","_id":"18086","title":"DeCAF: Decentralizable CGKA with fast healing"},{"year":"2024","researchdata_availability":"no","status":"public","intvolume":"      2024","type":"journal_article","issue":"4","date_created":"2025-01-29T13:39:34Z","date_published":"2024-07-01T00:00:00Z","oa":1,"fulldoi":"https://doi.org/10.56553/popets-2024-0134","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Proceedings on Privacy Enhancing Technologies","conference":{"location":"Bristol, UK/Virtual","start_date":"2024-07-15","name":"PETs: Privacy Enhancing Technologies Symposium ","end_date":"2024-07-20"},"article_type":"original","OA_type":"gold","file":[{"access_level":"open_access","date_created":"2025-01-29T13:44:47Z","file_name":"2024_ProcPrivacyEnhTech_Guenther.pdf","checksum":"348ed6adcf6ad2f925227bde1758cae6","date_updated":"2025-01-29T13:44:47Z","relation":"main_file","content_type":"application/pdf","file_id":"18962","success":1,"file_size":611567,"creator":"dernst"}],"quality_controlled":"1","supplementarymaterial":"no","volume":2024,"OA_place":"publisher","page":"636-648","license":"https://creativecommons.org/licenses/by/4.0/","das_tickbox":"0","author":[{"id":"ec98511c-eb8e-11eb-b029-edd25d7271a1","last_name":"Günther","first_name":"Christoph Ullrich","full_name":"Günther, Christoph Ullrich"},{"first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"day":"01","date_updated":"2026-10-16T08:29:47Z","ddc":["000"],"publisher":"Privacy Enhancing Technologies Symposium Advisory Board","_id":"18961","acknowledgement":"We thank Raluca-Georgia Diugan for her initial contributions and support afterward.\r\nThis research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/F85.","title":"Deniability in automated contact tracing: Impossibilities and possibilities","article_processing_charge":"No","publication_identifier":{"issn":["2299-0984"]},"abstract":[{"lang":"eng","text":"Automated contact tracing (ACT) emerged as a promising measure to curb the spread of Covid-19. Users enable ACT on their smartphones to automatically record contacts with other users. If a user tests positive for the disease, they report their diagnosis to alert their contacts.\r\nDesigning effective ACT protocols is challenging since they need to be efficient and secure while also ensuring users' privacy. As ACT protocols necessarily leak some information by design, defining privacy is difficult. For example, a user cannot deny having met another user. Ideally, however, the user can plausibly deny everything else, in particular, when they met. We call this privacy property contact-time deniability.\r\nWhile some early works discussed contact-time deniability informally, it has received little attention since then. We investigate deniability from a rigorous, theoretical point of view and arrive at the following impossibility result:\r\nA decentralized protocol with unidirectional communication cannot be contact-time deniable and replay-secure. This holds even if malicious users treat smartphones as black-boxes.\r\n Unidirectional protocols are usually very efficient and many proposals are unidirectional, e.g., the widely-deployed Google-Apple Exposure Notifications. So the impossibility result considerably constrains the design space of efficient, secure, and private ACT protocols. However, it can also be used as a guide; we discuss several possibilities to achieve contact-time deniability in practice."}],"file_date_updated":"2025-01-29T13:44:47Z","doi":"10.56553/popets-2024-0134","citation":{"apa":"Günther, C. U., &#38; Pietrzak, K. Z. (2024). Deniability in automated contact tracing: Impossibilities and possibilities. <i>Proceedings on Privacy Enhancing Technologies</i>. Bristol, UK/Virtual: Privacy Enhancing Technologies Symposium Advisory Board. <a href=\"https://doi.org/10.56553/popets-2024-0134\">https://doi.org/10.56553/popets-2024-0134</a>","mla":"Günther, Christoph Ullrich, and Krzysztof Z. Pietrzak. “Deniability in Automated Contact Tracing: Impossibilities and Possibilities.” <i>Proceedings on Privacy Enhancing Technologies</i>, vol. 2024, no. 4, Privacy Enhancing Technologies Symposium Advisory Board, 2024, pp. 636–48, doi:<a href=\"https://doi.org/10.56553/popets-2024-0134\">10.56553/popets-2024-0134</a>.","ama":"Günther CU, Pietrzak KZ. Deniability in automated contact tracing: Impossibilities and possibilities. <i>Proceedings on Privacy Enhancing Technologies</i>. 2024;2024(4):636-648. doi:<a href=\"https://doi.org/10.56553/popets-2024-0134\">10.56553/popets-2024-0134</a>","chicago":"Günther, Christoph Ullrich, and Krzysztof Z Pietrzak. “Deniability in Automated Contact Tracing: Impossibilities and Possibilities.” <i>Proceedings on Privacy Enhancing Technologies</i>. Privacy Enhancing Technologies Symposium Advisory Board, 2024. <a href=\"https://doi.org/10.56553/popets-2024-0134\">https://doi.org/10.56553/popets-2024-0134</a>.","short":"C.U. Günther, K.Z. Pietrzak, Proceedings on Privacy Enhancing Technologies 2024 (2024) 636–648.","ista":"Günther CU, Pietrzak KZ. 2024. Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. 2024(4), 636–648.","ieee":"C. U. Günther and K. Z. Pietrzak, “Deniability in automated contact tracing: Impossibilities and possibilities,” <i>Proceedings on Privacy Enhancing Technologies</i>, vol. 2024, no. 4. Privacy Enhancing Technologies Symposium Advisory Board, pp. 636–648, 2024."},"corr_author":"1","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"has_accepted_license":"1","project":[{"grant_number":"F8509","name":"Security and Privacy by Design for Complex Systems","_id":"34a34d57-11ca-11ed-8bc3-a2688a8724e1"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"06","oa_version":"Published Version","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"keyword":["Random Matrices","Spectrum","Central Limit Theorem","Resolvent","Free Probability"],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"article_processing_charge":"No","doi":"10.15479/at:ista:17164","citation":{"short":"J. Reker, Central Limit Theorems for Random Matrices: From Resolvents to Free Probability, Institute of Science and Technology Austria, 2024.","chicago":"Reker, Jana. “Central Limit Theorems for Random Matrices: From Resolvents to Free Probability.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17164\">https://doi.org/10.15479/at:ista:17164</a>.","ama":"Reker J. Central limit theorems for random matrices: From resolvents to free probability. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17164\">10.15479/at:ista:17164</a>","ieee":"J. Reker, “Central limit theorems for random matrices: From resolvents to free probability,” Institute of Science and Technology Austria, 2024.","ista":"Reker J. 2024. Central limit theorems for random matrices: From resolvents to free probability. Institute of Science and Technology Austria.","mla":"Reker, Jana. <i>Central Limit Theorems for Random Matrices: From Resolvents to Free Probability</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17164\">10.15479/at:ista:17164</a>.","apa":"Reker, J. (2024). <i>Central limit theorems for random matrices: From resolvents to free probability</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17164\">https://doi.org/10.15479/at:ista:17164</a>"},"file_date_updated":"2024-06-26T12:44:53Z","abstract":[{"text":"This thesis is structured into two parts. In the first part, we consider the random\r\nvariable X := Tr(f1(W)A1 . . . fk(W)Ak) where W is an N × N Hermitian Wigner matrix, k ∈ N, and we choose (possibly N-dependent) regular functions f1, . . . , fk as well as\r\nbounded deterministic matrices A1, . . . , Ak. In this context, we prove a functional central\r\nlimit theorem on macroscopic and mesoscopic scales, showing that the fluctuations of X\r\naround its expectation are Gaussian and that the limiting covariance structure is given\r\nby a deterministic recursion. We further give explicit error bounds in terms of the scaling\r\nof f1, . . . , fk and the number of traceless matrices among A1, . . . , Ak, thus extending\r\nthe results of Cipolloni, Erdős and Schröder [40] to products of arbitrary length k ≥ 2.