[{"publication_identifier":{"issn":["2663-337X"]},"citation":{"short":"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>","ieee":"G. Pascual Perez, “On the efficiency and security of secure group messaging,” Institute of Science and Technology Austria, 2024.","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>","ista":"Pascual Perez G. 2024. On the efficiency and security of secure group messaging. Institute of Science and Technology Austria.","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>.","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>."},"oa_version":"Published Version","corr_author":"1","title":"On the efficiency and security of secure group messaging","has_accepted_license":"1","date_published":"2024-09-18T00:00:00Z","month":"09","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"related_material":{"record":[{"id":"10408","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"11476"},{"id":"18086","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10049"}]},"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. "}],"department":[{"_id":"KrPi"},{"_id":"GradSch"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"18088","ec_funded":1,"publication_status":"published","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"}],"file_date_updated":"2024-09-19T12:36:08Z","date_created":"2024-09-18T12:59:49Z","doi":"10.15479/at:ista:18088","year":"2024","oa":1,"status":"public","degree_awarded":"PhD","type":"dissertation","page":"239","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","day":"18","ddc":["000"],"date_updated":"2026-04-07T13:01:26Z","author":[{"last_name":"Pascual Perez","orcid":"0000-0001-8630-415X","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","full_name":"Pascual Perez, Guillermo"}],"file":[{"access_level":"closed","checksum":"ce0dca715b3df48e52e2e891b6ac1bc5","date_updated":"2024-09-19T12:35:38Z","content_type":"application/x-zip-compressed","date_created":"2024-09-19T12:35:38Z","creator":"gpascual","file_name":"thesis_bundle.zip","file_size":11917734,"file_id":"18099","relation":"source_file"},{"file_size":2729427,"relation":"main_file","file_id":"18100","date_updated":"2024-09-19T12:36:08Z","access_level":"open_access","checksum":"4a2c72e90f1a0ef2a13cff800f8d1265","creator":"gpascual","date_created":"2024-09-19T12:36:08Z","content_type":"application/pdf","file_name":"thesis_gpasper.pdf"}],"article_processing_charge":"No","OA_place":"publisher"},{"has_accepted_license":"1","title":"Counting rational points over function fields","corr_author":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","citation":{"ista":"Glas J. 2024. Counting rational points over function fields. Institute of Science and Technology Austria.","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>.","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.","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>","ieee":"J. Glas, “Counting rational points over function fields,” Institute of Science and Technology Austria, 2024.","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>"},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","_id":"18132","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"department":[{"_id":"GradSch"},{"_id":"TiBr"}],"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"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18293"},{"status":"public","relation":"part_of_dissertation","id":"18294"},{"relation":"part_of_dissertation","status":"public","id":"18295"},{"relation":"part_of_dissertation","status":"public","id":"18173"}]},"project":[{"grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","name":"Rational curves via function field analytic number theory"}],"month":"09","date_published":"2024-09-23T00:00:00Z","page":"195","type":"dissertation","degree_awarded":"PhD","status":"public","oa":1,"year":"2024","doi":"10.15479/at:ista:18132","date_created":"2024-09-23T18:58:08Z","file_date_updated":"2024-09-25T14:08:57Z","supervisor":[{"full_name":"Browning, Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"OA_place":"publisher","article_processing_charge":"No","file":[{"access_level":"closed","checksum":"2f8cf5cefdab108b1979caa8146cae9a","date_updated":"2024-09-23T18:49:22Z","date_created":"2024-09-23T18:49:22Z","content_type":"application/x-zip-compressed","creator":"jglas","file_name":"PhDthesis (3).zip","file_size":5382106,"relation":"source_file","file_id":"18133"},{"creator":"jglas","content_type":"application/pdf","date_created":"2024-09-25T14:08:57Z","date_updated":"2024-09-25T14:08:57Z","access_level":"open_access","checksum":"08bb6f14c42b47ff25882a2ce3ea0d8a","success":1,"file_name":"example-phd.pdf","file_size":2380127,"relation":"main_file","file_id":"18140"}],"author":[{"full_name":"Glas, Jakob","first_name":"Jakob","last_name":"Glas","id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb"}],"date_updated":"2026-04-07T12:53:54Z","day":"23","ddc":["512"],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"publication_identifier":{"isbn":["978-3-99078-042-8"],"issn":["2663-337X"]},"citation":{"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>.","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>.","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","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>","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>","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024."