\r\nAnalyzing the underlying combinatorics leads to a non-recursive formula for the variance\r\nof X as well as the covariance of X and Y := Tr(fk+1(W)Ak+1 . . . fk+ℓ(W)Ak+ℓ) of similar\r\nbuild. When restricted to polynomials, these formulas reproduce recent results of Male,\r\nMingo, Peché, and Speicher [107], showing that the underlying combinatorics of noncrossing partitions and annular non-crossing permutations continue to stay valid beyond\r\nthe setting of second-order free probability theory. As an application, we consider the\r\nfluctuation of Tr(eitW A1e\r\n−itW A2)/N around its thermal value Tr(A1) Tr(A2)/N2 when t\r\nis large and give an explicit formula for the variance.\r\nThe second part of the thesis collects three smaller projects focusing on different random\r\nmatrix models. In the first project, we show that a class of weakly perturbed Hamiltonians\r\nof the form Hλ = H0 + λW, where W is a Wigner matrix, exhibits prethermalization.\r\nThat is, the time evolution generated by Hλ relaxes to its ultimate thermal state via an\r\nintermediate prethermal state with a lifetime of order λ\r\n−2\r\n. As the main result, we obtain\r\na general relaxation formula, expressing the perturbed dynamics via the unperturbed\r\ndynamics and the ultimate thermal state. The proof relies on a two-resolvent global law\r\nfor the deformed Wigner matrix Hλ.\r\nThe second project focuses on correlated random matrices, more precisely on a correlated N × N Hermitian random matrix with a polynomially decaying metric correlation\r\nstructure. A trivial a priori bound shows that the operator norm of this model is stochastically dominated by √\r\nN. However, by calculating the trace of the moments of the matrix\r\nand using the summable decay of the cumulants, the norm estimate can be improved to a\r\nbound of order one.\r\nIn the third project, we consider a multiplicative perturbation of the form UA(t) where U\r\nis a unitary random matrix and A = diag(t, 1, ..., 1). This so-called UA model was\r\nfirst introduced by Fyodorov [73] for its applications in scattering theory. We give a\r\ngeneral description of the eigenvalue trajectories obtained by varying the parameter t and\r\nintroduce a flow of deterministic domains that separates the outlier resulting from the\r\nrank-one perturbation from the typical eigenvalues for all sub-critical timescales. The\r\nresults are obtained under generic assumptions on U that hold for various unitary random\r\nmatrices, including the circular unitary ensemble (CUE) in the original formulation of\r\nthe model.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"title":"Central limit theorems for random matrices: From resolvents to free probability","_id":"17164","publisher":"Institute of Science and Technology Austria","date_updated":"2026-10-16T08:35:03Z","ddc":["519"],"degree_awarded":"PhD","doi_confirm":"1","author":[{"first_name":"Jana","full_name":"Reker, Jana","last_name":"Reker","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9"}],"day":"26","ec_funded":1,"OA_place":"publisher","das_tickbox":"0","page":"206","supervisor":[{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László"}],"supplementarymaterial":"no","file":[{"file_name":"ISTA_Thesis_JReker.pdf","access_level":"open_access","date_created":"2024-06-26T12:39:36Z","checksum":"fb16d86e1f2753dc3a9e14d2bdfd84cd","relation":"main_file","date_updated":"2024-06-26T12:44:53Z","file_id":"17176","content_type":"application/pdf","creator":"jreker","file_size":2783027},{"relation":"source_file","date_updated":"2024-06-26T12:44:53Z","checksum":"cb1e54009d47c1dcf5b866c4566fa27f","date_created":"2024-06-26T12:39:42Z","access_level":"closed","file_name":"ISTA_Thesis_JReker_SourceFiles.zip","file_size":3054878,"creator":"jreker","file_id":"17177","content_type":"application/zip"}],"publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:17164","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"date_created":"2024-06-24T11:23:29Z","oa":1,"date_published":"2024-06-26T00:00:00Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17173"},{"status":"public","id":"11135","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"17174"},{"relation":"part_of_dissertation","status":"public","id":"17047"},{"status":"public","id":"17154","relation":"part_of_dissertation"}]},"status":"public","researchdata_availability":"no","year":"2024","type":"dissertation"},{"file":[{"date_created":"2024-11-19T12:39:55Z","access_level":"open_access","file_name":"Roshan PhD thesis-Final.pdf","relation":"main_file","date_updated":"2024-11-19T12:39:55Z","checksum":"340f2bfe882c8a85e11ec0687ca15f5e","content_type":"application/pdf","file_id":"18570","success":1,"file_size":10960975,"creator":"rsatapat"},{"file_name":"Roshan PhD thesis-Final.docx","access_level":"closed","date_created":"2024-11-19T12:46:47Z","checksum":"0f846fce60d6ea511e07f77eff59a6a1","date_updated":"2024-12-13T10:27:25Z","relation":"source_file","file_id":"18571","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"rsatapat","file_size":36695917}],"supervisor":[{"last_name":"Jösch","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","first_name":"Maximilian A"}],"supplementarymaterial":"no","ec_funded":1,"OA_place":"publisher","das_tickbox":"0","license":"https://creativecommons.org/licenses/by-sa/4.0/","page":"114","doi_confirm":"1","author":[{"full_name":"Satapathy, Roshan K","first_name":"Roshan K","orcid":"0009-0006-2974-5075","last_name":"Satapathy","id":"46046B7A-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"day":"20","related_material":{"record":[{"status":"public","id":"18444","relation":"part_of_dissertation"}]},"researchdata_availability":"no","year":"2024","status":"public","type":"dissertation","date_created":"2024-11-19T12:34:30Z","oa":1,"date_published":"2024-11-20T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18568","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"11","language":[{"iso":"eng"}],"_id":"18568","publisher":"Institute of Science and Technology Austria","date_updated":"2026-10-16T10:11:24Z","ddc":["573"],"degree_awarded":"PhD","acknowledgement":"I am incredibly thankful for the outstanding support provided by ISTA, especially the Machine Shop team, who made conducting research much easier and more efficient. I am also grateful for the funding provided by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization of neuronal processing”.","title":"Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster","article_processing_charge":"No","citation":{"apa":"Satapathy, R. K. (2024). <i>Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>","mla":"Satapathy, Roshan K. <i>Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>.","ama":"Satapathy RK. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>","chicago":"Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>.","short":"R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria, 2024.","ista":"Satapathy RK. 2024. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. Institute of Science and Technology Austria.","ieee":"R. K. Satapathy, “Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria, 2024."},"doi":"10.15479/at:ista:18568","file_date_updated":"2024-12-13T10:27:25Z","publication_identifier":{"isbn":["978-3-99078-047-3"],"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Locomotion is ubiquitous in the animal kingdom because an animal's survival depends on its ability to navigate its environment to find food, avoid predators and locate potential mates. These behaviours require control mechanisms that can extract information from the environment, particularly visual cues. Selective evolutionary pressures have thus refined such visuomotor transformations in a species-specific manner to meet the specific ecological and ethological challenges of each organism. However, a common challenge across organisms as visual information processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise disparate pieces of information into a coherent percept or unified picture of the world. In this thesis, I investigate how disparate visual information is combined in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor this, I first designed and built a behavioural setup to record locomotion and present visual stimuli to freely-walking fruit flies in a closed-loop manner. This setup allowed the investigation of innate visually-guided behaviours, including the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I investigated the optomotor response, a reflexive visual stabilisation behaviour in which flies turn in the direction of global motion to minimise retinal