},"oa_version":"Published Version","corr_author":"1","title":"Energies of dilute Fermi gases and universalities in BCS theory","has_accepted_license":"1","date_published":"2024-09-23T00:00:00Z","month":"09","project":[{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"related_material":{"record":[{"id":"11732","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14542"},{"id":"18107","relation":"part_of_dissertation","status":"public"},{"id":"17240","status":"public","relation":"part_of_dissertation"},{"id":"14931","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"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 $d=1,2,3$.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"_id":"18135","ec_funded":1,"publication_status":"published","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"file_date_updated":"2024-09-26T13:12:55Z","date_created":"2024-09-24T10:56:25Z","doi":"10.15479/at:ista:18135","oa":1,"year":"2024","status":"public","degree_awarded":"PhD","page":"353","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","ddc":["515","539"],"day":"23","date_updated":"2026-04-16T08:17:55Z","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"file":[{"relation":"main_file","file_id":"18147","file_size":3648831,"success":1,"file_name":"Lauritsen-thesis-final.pdf","creator":"alaurits","date_created":"2024-09-26T13:11:24Z","content_type":"application/pdf","date_updated":"2024-09-26T13:11:24Z","checksum":"c7bc3b31e430d57c65393051ca439575","access_level":"open_access"},{"file_name":"Lauritsen-thesis-source.zip","creator":"alaurits","date_created":"2024-09-26T13:12:55Z","content_type":"application/x-zip-compressed","date_updated":"2024-09-26T13:12:55Z","access_level":"closed","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","file_id":"18148","relation":"source_file","file_size":1625888}],"article_processing_charge":"No","OA_place":"publisher"},{"article_processing_charge":"No","file":[{"file_id":"18467","relation":"main_file","file_size":1672547,"success":1,"file_name":"MASisak_dissertation.pdf","date_updated":"2024-10-23T14:42:45Z","access_level":"open_access","checksum":"8c4893e726aaa4b3efb82758da9b6851","creator":"msisak","content_type":"application/pdf","date_created":"2024-10-23T14:42:45Z"},{"date_updated":"2024-10-24T08:09:13Z","access_level":"closed","checksum":"1831b072e861a1e5481024ca9d02b036","creator":"msisak","content_type":"application/x-zip-compressed","date_created":"2024-10-23T14:43:56Z","file_name":"MASisak_source.zip","file_size":617913,"relation":"source_file","file_id":"18468"}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T12:42:44Z","day":"24","ddc":["516"],"OA_type":"free access","author":[{"full_name":"Sisak, Maria A","last_name":"Sisak","first_name":"Maria A","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425"}],"doi":"10.15479/at:ista:18443","status":"public","oa":1,"year":"2024","degree_awarded":"PhD","page":"178","type":"dissertation","supervisor":[{"full_name":"Hausel, Tamás","last_name":"Hausel","orcid":"0000-0002-9582-2634","first_name":"Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file_date_updated":"2024-10-24T08:09:13Z","keyword":["hyperkaehler geometry","branes","mirror symmetry","T-duality"],"date_created":"2024-10-19T12:00:37Z","_id":"18443","publication_status":"published","project":[{"name":"Branes on hyperkähler manifolds","grant_number":"26069","_id":"6286e8c4-2b32-11ec-9570-f5297902f67f"}],"date_published":"2024-10-24T00:00:00Z","month":"10","department":[{"_id":"GradSch"},{"_id":"TaHa"}],"abstract":[{"lang":"eng","text":"In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli spaces. As a consequence, they\r\nconjecture an equivalence between categories of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler structures and the\r\ncorresponding branes on affine torus bundles. We use the techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles and connections. This T-duality in the appropriate context specializes to\r\nT-duality between BBB and BAA-branes.\r\n"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","title":"T-dual branes on hyperkähler manifolds","corr_author":"1","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"citation":{"ieee":"M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science and Technology Austria, 2024.","apa":"Sisak, M. A. (2024). <i>T-dual branes on hyperkähler manifolds</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>","ama":"Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>","short":"M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science and Technology Austria, 2024.","mla":"Sisak, Maria A. <i>T-Dual Branes on Hyperkähler Manifolds</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>.","chicago":"Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>.","ista":"Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria."}},{"oa_version":"Published Version","title":"Compressing large neural networks : Algorithms, systems and scaling laws","corr_author":"1","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"citation":{"mla":"Frantar, Elias. <i>Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17485\">10.15479/at:ista:17485</a>.","chicago":"Frantar, Elias. “Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17485\">https://doi.org/10.15479/at:ista:17485</a>.","ista":"Frantar E. 2024. Compressing large neural networks : Algorithms, systems and scaling laws. Institute of Science and Technology Austria.","apa":"Frantar, E. (2024). <i>Compressing large neural networks : Algorithms, systems and scaling laws</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17485\">https://doi.org/10.15479/at:ista:17485</a>","ieee":"E. Frantar, “Compressing large neural networks : Algorithms, systems and scaling laws,” Institute of Science and Technology Austria, 2024.","ama":"Frantar E. Compressing large neural networks : Algorithms, systems and scaling laws. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17485\">10.15479/at:ista:17485</a>","short":"E. Frantar, Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws, Institute of Science and Technology Austria, 2024."},"acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"17485","ec_funded":1,"publication_status":"published","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"date_published":"2024-09-05T00:00:00Z","month":"09","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"abstract":[{"lang":"eng","text":"Large language models (LLMs) have made tremendous progress in the past few years, from being able to generate coherent text to matching or surpassing humans in a wide variety of creative, knowledge or reasoning tasks. Much of this can be attributed to massively increased scale, both in the size of the model as well as the amount of training data, from 100s of millions to 100s of billions, or even trillions. This trend is expected to continue, which, although exciting, also raises major practical concerns. Already today's 100+ billion parameter LLMs require top-of-the-line hardware just to run. Hence, it is clear that sustaining these developments will require significant efficiency advances.\r\n\r\nHistorically, one of the most practical ways of improving model efficiency has been compression, especially in the form of sparsity or quantization. While this has been studied extensively in the past, existing accurate methods are all designed for models around 100 million parameters; scaling them up to ones literally 1000x larger is highly challenging. In this thesis, we introduce a new unified sparsification and quantization approach OBC, which through additional algorithmic enhancements leads to GPTQ and SparseGPT, the first techniques fast and accurate enough to compress 100+ billion parameter models to 4- or even 3-bit precision and 50% weight-sparsity, respectively. Additionally, we show how weight-only quantizion does not just bring space savings but also up to 4.5x faster generation speed, via custom GPU kernels.\r\n\r\nIn fact, we show for the first time that it is possible to develop an FP16 times INT4 mixed-precision matrix multiplication kernel, called Marlin, which comes close to simultaneously maximizing both memory and compute utilization, making weight-only quantization highly practical even for multi-user serving. Further, we demonstrate that GPTQ can be scaled to widely overparametrized trillion-parameter models, where extreme sub-1-bit compression rates can be achieved without any inference slow-down, by co-designing a bespoke entropy coding scheme together with an efficient kernel.\r\n\r\nFinally, we also study compression from the perspective of someone with access to massive amounts of compute resources for training large models completely from scratch. Here the key questions evolve around the joint scaling behavior between compression, model size, and amount of training data used. Based on extensive experimental results for both vision and text models, we introduce the first scaling law which accurately captures the relationship between weight-sparsity, number of non-zero weights and data. This further allows us to characterize the optimal sparsity, which we find to increase the longer a fixed cost model is being trained.\r\n\r\nOverall, this thesis presents contributions to three different angles of large model efficiency: affordable but accurate algorithms, highly efficient systems implementations, and fundamental scaling laws for compressed training."}],"related_material":{"record":[{"id":"17378","status":"public","relation":"part_of_dissertation"},{"id":"17087","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14458"},{"relation":"part_of_dissertation","status":"public","id":"18062"},{"id":"18061","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/at:ista:17485","status":"public","oa":1,"year":"2024","degree_awarded":"PhD","page":"129","type":"dissertation","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"file_date_updated":"2024-09-06T16:24:59Z","date_created":"2024-09-02T11:01:48Z","article_processing_charge":"No","file":[{"file_name":"thesis-final.zip","creator":"efrantar","content_type":"application/zip","date_created":"2024-09-05T12:04:11Z","date_updated":"2024-09-05T12:04:11Z","checksum":"5d785645805a78c5b4ce7cc3df557b09","access_level":"closed","relation":"source_file","file_id":"17570","file_size":1615167},{"file_name":"frantar_thesis_final.pdf","success":1,"access_level":"open_access","checksum":"a9dd1c2d23734986924eb44ebb55fd8f","date_updated":"2024-09-06T16:24:59Z","content_type":"application/pdf","date_created":"2024-09-06T16:24:59Z","creator":"efrantar","relation":"main_file","file_id":"17880","file_size":2376611}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"05","ddc":["000"],"date_updated":"2026-07-07T13:22:38Z","author":[{"first_name":"Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"}]},{"article_processing_charge":"No","file":[{"relation":"main_file","file_id":"18686","file_size":7752253,"success":1,"file_name":"Teresa_Heiss_PhD_Thesis_final.pdf","creator":"theiss","date_created":"2024-12-19T10:24:46Z","content_type":"application/pdf","date_updated":"2024-12-19T10:24:46Z","access_level":"open_access","checksum":"247bb057aed2fba1cd4711917aaa2d77"},{"date_updated":"2024-12-19T10:24:50Z","checksum":"9648b45c07a008ee11a07f99856a139d","access_level":"closed","creator":"theiss","date_created":"2024-12-19T10:24:50Z","content_type":"application/zip","file_name":"PhD_Thesis.zip","file_size":17197731,"file_id":"18687","relation":"source_file"}],"OA_place":"publisher","day":"17","ddc":["514","516","004"],"date_updated":"2026-07-07T13:43:27Z","author":[{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","orcid":"0000-0002-1780-2689","first_name":"Teresa","full_name":"Heiss, Teresa"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"I