slip. This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs); a complex network of optic-flow-sensitive neurons essential for self-motion estimation. Using a novel genetic mutant, I demonstrate that electrical coupling between two LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between smooth optomotor turning and saccadic anti-optomotor responses. These findings underscore the critical role of binocular motion cue integration in guiding course control. Finally, I developed a novel behavioural paradigm in which a sexually aroused male fruit fly is presented with an optomotor distractor. This setup creates competition between two visual behaviours, courtship tracking and the  optomotor response, enabling me to explore how the visual system resolves this conflict. In this setting, males\r\nengaged in courtship selectively suppress their optomotor response based on the female's location. Furthermore, when this experiment is replicated with an “artificial female”, optogenetically aroused males alternate between tracking and optomotor responses. The probability and dynamics of this switching are determined by the relative strengths of the two competing stimuli. In summary, the results presented in this thesis explore two mechanisms – integration and competition - through which visual information is combined in the brain of the fruit fly to drive locomotion."}],"corr_author":"1","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"MaJö"}]},{"author":[{"orcid":"0009-0006-2974-5075","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy","full_name":"Satapathy, Roshan K","first_name":"Roshan K"},{"first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","last_name":"Symonova","first_name":"Olga","full_name":"Symonova, Olga"},{"first_name":"Victoria","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva"}],"month":"09","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Published Version","project":[{"grant_number":"429960716","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","name":"Evolution of Sensorimotor Transformation Across Diptera"}],"file":[{"access_level":"open_access","date_created":"2024-09-03T17:39:32Z","file_name":"BehaviouralData.zip","checksum":"df9d6c8ddffa046c3b1639281f83cfcf","date_updated":"2024-09-03T17:39:32Z","relation":"main_file","content_type":"application/x-zip-compressed","file_id":"17489","success":1,"file_size":965778072,"creator":"rsatapat"}],"corr_author":"1","keyword":["drosophila","behaviour","locomotion","gap junctions"],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:17488","article_processing_charge":"No","citation":{"ieee":"R. K. Satapathy, M. A. Jösch, O. Symonova, and V. Pokusaeva, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies.” Institute of Science and Technology Austria, 2024.","ista":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>.","chicago":"Satapathy, Roshan K, Maximilian A Jösch, Olga Symonova, and Victoria Pokusaeva. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>.","short":"R.K. Satapathy, M.A. Jösch, O. Symonova, V. Pokusaeva, (2024).","ama":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>","mla":"Satapathy, Roshan K., et al. <i>Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>.","apa":"Satapathy, R. K., Jösch, M. A., Symonova, O., &#38; Pokusaeva, V. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>"},"file_date_updated":"2024-09-03T17:39:32Z","doi":"10.15479/AT:ISTA:17488","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Behavioural data for Pokusaeva, Satapathy et al. Relevant information can be found in the 'README.txt' file.","lang":"eng"}],"date_created":"2024-09-03T17:42:46Z","oa":1,"date_published":"2024-09-01T00:00:00Z","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","_id":"17488","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"18444"}]},"publisher":"Institute of Science and Technology Austria","date_updated":"2026-10-16T10:11:24Z","year":"2024","status":"public","ddc":["570"],"type":"research_data"},{"date_published":"2024-07-09T00:00:00Z","oa":1,"date_created":"2024-07-09T09:14:24Z","type":"dissertation","researchdata_availability":"no","year":"2024","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"10545","status":"public"},{"relation":"part_of_dissertation","id":"10067","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13125"},{"id":"11471","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"17222","relation":"part_of_dissertation"}]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.15479/at:ista:17208","publication_status":"published","supplementarymaterial":"no","supervisor":[{"first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"file":[{"file_id":"17212","content_type":"application/zip","creator":"rmedinar","file_size":"14218691","file_name":"Raimel_Thesis-Final.zip","date_created":"2024-07-09T09:21:44Z","access_level":"closed","relation":"source_file","date_updated":"2024-07-10T11:34:09Z","checksum":"6f45273d04f4418bc2adc018baed0525"},{"date_created":"2024-07-17T09:23:24Z","access_level":"open_access","file_name":"Raimel_Thesis-20_pdfa.pdf","date_updated":"2024-07-17T09:23:24Z","relation":"main_file","checksum":"6724a95bec772dbabc0111b9f08a805e","content_type":"application/pdf","file_id":"17275","success":1,"file_size":11253627,"creator":"rmedinar"}],"day":"09","acknowledged_ssus":[{"_id":"ScienComp"}],"doi_confirm":"1","author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A"}],"page":"133","das_tickbox":"0","OA_place":"publisher","ec_funded":1,"title":"Exploring the optimization landscape of variational quantum algorithms","degree_awarded":"PhD","ddc":["539"],"date_updated":"2026-10-16T12:14:52Z","_id":"17208","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"has_accepted_license":"1","keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"corr_author":"1","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization.  We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration."}],"doi":"10.15479/at:ista:17208","citation":{"mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>.","apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>","short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria."},"file_date_updated":"2024-07-17T09:23:24Z","article_processing_charge":"No","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"month":"07","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version"},{"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"fulldoi":"https://doi.org/10.15479/at:ista:14711","publication_status":"published","type":"dissertation","researchdata_availability":"no","year":"2024","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"10787","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10658"},{"id":"14732","relation":"part_of_dissertation","status":"public"}]},"date_published":"2024-01-19T00:00:00Z","oa":1,"date_created":"2023-12-26T22:49:53Z","page":"183","das_tickbox":"0","OA_place":"publisher","ec_funded":1,"day":"19","acknowledged_ssus":[{"_id":"SSU"}],"author":[{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","last_name":"Olusanya","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O"}],"doi_confirm":"1","file":[{"creator":"oolusany","file_size":16986244,"content_type":"application/zip","file_id":"14730","date_updated":"2024-01-03T18:30:13Z","relation":"source_file","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","date_created":"2024-01-03T18:30:13Z","access_level":"closed"},{"date_updated":"2024-01-03T18:31:34Z","relation":"main_file","checksum":"0e331585e3cd4823320aab4e69e64ccf","date_created":"2024-01-03T18:31:34Z","access_level":"open_access","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","file_size":6460403,"creator":"oolusany","content_type":"application/pdf","file_id":"14731","success":1}],"supplementarymaterial":"yes","supervisor":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"}],"abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2024-01-03T18:31:34Z","citation":{"apa":"Olusanya, O. O. (2024). <i>Local adaptation, genetic load and extinction in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>","mla":"Olusanya, Oluwafunmilola O. <i>Local Adaptation, Genetic Load and Extinction in Metapopulations</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>."},"doi":"10.15479/at:ista:14711","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"corr_author":"1","degree_awarded":"PhD","date_updated":"2026-10-21T08:24:47Z","ddc":["576"],"_id":"14711","publisher":"Institute of Science and Technology Austria","title":"Local adaptation, genetic load and extinction in metapopulations","oa_version":"Published Version","month":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896"},{"name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380"}]},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18135","oa":1,"date_published":"2024-09-23T00:00:00Z","date_created":"2024-09-24T10:56:25Z","type":"dissertation","related_material":{"record":[{"status":"public","id":"11732","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14542"},{"relation":"part_of_dissertation","id":"18107","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17240"},{"id":"14931","status":"public","relation":"part_of_dissertation"}]},"year":"2024","researchdata_availability":"no","status":"public","day":"23","doi_confirm":"1","author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard"}],"das_tickbox":"0","page":"353","ec_funded":1,"OA_place":"publisher","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"supplementarymaterial":"no","file":[{"creator":"alaurits","file_size":3648831,"success":1,"content_type":"application/pdf","file_id":"18147","date_updated":"2024-09-26T13:11:24Z","relation":"main_file","checksum":"c7bc3b31e430d57c65393051ca439575","file_name":"Lauritsen-thesis-final.pdf","date_created":"2024-09-26T13:11:24Z","access_level":"open_access"},{"file_size":1625888,"creator":"alaurits","file_id":"18148","content_type":"application/x-zip-compressed","date_updated":"2024-09-26T13:12:55Z","relation":"source_file","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","date_created":"2024-09-26T13:12:55Z","access_level":"closed","file_name":"Lauritsen-thesis-source.zip"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","citation":{"ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024.","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>."},"doi":"10.15479/at:ista:18135","file_date_updated":"2024-09-26T13:12:55Z","abstract":[{"lang":"eng","text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$."}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"article_processing_charge":"No","title":"Energies of dilute Fermi gases and universalities in BCS theory","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","_id":"18135","date_updated":"2026-10-21T08:29:08Z","ddc":["515","539"],"month":"09","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","project":[{"name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}]},{"fulldoi":"https://doi.org/10.15479/at:ista:18674","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2024-12-18T14:24:43Z","date_published":"2024-12-18T00:00:00Z","oa":1,"researchdata_availability":"no","year":"2024","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11160"},{"status":"public","relation":"part_of_dissertation","id":"13267"},{"id":"18677","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14257"}]},"type":"dissertation","author":[{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"}],"doi_confirm":"1","day":"18","acknowledged_ssus":[{"_id":"Bio"}],"OA_place":"publisher","ec_funded":1,"page":"217","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","das_tickbox":"0","supplementarymaterial":"no","supervisor":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G"}],"file":[{"checksum":"1b42b8073e2bc09fc504da52372248c1","date_updated":"2024-12-18T14:17:34Z","relation":"main_file","file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","access_level":"open_access","date_created":"2024-12-18T14:17:34Z","creator":"jlyudchi","file_size":160536833,"success":1,"content_type":"application/pdf","file_id":"18675"},{"date_updated":"2024-12-18T14:41:53Z","relation":"source_file","checksum":"b4da84624060745519723698f7ddf54b","date_created":"2024-12-18T14:21:06Z","access_level":"closed","file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","file_size":99172203,"creator":"jlyudchi","file_id":"18676","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"isbn":[" 978-3-99078-051-0"],"issn":["2663-337X"]},"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue.","lang":"eng"}],"doi":"10.15479/at:ista:18674","file_date_updated":"2024-12-18T14:41:53Z","citation":{"apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024.","ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024.","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>."},"title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","date_updated":"2026-10-21T08:36:19Z","ddc":["004"],"publisher":"Institute of Science and Technology Austria","_id":"18674","degree_awarded":"PhD","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","oa_version":"Published Version","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}]},{"publication_status":"published","fulldoi":"https://doi.org/10.1002/anie.202316476","publication":"Angewandte Chemie International Edition","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2023-12-15T16:10:13Z","oa":1,"date_published":"2024-07-08T00:00:00Z","intvolume":"        63","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20607"}]},"year":"2024","researchdata_availability":"no","status":"public","issue":"28","type":"journal_article","author":[{"full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","last_name":"Jethwa"},{"full_name":"Mondal, Soumyadip","first_name":"Soumyadip","last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","first_name":"Bhargavi","full_name":"Pant, Bhargavi"},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"isi":1,"day":"08","ec_funded":1,"das_tickbox":"0","volume":63,"supplementarymaterial":"no","article_type":"review","pmid":1,"quality_controlled":"1","file":[{"creator":"dernst","file_size":4766445,"success":1,"file_id":"17261","content_type":"application/pdf","relation":"main_file","date_updated":"2024-07-16T11:54:46Z","checksum":"fe2c23454279eb9d76ed6ca9970c21c7","file_name":"2024_AngChemieInt_Jethwa.pdf","date_created":"2024-07-16T11:54:46Z","access_level":"open_access"}],"corr_author":"1","keyword":["General Chemistry","Catalysis"],"has_accepted_license":"1","department":[{"_id":"StFr"},{"_id":"GradSch"}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1002/anie.202316476","file_date_updated":"2024-07-16T11:54:46Z","citation":{"ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. 2024;63(28). doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>","chicago":"Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>.","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition 63 (2024).","ista":"Jethwa RB, Mondal S, Pant B, Freunberger SA. 2024. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 63(28), e202316476.","ieee":"R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28. Wiley, 2024.","apa":"Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2024). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>","mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28, e202316476, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>."},"abstract":[{"lang":"eng","text":"The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity."}],"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","publisher":"Wiley","_id":"14687","ddc":["540"],"date_updated":"2026-10-21T10:25:05Z","acknowledgement":"S.A.F. is indebted to ISTA for support. R.B.J. thanks the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 for funding. B.P. thanks Alistore ERI for providing a PhD scholarship.","external_id":{"isi":["001241932700001"],"pmid":["38095355"]},"month":"07","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","oa_version":"Published Version","article_number":"e202316476","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}]},{"oa_version":"Published Version","month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","ddc":["000","570"],"date_updated":"2026-10-21T10:52:44Z","_id":"18847","publisher":"Curran Associates","external_id":{"arxiv":["2405.17151"]},"acknowledgement":"We thank Piersilvio De Bartolomeis, and the full Causal Learning and Artificial Intelligence (CLAI) group at ISTA for the extremely helpful discussions. Riccardo Cadei was supported by a Google Research Scholar Award and a Google Initiated Gift to Francesco Locatello. We thank the Social Immunity team at ISTA particularly Michaela Hönigsberger and Wilfrid Jean Louis, for supporting the ecological experiment and Farnaz Beikzadeh Abbasi, Luisa Fiebig and Martin Estermann for annotating ant behavior in ISTAnt.","title":"Smoke and mirrors in causal downstream tasks","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Machine Learning and AI have the potential to transform data-driven\r\nscientific discovery, enabling accurate predictions for several scientific\r\nphenomena. As many scientific questions are inherently causal, this paper looks\r\nat the causal inference task of treatment effect estimation, where the outcome\r\nof interest is recorded in high-dimensional observations in a Randomized\r\nControlled Trial (RCT). Despite being the simplest possible causal setting and\r\na perfect fit for deep learning, we theoretically find that many common choices\r\nin the literature may lead to biased estimates. To test the practical impact of\r\nthese considerations, we recorded ISTAnt, the first real-world benchmark for\r\ncausal inference downstream tasks on high-dimensional observations as an RCT\r\nstudying how garden ants (Lasius neglectus) respond to microparticles applied\r\nonto their colony members by hygienic grooming. Comparing 6 480 models\r\nfine-tuned from state-of-the-art visual backbones, we find that the sampling\r\nand modeling choices significantly affect the accuracy of the causal estimate,\r\nand that classification accuracy is not a proxy thereof. We further validated\r\nthe analysis, repeating it on a synthetically generated visual data set\r\ncontrolling the causal model. Our results suggest that future benchmarks should\r\ncarefully consider real downstream scientific questions, especially causal\r\nones. Further, we highlight guidelines for representation learning methods to\r\nhelp answer causal questions in the sciences."}],"file_date_updated":"2025-01-27T11:42:24Z","citation":{"mla":"Cadei, Riccardo, et al. “Smoke and Mirrors in Causal Downstream Tasks.” <i>ICML 2024 Workshop AI4Science</i>, vol. 38, Curran Associates, 2024.","apa":"Cadei, R., Lindorfer, L., Cremer, S., Schmid, C., &#38; Locatello, F. (2024). Smoke and mirrors in causal downstream tasks. In <i>ICML 2024 Workshop AI4Science</i> (Vol. 38). Curran Associates.","chicago":"Cadei, Riccardo, Lukas Lindorfer, Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Smoke and Mirrors in Causal Downstream Tasks.” In <i>ICML 2024 Workshop AI4Science</i>, Vol. 38. Curran Associates, 2024.","short":"R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, F. Locatello, in:, ICML 2024 Workshop AI4Science, Curran Associates, 2024.","ama":"Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. Smoke and mirrors in causal downstream tasks. In: <i>ICML 2024 Workshop AI4Science</i>. Vol 38. Curran Associates; 2024.","ieee":"R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, and F. Locatello, “Smoke and mirrors in causal downstream tasks,” in <i>ICML 2024 Workshop AI4Science</i>, 2024, vol. 38.","ista":"Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. 2024. Smoke and mirrors in causal downstream tasks. ICML 2024 Workshop AI4Science. ICML: International Conference on Machine Learning vol. 38."},"corr_author":"1","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"has_accepted_license":"1","OA_type":"gold","file":[{"creator":"dernst","file_size":4453014,"success":1,"file_id":"18896","content_type":"application/pdf","checksum":"beedf05388bbdb7ddda81ec3d5ec7026","date_updated":"2025-01-27T11:42:24Z","relation":"main_file","file_name":"2024_ICML_Cadei.pdf","access_level":"open_access","date_created":"2025-01-27T11:42:24Z"}],"quality_controlled":"1","supplementarymaterial":"yes","volume":38,"OA_place":"publisher","das_tickbox":"0","author":[{"full_name":"Cadei, Riccardo","first_name":"Riccardo","last_name":"Cadei","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b"},{"first_name":"Lukas","full_name":"Lindorfer, Lukas","last_name":"Lindorfer","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia"},{"first_name":"Cordelia","full_name":"Schmid, Cordelia","last_name":"Schmid"},{"first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"}],"day":"25","status":"public","year":"2024","researchdata_availability":"yes","intvolume":"        38","related_material":{"record":[{"id":"18895","status":"public","relation":"research_data"},{"id":"19509","status":"public","relation":"later_version"}],"link":[{"relation":"software","url":"https://github.com/CausalLearningAI/ISTAnt"}]},"type":"conference","date_created":"2025-01-14T07:27:26Z","date_published":"2024-09-25T00:00:00Z","oa":1,"publication_status":"published","arxiv":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"ICML 2024 Workshop AI4Science","conference":{"start_date":"2024-07-26","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-26"}},{"corr_author":"1","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2","doi":"10.6084/M9.FIGSHARE.26484934.V2","citation":{"apa":"Cadei, R., Locatello, F., Cremer, S., Lindorfer, L., &#38; Schmid, C. (2024). ISTAnt. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>","mla":"Cadei, Riccardo, et al. <i>ISTAnt</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","ama":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. ISTAnt. 2024. doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>","chicago":"Cadei, Riccardo, Francesco Locatello, Sylvia Cremer, Lukas Lindorfer, and Cordelia Schmid. “ISTAnt.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>.","short":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, C. Schmid, (2024).","ista":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. 2024. ISTAnt, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","ieee":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, and C. Schmid, “ISTAnt.” Institute of Science and Technology Austria, 2024."},"abstract":[{"lang":"eng","text":"ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \\citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see 'annotations' folder). In one of the videos, one of the nestmates' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see 'video' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see 'experiments_settings.csv' file)."}],"date_created":"2025-01-27T11:45:43Z","oa":1,"title":"ISTAnt","date_published":"2024-10-23T00:00:00Z","publisher":"Institute of Science and Technology Austria","_id":"18895","related_material":{"record":[{"id":"18847","status":"public","relation":"used_in_publication"}]},"status":"public","date_updated":"2026-10-21T10:52:44Z","ddc":["570"],"year":"2024","type":"research_data_reference","author":[{"first_name":"Riccardo","full_name":"Cadei, Riccardo","last_name":"Cadei","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M","first_name":"Sylvia M"},{"full_name":"Lindorfer, Lukas","first_name":"Lukas","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","last_name":"Lindorfer"},{"full_name":"Schmid, Cordelia","first_name":"Cordelia","last_name":"Schmid"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","day":"23","main_file_link":[{"open_access":"1","url":"https://10.6084/M9.FIGSHARE.26484934.V2"}],"OA_place":"repository","oa_version":"Published Version","OA_type":"gold"},{"date_created":"2024-06-23T15:07:06Z","date_published":"2024-06-25T00:00:00Z","oa":1,"researchdata_availability":"no","status":"public","year":"2024","related_material":{"record":[{"relation":"part_of_dissertation","id":"17157","status":"public"}]},"type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:17156","publication_status":"published","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"supplementarymaterial":"no","supervisor":[{"last_name":"Hausel","orcid":"0000-0002-9582-2634","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás","first_name":"Tamás"}],"file":[{"file_name":"thesis.zip","access_level":"closed","date_created":"2024-06-26T20:56:27Z","checksum":"1610063569f5452f8a5acef728c2fc26","date_updated":"2024-06-26T21:00:14Z","relation":"source_file","content_type":"application/zip","file_id":"17179","creator":"krychlew","file_size":2761814},{"relation":"main_file","date_updated":"2024-06-26T20:58:24Z","checksum":"7bbadb1fbc9ed2a1ecf54597f88af99c","date_created":"2024-06-26T20:58:24Z","access_level":"open_access","file_name":"thesis.pdf","file_size":3695952,"creator":"krychlew","file_id":"17180","content_type":"application/pdf"}],"doi_confirm":"1","author":[{"full_name":"Rychlewicz, Kamil P","first_name":"Kamil P","last_name":"Rychlewicz","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425"}],"day":"25","OA_place":"publisher","page":"117","das_tickbox":"0","title":"Equivariant cohomology and rings of functions","date_updated":"2026-10-21T11:00:25Z","ddc":["516"],"publisher":"Institute of Science and Technology Austria","_id":"17156","degree_awarded":"PhD","keyword":["equivariant cohomology","zero schemes","algebraic groups","Lie algebras"],"corr_author":"1","alternative_title":["ISTA Thesis"],"department":[{"_id":"TaHa"},{"_id":"GradSch"}],"has_accepted_license":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This dissertation is the summary of the author’s work, concerning the relations between\r\ncohomology rings of algebraic varieties and rings of functions on zero schemes and fixed\r\npoint schemes. For most of the thesis, the focus is on smooth complex varieties with\r\nan action of a principally paired group, e.g. a parabolic subgroup of a reductive group.