was supported by the European Research Council (ERC) Horizon 2020 project\r\n“Alpha Shape Theory Extended” No. 788183 and by the Pöttinger Scholarship. In addition,\r\nI am very thankful for having been able to attend the second Workshop for Women in\r\nComputational Topology in July 2019, funded by the Mathematical Sciences Institute at\r\nANU, the US National Science Foundation through the award CCF-1841455, the Australian\r\nMathematical Sciences Institute and the Association for Women in Mathematics. Two of the\r\nprojects presented in this thesis started there. One of them reached completion thanks to\r\nfunding from the MSRI Summer Research in Mathematics program awarded to me and my\r\ncollaborators in 2020.","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","type":"dissertation","page":"111","doi":"10.15479/at:ista:18667","status":"public","year":"2024","oa":1,"file_date_updated":"2024-12-19T10:24:50Z","keyword":["persistent homology","topological data analysis","periodic","crystalline materials","images","fingerprint"],"date_created":"2024-12-17T16:17:55Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","_id":"18667","ec_funded":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020"}],"month":"12","date_published":"2024-12-17T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"related_material":{"record":[{"id":"10828","status":"public","relation":"part_of_dissertation"},{"id":"11440","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"18673"},{"id":"9345","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Many chemical and physical properties of materials are determined by the material’s shape,\r\nfor example the size of its pores and the width of its tunnels. This makes materials science\r\na prime application area for geometrical and topological methods. Nevertheless many\r\nmethods in topological data analysis have not been satisfyingly extended to the needs of\r\nmaterials science. This thesis provides new methods and new mathematical theorems\r\ntargeted at those specific needs by answering four different research questions. While the\r\nmotivation for each of the research questions arises from materials science, the methods\r\nare versatile and can be applied in different areas as well. \r\n\r\nThe first research question is concerned with image data, for example a three-dimensional\r\ncomputed tomography (CT) scan of a material, like sand or stone. There are two commonly\r\nused topologies for digital images and depending on the application either of them might be\r\nrequired. However, software for computing the topological data analysis method persistence\r\nhomology, usually supports only one of the two topologies. We answer the question how to\r\ncompute persistent homology of an image with respect to one of the two topologies using\r\nsoftware that is intended for the other topology. \r\n\r\nThe second research question is concerned with image data as well, and asks how much\r\nof the topological information of an image is lost when the resolution is coarsened. As\r\ncomputer tomography scanners are more expensive the higher the resolution, it is an\r\nimportant question in materials science to know which resolution is enough to get satisfying\r\npersistent homology. We give theoretical bounds on the information loss based on different\r\ngeometrical properties of the object to be scanned. In addition, we conduct experiments on\r\nsand and stone CT image data. \r\n\r\nThe third research question is motivated by comparing crystalline materials efficiently. As\r\nthe atoms within a crystal repeat periodically, crystalline materials are either modeled by\r\nunmanageable infinite periodic point sets, or by one of their fundamental domains, which is\r\nunstable under perturbation. Therefore a fingerprint of crystalline materials is needed, with\r\nappropriate properties such that comparing the crystals can be eased by comparing the\r\nfingerprints instead. We define the density fingerprint and prove the necessary properties. \r\n\r\nThe fourth research question is motivated by studying the hole-structure or connectedness,\r\ni.e. persistent homology or merge trees, of crystalline materials. A common way to deal\r\nwith periodicity is to take a fundamental domain and identify opposite boundaries to form a\r\ntorus. However, computing persistent homology or merge trees on that torus loses some\r\nof the information materials scientists are interested in and is additionally not stable under\r\ncertain noise. We therefore decorate the merge tree stemming from the torus with additional\r\ninformation describing the density and growth rate of the periodic copies of a component\r\nwithin a growing spherical window. We prove all desired properties, like stability and efficient\r\ncomputability."}],"title":"New methods for applying topological data analysis to materials science","corr_author":"1","has_accepted_license":"1","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-052-7"]},"citation":{"chicago":"Heiss, Teresa. “New Methods for Applying Topological Data Analysis to Materials Science.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>.","mla":"Heiss, Teresa. <i>New Methods for Applying Topological Data Analysis to Materials Science</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>.","ista":"Heiss T. 2024. New methods for applying topological data analysis to materials science. Institute of Science and Technology Austria.","ama":"Heiss T. New methods for applying topological data analysis to materials science. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>","ieee":"T. Heiss, “New methods for applying topological data analysis to materials science,” Institute of Science and Technology Austria, 2024.","apa":"Heiss, T. (2024). <i>New methods for applying topological data analysis to materials science</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>","short":"T. Heiss, New Methods for Applying Topological Data Analysis to Materials Science, Institute of Science and Technology Austria, 2024."}},{"oa_version":"Published Version","has_accepted_license":"1","corr_author":"1","title":"Towards a quantum entanglement enhanced atom interferomter","citation":{"mla":"Li, Vyacheslav. <i>Towards a Quantum Entanglement Enhanced Atom Interferomter</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>.","chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>.","ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","apa":"Li, V. (2024). <i>Towards a quantum entanglement enhanced atom interferomter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>","short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"]},"_id":"17225","publication_status":"published","related_material":{"record":[{"id":"11438","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"text":"This thesis describes the development of an atom interferometer designed to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision measurements beyond\r\nthe standard quantum limit. While the project remains ongoing, significant progress has been\r\nmade.\r\nA key contribution of this work is the development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ framework. This software enables precise timing and control\r\nwithout requiring prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe interface offers user friendly visual comprehension of the experimental sequence and\r\nextended capabilities, allowing researchers to scan variables with a simple click of a mouse.\r\nThe main proposed project is to implement atom interferometric sequence with squeezed input\r\nstates inside of a dipole trap generated by a high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional atomic cloud split while maintaining relatively strong confinement\r\nin other directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro kelvin temperatures, load\r\nthem into the dipole trap and state prepare them to be used for squeezing and interferometric\r\nsequence.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"OnHo"}],"month":"07","date_published":"2024-07-11T00:00:00Z","project":[{"name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","grant_number":"101087907"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"oa":1,"year":"2024","status":"public","doi":"10.15479/at:ista:17225","type":"dissertation","page":"79","degree_awarded":"PhD","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hosten, Onur","first_name":"Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"date_created":"2024-07-11T09:46:48Z","file_date_updated":"2024-07-11T10:26:22Z","OA_place":"publisher","file":[{"creator":"vli","content_type":"application/pdf","date_created":"2024-07-11T10:26:22Z","date_updated":"2024-07-11T10:26:22Z","access_level":"open_access","checksum":"15b2dbe8d2c9ed7ca5dd413827928077","success":1,"file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","file_size":6729761,"file_id":"17228","relation":"main_file"},{"date_updated":"2024-07-11T10:26:22Z","checksum":"16e904a11d8d0ebb167cb654ddfc7fe5","access_level":"closed","creator":"vli","date_created":"2024-07-11T10:26:22Z","content_type":"application/x-zip-compressed","file_name":"PhD Thesis Vyacheslav Li.zip","file_size":9542859,"file_id":"17229","relation":"source_file"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Li, Vyacheslav","first_name":"Vyacheslav","last_name":"Li","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87"}],"day":"11","ddc":["530"],"date_updated":"2026-07-08T08:50:57Z"},{"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"date_created":"2024-06-07T16:14:13Z","file_date_updated":"2025-01-10T23:30:10Z","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"status":"public","oa":1,"year":"2024","doi":"10.15479/at:ista:17119","page":"105","type":"dissertation","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen"}],"day":"20","date_updated":"2026-04-07T13:21:37Z","ddc":["576"],"OA_place":"publisher","article_processing_charge":"No","file":[{"file_name":"thesis.zip","creator":"rkelemen","embargo_to":"open_access","content_type":"application/zip","date_created":"2024-06-07T16:09:17Z","date_updated":"2025-01-10T23:30:10Z","checksum":"fab59146e3b3dc2e5d214576984a2a63","access_level":"closed","file_id":"17121","relation":"source_file","file_size":180557931},{"file_id":"17213","relation":"main_file","file_size":19405484,"file_name":"thesis_to_archive.pdf","embargo":"2025-01-10","date_created":"2024-07-10T08:00:20Z","content_type":"application/pdf","creator":"rkelemen","access_level":"open_access","checksum":"91cc4c25a792239e8a7688e8aec7c62a","date_updated":"2025-01-10T23:30:10Z"}],"citation":{"ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>"},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"oa_version":"Published Version","has_accepted_license":"1","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"related_material":{"record":[{"id":"542","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10767"}]},"abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"},{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"month":"06","date_published":"2024-06-20T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"ec_funded":1,"_id":"17119","publication_status":"published"},{"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"citation":{"short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>."