\r\nThe fundamental theorem 5.2.11 from co-authored article [66] says that if the principal\r\nnilpotent has a unique zero, then the zero scheme over the Kostant section is isomorphic\r\nto the spectrum of the equivariant cohomology ring, remembering the grading in terms of\r\na C^* action. A similar statement is proved also for the G-invariant functions on the total\r\nzero scheme over the whole Lie algebra. Additionally, we are able to prove an analogous\r\nresult for the GKM spaces, which poses the question on a joint generalisation.\r\nWe also tackle the situation of a singular variety. As long as it is embedded in a smooth\r\nvariety with regular action, we are able to study its cohomology as well by means of\r\nthe zero scheme. In case of e.g. Schubert varieties this determines the cohomology ring\r\ncompletely. In largest generality, this allows us to see a significant part of the cohomology\r\nring.\r\nWe also show (Theorem 6.2.1) that the cohomology ring of spherical varieties appears as\r\nthe ring of functions on the zero scheme. The computational aspect is not easy, but one\r\ncan hope that this can bring some concrete information about such cohomology rings.\r\nLastly, the K-theory conjecture 6.3.1 is studied, with some results attained for GKM\r\nspaces.\r\nThe thesis includes also an introduction to group actions on algebraic varieties. In\r\nparticular, the vector fields associated to the actions are extensively studied. We also\r\nprovide a version of the Kostant section for arbitrary principally paired group, which\r\nparametrises the regular orbits in the Lie algebra of an algebraic group. Before proving\r\nthe main theorem, we also include a historical overview of the field. In particular we bring\r\ntogether the results of Akyildiz, Carrell and Lieberman on non-equivariant cohomology\r\nrings."}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:17156","citation":{"mla":"Rychlewicz, Kamil P. <i>Equivariant Cohomology and Rings of Functions</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17156\">10.15479/at:ista:17156</a>.","apa":"Rychlewicz, K. P. (2024). <i>Equivariant cohomology and rings of functions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17156\">https://doi.org/10.15479/at:ista:17156</a>","ieee":"K. P. Rychlewicz, “Equivariant cohomology and rings of functions,” Institute of Science and Technology Austria, 2024.","ista":"Rychlewicz KP. 2024. Equivariant cohomology and rings of functions. Institute of Science and Technology Austria.","chicago":"Rychlewicz, Kamil P. “Equivariant Cohomology and Rings of Functions.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17156\">https://doi.org/10.15479/at:ista:17156</a>.","short":"K.P. Rychlewicz, Equivariant Cohomology and Rings of Functions, Institute of Science and Technology Austria, 2024.","ama":"Rychlewicz KP. Equivariant cohomology and rings of functions. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17156\">10.15479/at:ista:17156</a>"},"file_date_updated":"2024-06-26T21:00:14Z","project":[{"grant_number":"26525","name":"Topology of open smooth varieties with a torus action","_id":"34cd0f74-11ca-11ed-8bc3-bf0492a14a24"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"supervisor":[{"full_name":"Browning, Timothy D","first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"supplementarymaterial":"no","file":[{"checksum":"2f8cf5cefdab108b1979caa8146cae9a","relation":"source_file","date_updated":"2024-09-23T18:49:22Z","access_level":"closed","date_created":"2024-09-23T18:49:22Z","file_name":"PhDthesis (3).zip","file_size":5382106,"creator":"jglas","file_id":"18133","content_type":"application/x-zip-compressed"},{"file_name":"example-phd.pdf","access_level":"open_access","date_created":"2024-09-25T14:08:57Z","checksum":"08bb6f14c42b47ff25882a2ce3ea0d8a","date_updated":"2024-09-25T14:08:57Z","relation":"main_file","success":1,"content_type":"application/pdf","file_id":"18140","creator":"jglas","file_size":2380127}],"day":"23","author":[{"last_name":"Glas","id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","full_name":"Glas, Jakob","first_name":"Jakob"}],"doi_confirm":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","das_tickbox":"0","page":"195","OA_place":"publisher","oa":1,"date_published":"2024-09-23T00:00:00Z","date_created":"2024-09-23T18:58:08Z","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"18294"},{"id":"18293","status":"public","relation":"part_of_dissertation"},{"id":"18173","status":"public","relation":"part_of_dissertation"},{"id":"18295","relation":"part_of_dissertation","status":"public"}]},"researchdata_availability":"no","year":"2024","status":"public","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18132","project":[{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"09","oa_version":"Published Version","title":"Counting rational points over function fields","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","_id":"18132","ddc":["512"],"date_updated":"2026-10-21T11:02:28Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","citation":{"ama":"Glas J. Counting rational points over function fields. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18132\">10.15479/at:ista:18132</a>","chicago":"Glas, Jakob. “Counting Rational Points over Function Fields.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18132\">https://doi.org/10.15479/at:ista:18132</a>.","short":"J. Glas, Counting Rational Points over Function Fields, Institute of Science and Technology Austria, 2024.","ista":"Glas J. 2024. Counting rational points over function fields. Institute of Science and Technology Austria.","ieee":"J. Glas, “Counting rational points over function fields,” Institute of Science and Technology Austria, 2024.","apa":"Glas, J. (2024). <i>Counting rational points over function fields</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18132\">https://doi.org/10.15479/at:ista:18132</a>","mla":"Glas, Jakob. <i>Counting Rational Points over Function Fields</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18132\">10.15479/at:ista:18132</a>."},"file_date_updated":"2024-09-25T14:08:57Z","doi":"10.15479/at:ista:18132","abstract":[{"lang":"eng","text":"In this thesis, we are dealing with both arithmetic and geometric problems coming from the\r\nstudy of rational points with a particular focus on function fields over finite fields:\r\n(1) Using the circle method we produce upper bounds for the number of rational points of\r\nbounded height on diagonal cubic surfaces and fourfolds over Fq(t). This is based on\r\njoint work with Leonhard Hochfilzer.\r\n(2) We study rational points on smooth complete intersections X defined by cubic and\r\nquadratic hypersurfaces over Fq(t). We refine the Farey dissection of the “unit square”\r\ndeveloped by Vishe [202] and use the circle method with a Kloosterman refinement to\r\nestablish an asymptotic formula for the number of rational points of bounded height on\r\nX when dim(X) ≥ 23. Under the same hypotheses, we also verify weak approximation.\r\n(3) In joint work with Hochfilzer, we obtain upper bounds for the number of rational points of\r\nbounded height on del Pezzo surfaces of low degree over any global field. Our approach\r\nis to take hyperplane sections, which reduces the problem to uniform estimates for the\r\nnumber of rational points on curves.