},"publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"has_accepted_license":"1","title":"Biochemical and structural insights into ADAR1 RNA editing","corr_author":"1","oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"month":"10","date_published":"2024-10-29T00:00:00Z","publication_status":"published","_id":"18477","date_created":"2024-10-27T07:35:13Z","file_date_updated":"2025-10-29T23:30:02Z","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"page":"124","type":"dissertation","degree_awarded":"PhD","status":"public","oa":1,"year":"2024","doi":"10.15479/at:ista:18477","author":[{"id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek","first_name":"Beata M","full_name":"Kaczmarek, Beata M"}],"day":"29","date_updated":"2026-04-07T13:23:59Z","ddc":["572"],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","article_processing_charge":"No","file":[{"file_size":23136626,"file_id":"18485","relation":"source_file","creator":"bkaczmar","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-10-29T11:56:36Z","date_updated":"2025-10-29T23:30:02Z","access_level":"closed","checksum":"2053294ea4d770c495e4cc501e2a218b","file_name":"20241029_PhD_thesis_BKaczmarek.docx"},{"file_id":"18486","relation":"main_file","file_size":11707360,"file_name":"20241029_PhD_thesis_BKaczmarek.pdf","embargo":"2025-10-29","content_type":"application/pdf","date_created":"2024-10-29T11:56:44Z","creator":"bkaczmar","access_level":"open_access","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","date_updated":"2025-10-29T23:30:02Z"}]},{"publication_identifier":{"issn":["2663-337X"]},"citation":{"short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>."},"title":"Adaptive hierarchical representations in the hippocampus","corr_author":"1","has_accepted_license":"1","oa_version":"Published Version","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"month":"01","date_published":"2024-01-19T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"abstract":[{"text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour.","lang":"eng"}],"publication_status":"published","_id":"14821","ec_funded":1,"file_date_updated":"2025-01-19T23:30:04Z","date_created":"2024-01-16T14:25:21Z","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"degree_awarded":"PhD","type":"dissertation","page":"89","doi":"10.15479/at:ista:14821","status":"public","oa":1,"year":"2024","ddc":["570"],"date_updated":"2026-04-07T13:21:56Z","day":"19","author":[{"full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","first_name":"Heloisa","orcid":"0009-0004-2973-278X","last_name":"Chiossi"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","file":[{"file_size":8656268,"relation":"source_file","file_id":"14838","date_created":"2024-01-19T11:04:05Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","creator":"hchiossi","checksum":"d3fa3de1abd5af5204c13e9d55375615","access_level":"closed","date_updated":"2025-01-19T23:30:04Z","file_name":"PhD_Thesis_190124.docx"},{"file_name":"PhD_Thesis_190124.pdf","embargo":"2025-01-19","content_type":"application/pdf","date_created":"2024-01-19T11:03:59Z","creator":"hchiossi","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","access_level":"open_access","date_updated":"2025-01-19T23:30:04Z","file_id":"14839","relation":"main_file","file_size":6567275}],"OA_place":"publisher"},{"oa_version":"Published Version","has_accepted_license":"1","corr_author":"1","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"ec_funded":1,"_id":"15101","publication_status":"published","related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"month":"03","date_published":"2024-03-11T00:00:00Z","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","oa":1,"status":"public","doi":"10.15479/at:ista:15101","type":"dissertation","page":"84","degree_awarded":"PhD","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"date_created":"2024-03-11T10:09:54Z","file_date_updated":"2024-04-02T22:30:03Z","OA_place":"publisher","file":[{"date_created":"2024-03-11T14:10:58Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","creator":"jchen","access_level":"closed","checksum":"db4947474ffa271e66c254b6fe876a55","date_updated":"2024-04-02T22:30:03Z","file_name":"Thesis_Jingjing CHEN.docx","file_size":11271363,"relation":"source_file","file_id":"15104"},{"relation":"main_file","file_id":"15105","file_size":16627311,"file_name":"Thesis_Jingjing CHEN_merged.pdf","embargo":"2024-04-01","content_type":"application/pdf","date_created":"2024-03-11T14:11:06Z","creator":"jchen","access_level":"open_access","checksum":"a5eeae8b5702cd540f5d03469bc33dde","date_updated":"2024-04-02T22:30:03Z"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","author":[{"id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"JingJing","full_name":"Chen, JingJing"}],"day":"11","ddc":["570"],"date_updated":"2026-04-07T13:24:22Z"},{"corr_author":"1","title":"Visualizing the neuronal transcriptional landscape with tissue context","has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"citation":{"ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria."},"publication_status":"published","_id":"18471","ec_funded":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-10-28T00:00:00Z","month":"10","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets"}],"abstract":[{"lang":"eng","text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. "}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"degree_awarded":"PhD","page":"97","type":"dissertation","doi":"10.15479/at:ista:18471","year":"2024","oa":1,"status":"public","file_date_updated":"2025-05-05T22:30:04Z","date_created":"2024-10-26T20:02:42Z","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"file":[{"file_size":183077763,"relation":"source_file","file_id":"18475","creator":"nagudelo","embargo_to":"open_access","date_created":"2024-10-26T22:29:06Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-05-05T22:30:04Z","checksum":"6d7c7725d040d8debc070dcb35ac965d","access_level":"closed","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx"},{"embargo":"2025-05-05","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","creator":"nagudelo","date_created":"2024-10-26T23:13:33Z","content_type":"application/pdf","date_updated":"2025-05-05T22:30:04Z","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","access_level":"open_access","relation":"main_file","file_id":"18476","file_size":47027710}],"article_processing_charge":"No","OA_place":"publisher","ddc":["570"],"day":"28","date_updated":"2026-04-14T08:34:37Z","author":[{"last_name":"Agudelo Duenas","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria"},{"oa_version":"Published Version","corr_author":"1","title":"Visual adaptations to natural statistics","has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-050-3"],"issn":["2663-337X"]},"citation":{"chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"_id":"18574","ec_funded":1,"OA_embargo":"12","publication_status":"published","month":"11","date_published":"2024-11-22T00:00:00Z","project":[{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","grant_number":"101086580","_id":"bdaf81a8-d553-11ed-ba76-c95961984540"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12349"},{"relation":"research_data","status":"public","id":"12370"}]},"abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"doi":"10.15479/at:ista:18574","oa":1,"year":"2024","status":"public","degree_awarded":"PhD","page":"86","type":"dissertation","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2025-11-11T23:30:02Z","date_created":"2024-11-20T21:30:44Z","file":[{"relation":"source_file","file_id":"18589","file_size":75512262,"file_name":"PhD Thesis - Divyansh Gupta.zip","date_updated":"2025-11-11T23:30:02Z","checksum":"ebb000d361c36b22ed6e639a931c6b7c","access_level":"closed","creator":"dgupta","embargo_to":"open_access","date_created":"2024-11-25T14:44:03Z","content_type":"application/zip"},{"relation":"main_file","file_id":"18591","file_size":6412619,"embargo":"2025-11-11","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","creator":"dgupta","date_created":"2024-11-26T11:43:19Z","content_type":"application/pdf","date_updated":"2025-11-11T23:30:02Z","checksum":"1282401eb71598bc311058b0fcefc6a1","access_level":"open_access"}],"article_processing_charge":"No","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","date_updated":"2026-04-07T13:24:48Z","day":"22","ddc":["573"],"author":[{"last_name":"Gupta","orcid":"0000-0001-7400-6665","first_name":"Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Divyansh"}]},{"_id":"18531","publication_status":"published","OA_embargo":"6","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12521"},{"status":"public","relation":"part_of_dissertation","id":"18549"}]},"abstract":[{"lang":"eng","text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. "}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"month":"11","date_published":"2024-11-11T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","has_accepted_license":"1","corr_author":"1","title":"Early stages of sex chromosome evolution","citation":{"chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"OA_place":"publisher","file":[{"file_size":26870629,"title":"Early stages of sex chromosome evolution","relation":"source_file","file_id":"18551","checksum":"3e48b163c22114ef5d5371f758668289","access_level":"closed","date_updated":"2025-05-11T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-11-13T12:15:28Z","embargo_to":"open_access","creator":"amrnjava","file_name":"AMrnjavac_thesis_library.docx"},{"relation":"main_file","file_id":"18552","file_size":4228766,"title":"Early stages of sex chromosome evolution","embargo":"2025-05-11","file_name":"AMrnjavac_thesis_library.pdf","creator":"amrnjava","content_type":"application/pdf","date_created":"2024-11-13T12:15:54Z","date_updated":"2025-05-11T22:30:04Z","access_level":"open_access","checksum":"3ead60c1b678e7dcf018043aef3b5db2"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"}],"ddc":["576"],"date_updated":"2026-04-07T13:22:45Z","day":"11","oa":1,"year":"2024","status":"public","doi":"10.15479/at:ista:18531","page":"181","type":"dissertation","degree_awarded":"PhD","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"date_created":"2024-11-11T08:40:45Z","keyword":["Sex chromosomes","evolution","selection","sheltering"],"file_date_updated":"2025-05-11T22:30:04Z"},{"publication_identifier":{"issn":["2663-337X"]},"citation":{"ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","mla":"Machnik, Nick N. <i>Algorithms for Causal Learning and Comparative Analysis for Genomic Data</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>.","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>.","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","apa":"Machnik, N. N. (2024). <i>Algorithms for causal learning and comparative analysis for genomic data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>"},"title":"Algorithms for causal learning and comparative