\r\n(4) We develop a version of the circle method capable of counting Fq-points on jet schemes\r\nof moduli spaces of rational curves on hypersurfaces. Combining this with a spreading\r\nout argument and a result of Mustaţă [150], this allows us to show that these moduli\r\nspaces only have canonical singularities under suitable assumptions on the degree and the\r\ndimension.\r\nIn addition, we give an overview of guiding questions and conjectures in the field of rational\r\npoints and explain the basic mechanism underlying the circle method.\r\n"}],"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No"},{"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"scopus_import":"1","month":"10","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. This work is sponsored in part by the United States NSF CCF-2118356 award. This research was partially funded by A-IQ Ready (Chips JU, grant agreement No. 101096658).","APC_amount":"2748 EUR","external_id":{"isi":["001420093700018"],"arxiv":["2408.05033"]},"_id":"18521","publisher":"Springer Nature","date_updated":"2026-10-21T13:14:54Z","ddc":["000"],"has_accepted_license":"1","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"corr_author":"1","alternative_title":["LNCS"],"doi":"10.1007/978-3-031-74234-7_18","citation":{"ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In: <i>24th International Conference on Runtime Verification</i>. Vol 15191. Springer Nature; 2024:282-301. doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” In <i>24th International Conference on Runtime Verification</i>, 15191:282–301. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>.","ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy,” in <i>24th International Conference on Runtime Verification</i>, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301.","apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., &#38; Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In <i>24th International Conference on Runtime Verification</i> (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>","mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” <i>24th International Conference on Runtime Verification</i>, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>."},"file_date_updated":"2024-11-11T09:42:28Z","abstract":[{"text":"In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples.","lang":"eng"}],"publication_identifier":{"isbn":["9783031742330"],"eissn":["1611-3349"],"issn":["0302-9743"]},"article_processing_charge":"Yes (in subscription journal)","volume":15191,"supplementarymaterial":"no","quality_controlled":"1","file":[{"access_level":"open_access","date_created":"2024-11-11T09:42:28Z","file_name":"2024_LNCS_Bonakdarpour.pdf","checksum":"7b8ca21b8c19ab796fa445b0e54003ca","relation":"main_file","date_updated":"2024-11-11T09:42:28Z","file_id":"18539","content_type":"application/pdf","success":1,"file_size":1897101,"creator":"dernst"}],"OA_type":"hybrid","day":"12","author":[{"full_name":"Bonakdarpour, Borzoo","first_name":"Borzoo","last_name":"Bonakdarpour"},{"full_name":"Momtaz, Anik","first_name":"Anik","last_name":"Momtaz"},{"last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"first_name":"Naci E","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"isi":1,"das_tickbox":"0","page":"282-301","ec_funded":1,"OA_place":"publisher","oa":1,"date_published":"2024-10-12T00:00:00Z","date_created":"2024-11-10T23:01:58Z","type":"conference","intvolume":"     15191","status":"public","year":"2024","researchdata_availability":"no","conference":{"location":"Istanbul, Turkey","name":"RV: Conference on Runtime Verification","end_date":"2024-10-17","start_date":"2024-10-15"},"publication":"24th International Conference on Runtime Verification","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"publication_status":"published","fulldoi":"https://doi.org/10.1007/978-3-031-74234-7_18"},{"scopus_import":"1","month":"09","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","article_number":"29","project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"has_accepted_license":"1","corr_author":"1","alternative_title":["LIPIcs"],"abstract":[{"text":"We study the following refinement relation between nondeterministic state-transition models: model ℬ strategically dominates model 𝒜 iff every deterministic refinement of 𝒜 is language contained in some deterministic refinement of ℬ. While language containment is trace inclusion, and the (fair) simulation preorder coincides with tree inclusion, strategic dominance falls strictly between the two and can be characterized as \"strategy inclusion\" between 𝒜 and ℬ: every strategy that resolves the nondeterminism of 𝒜 is dominated by a strategy that resolves the nondeterminism of ℬ. Strategic dominance can be checked in 2-ExpTime by a decidable first-order Presburger logic with quantification over words and strategies, called resolver logic. We give several other applications of resolver logic, including checking the co-safety, co-liveness, and history-determinism of boolean and quantitative automata, and checking the inclusion between hyperproperties that are specified by nondeterministic boolean and quantitative automata.","lang":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773393"]},"citation":{"mla":"Henzinger, Thomas A., et al. “Strategic Dominance: A New Preorder for Nondeterministic Processes.” <i>35th International Conference on Concurrency Theory</i>, vol. 311, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2024.29\">10.4230/LIPIcs.CONCUR.2024.29</a>.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2024). Strategic dominance: A new preorder for nondeterministic processes. In <i>35th International Conference on Concurrency Theory</i> (Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2024.29\">https://doi.org/10.4230/LIPIcs.CONCUR.2024.29</a>","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Strategic dominance: A new preorder for nondeterministic processes,” in <i>35th International Conference on Concurrency Theory</i>, Calgary, Canada, 2024, vol. 311.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2024. Strategic dominance: A new preorder for nondeterministic processes. 35th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 311, 29.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 35th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Strategic Dominance: A New Preorder for Nondeterministic Processes.” In <i>35th International Conference on Concurrency Theory</i>, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2024.29\">https://doi.org/10.4230/LIPIcs.CONCUR.2024.29</a>.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Strategic dominance: A new preorder for nondeterministic processes. In: <i>35th International Conference on Concurrency Theory</i>. Vol 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2024.29\">10.4230/LIPIcs.CONCUR.2024.29</a>"},"file_date_updated":"2024-09-17T07:48:56Z","doi":"10.4230/LIPIcs.CONCUR.2024.29","article_processing_charge":"Yes","title":"Strategic dominance: A new preorder for nondeterministic processes","external_id":{"isi":["001556847400029"],"arxiv":["2407.10473"]},"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","ddc":["000"],"date_updated":"2026-10-21T13:15:11Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"18068","day":"01","isi":1,"author":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi"},{"first_name":"Naci E","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"das_tickbox":"0","OA_place":"publisher","ec_funded":1,"supplementarymaterial":"no","volume":311,"file":[{"success":1,"content_type":"application/pdf","file_id":"18081","creator":"dernst","file_size":964124,"file_name":"2024_LIPICS_Henzinger.pdf","access_level":"open_access","date_created":"2024-09-17T07:48:56Z","checksum":"555bd343e1fb38adeab8fc465ff4fad8","relation":"main_file","date_updated":"2024-09-17T07:48:56Z"}],"quality_controlled":"1","OA_type":"gold","conference":{"location":"Calgary, Canada","name":"CONCUR: Conference on Concurrency Theory","end_date":"2024-09-13","start_date":"2024-09-09"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"35th International Conference on Concurrency Theory","fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2024.29","publication_status":"published","arxiv":1,"date_published":"2024-09-01T00:00:00Z","oa":1,"date_created":"2024-09-15T22:01:40Z","type":"conference","status":"public","researchdata_availability":"no","year":"2024","intvolume":"       311"},{"scopus_import":"1","month":"06","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"corr_author":"1","file_date_updated":"2025-01-27T14:17:37Z","citation":{"apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2024). Eight-partitioning points in 3D, and efficiently too. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 8:1-8:15). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">https://doi.org/10.4230/LIPIcs.SoCG.2024.8</a>","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">10.4230/LIPIcs.SoCG.2024.8</a>.","ista":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2024. Eight-partitioning points in 3D, and efficiently too. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry vol. 293, 8:1-8:15.","ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 8:1-8:15.","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:8:1-8:15. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">10.4230/LIPIcs.SoCG.2024.8</a>","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” In <i>40th International Symposium on Computational Geometry</i>, 293:8:1-8:15. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">https://doi.org/10.4230/LIPIcs.SoCG.2024.8</a>.","short":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15."},"doi":"10.4230/LIPIcs.SoCG.2024.8","abstract":[{"lang":"eng","text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in ℝ³ consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument.\r\nWe prove the following variant of this result: Any mass distribution (or point set) in ℝ³ admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction.\r\nMoreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2})."}],"publication_identifier":{"isbn":["9783959773164"]},"article_processing_charge":"Yes","title":"Eight-partitioning points in 3D, and efficiently too","acknowledgement":"Aronov, Boris: Work has been supported by NSF grants CCF 15-40656 and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of this research was conducted while BA was visiting ISTA in the summers of 2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting Professorship.\r\nBasit, Abdul: Work has been supported by Australian Research Council grant DP220102212.\r\nRamesh, Indu: Work supported by a Tandon School of Engineering Fellowship and by NSF Grant CCF-20-08551.\r\nBA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work.","external_id":{"arxiv":["2403.02627"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"18917","ddc":["510"],"date_updated":"2026-10-21T13:38:17Z","day":"06","author":[{"first_name":"Boris","full_name":"Aronov, Boris","last_name":"Aronov"},{"last_name":"Basit","full_name":"Basit, Abdul","first_name":"Abdul"},{"last_name":"Ramesh","first_name":"Indu","full_name":"Ramesh, Indu"},{"full_name":"Tasinato, Gianluca","first_name":"Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","last_name":"Tasinato"},{"first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"das_tickbox":"0","page":"8:1-8:15","OA_place":"publisher","volume":293,"supplementarymaterial":"no","quality_controlled":"1","file":[{"date_created":"2025-01-27T14:17:37Z","access_level":"open_access","file_name":"2024_LIPICs_Aronov.pdf","relation":"main_file","date_updated":"2025-01-27T14:17:37Z","checksum":"443aa29ea5d948e917cfccd681dcf176","file_id":"18918","content_type":"application/pdf","success":1,"file_size":880725,"creator":"dernst"}],"OA_type":"gold","conference":{"location":"Athens, Greece","start_date":"2024-06-11","name":"SoCG: Symposium on Computational Geometry","end_date":"2024-06-14"},"publication":"40th International Symposium on Computational Geometry","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"publication_status":"published","fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2024.8","oa":1,"date_published":"2024-06-06T00:00:00Z","date_created":"2025-01-27T14:19:17Z","type":"conference","intvolume":"       293","related_material":{"record":[{"relation":"later_version","id":"19860","status":"public"}]},"researchdata_availability":"no","status":"public","year":"2024"},{"title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","_id":"17206","publisher":"Institute of Science and Technology Austria","date_updated":"2026-09-24T11:19:04Z","ddc":["570"],"degree_awarded":"PhD","corr_author":"1","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"article_processing_charge":"No","file_date_updated":"2025-01-11T23:30:04Z","doi":"10.15479/at:ista:17206","citation":{"ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>","chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","short":"J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.","ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","ieee":"J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.","apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>."},"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. ","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"month":"07","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","date_created":"2024-07-05T14:15:29Z","oa":1,"date_published":"2024-07-05T00:00:00Z","status":"public","researchdata_availability":"no","year":"2024","type":"dissertation","publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:17206","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"supplementarymaterial":"no","file":[{"access_level":"closed","date_created":"2024-07-11T07:18:01Z","file_name":"ThesisRaices2024_postDefense.docx","embargo_to":"open_access","checksum":"d5e9234bde8667b005a8cfe18bb467d3","date_updated":"2025-01-11T23:30:04Z","relation":"source_file","file_id":"17223","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":13788479,"creator":"cchlebak"},{"creator":"cchlebak","file_size":5580296,"content_type":"application/pdf","file_id":"17224","embargo":"2025-01-11","date_updated":"2025-01-11T23:30:04Z","relation":"main_file","checksum":"f5ed0139aa3e11ce58369f0915647c5c","file_name":"ThesisRaices2024_nosignature.pdf","date_created":"2024-07-11T07:22:32Z","access_level":"open_access"}],"doi_confirm":"1","author":[{"full_name":"Raices, Julia","first_name":"Julia","last_name":"Raices","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"day":"05","ec_funded":1,"OA_place":"publisher","das_tickbox":"0","page":"82"},{"publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18101","oa":1,"date_published":"2024-09-26T00:00:00Z","date_created":"2024-09-20T10:21:03Z","type":"dissertation","status":"public","researchdata_availability":"unclear","year":"2024","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"day":"26","doi_confirm":"1","author":[{"full_name":"Porley, Dario J","first_name":"Dario J","last_name":"Porley","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87"}],"page":"131","ec_funded":1,"OA_place":"publisher","supervisor":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"supplementarymaterial":"unclear","file":[{"file_size":14213128,"creator":"dporley","file_id":"18149","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"3b8b0bacfe61112f3852744f3170e468","date_updated":"2025-03-25T23:30:03Z","relation":"source_file","access_level":"closed","date_created":"2024-09-26T13:40:33Z","file_name":"PhD_thesis_DPorley_final_20240919.docx","embargo_to":"open_access"},{"embargo":"2025-03-25","checksum":"6c3a652a8eede874118e11d66a63652f","relation":"main_file","date_updated":"2025-03-25T23:30:03Z","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","access_level":"open_access","date_created":"2024-09-26T13:41:39Z","creator":"dporley","file_size":18583031,"file_id":"18150","content_type":"application/pdf"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","citation":{"mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>"},"file_date_updated":"2025-03-25T23:30:03Z","doi":"10.15479/at:ista:18101","abstract":[{"lang":"eng","text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies."}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"article_processing_charge":"No","title":"Structural characterization of spumavirus capsid assemblies","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","_id":"18101","ddc":["570"],"date_updated":"2026-10-02T11:20:53Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"09","oa_version":"Published Version","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"25762","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A"}]}]