analysis for genomic data","corr_author":"1","has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"date_published":"2024-12-11T00:00:00Z","month":"12","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"18648"},{"id":"8707","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"text":"This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe efects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size diferences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n","lang":"eng"}],"publication_status":"published","_id":"18642","file_date_updated":"2025-06-12T22:30:02Z","date_created":"2024-12-10T13:49:15Z","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"}],"degree_awarded":"PhD","page":"138","type":"dissertation","doi":"10.15479/at:ista:18642","status":"public","oa":1,"year":"2024","day":"11","ddc":["576"],"date_updated":"2026-04-07T13:23:06Z","author":[{"full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742","first_name":"Nick N","last_name":"Machnik","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","file":[{"file_size":12845009,"file_id":"18649","relation":"main_file","access_level":"open_access","checksum":"d45e4d170f9a70a1f69b44b99bd058e4","date_updated":"2025-06-12T22:30:02Z","date_created":"2024-12-11T11:59:54Z","content_type":"application/pdf","creator":"nmachnik","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","embargo":"2025-06-12"},{"file_size":14189810,"relation":"source_file","file_id":"18650","access_level":"closed","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","date_updated":"2025-06-12T22:30:02Z","content_type":"application/zip","date_created":"2024-12-11T11:59:34Z","embargo_to":"open_access","creator":"nmachnik","file_name":"thesis.zip"}],"OA_place":"publisher"},{"publication_status":"published","_id":"18661","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png"},"date_published":"2024-12-17T00:00:00Z","month":"12","abstract":[{"text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n","lang":"eng"}],"related_material":{"record":[{"id":"18670","status":"public","relation":"part_of_dissertation"}]},"department":[{"_id":"GradSch"},{"_id":"AnSa"}],"corr_author":"1","title":"Archaeal membranes : In silico modelling and design","has_accepted_license":"1","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-sa/4.0/","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"citation":{"short":"M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes : In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.","ama":"Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes : In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>."},"file":[{"file_id":"18671","relation":"source_file","file_size":19161387,"file_name":"2024_msfa_thesis.zip","checksum":"eca06497a29078558395455c890a32d9","access_level":"closed","date_updated":"2025-06-18T22:30:03Z","content_type":"application/zip","date_created":"2024-12-18T12:27:01Z","embargo_to":"open_access","creator":"mamaral"},{"relation":"main_file","file_id":"18672","file_size":16530084,"embargo":"2025-06-18","file_name":"2024_msfa_thesis.pdf","date_updated":"2025-06-18T22:30:03Z","access_level":"open_access","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","creator":"mamaral","content_type":"application/pdf","date_created":"2024-12-18T12:26:30Z"}],"article_processing_charge":"No","OA_place":"publisher","ddc":["572","530"],"date_updated":"2026-04-07T13:22:29Z","day":"17","author":[{"full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","type":"dissertation","page":"57","doi":"10.15479/at:ista:18661","year":"2024","oa":1,"status":"public","file_date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-16T10:53:39Z","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"language":[{"iso":"eng"}]},{"has_accepted_license":"1","corr_author":"1","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"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>.","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>.","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>","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>","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."},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","ec_funded":1,"_id":"17206","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png"},"abstract":[{"lang":"eng","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. "}],"department":[{"_id":"BeVi"},{"_id":"GradSch"}],"date_published":"2024-07-05T00:00:00Z","month":"07","project":[{"call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"page":"82","type":"dissertation","degree_awarded":"PhD","oa":1,"year":"2024","status":"public","doi":"10.15479/at:ista:17206","date_created":"2024-07-05T14:15:29Z","file_date_updated":"2025-01-11T23:30:04Z","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"OA_place":"publisher","file":[{"access_level":"closed","checksum":"d5e9234bde8667b005a8cfe18bb467d3","date_updated":"2025-01-11T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-07-11T07:18:01Z","embargo_to":"open_access","creator":"cchlebak","file_name":"ThesisRaices2024_postDefense.docx","file_size":13788479,"file_id":"17223","relation":"source_file"},{"embargo":"2025-01-11","file_name":"ThesisRaices2024_nosignature.pdf","creator":"cchlebak","content_type":"application/pdf","date_created":"2024-07-11T07:22:32Z","date_updated":"2025-01-11T23:30:04Z","checksum":"f5ed0139aa3e11ce58369f0915647c5c","access_level":"open_access","relation":"main_file","file_id":"17224","file_size":5580296}],"article_processing_charge":"No","author":[{"last_name":"Raices","first_name":"Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","full_name":"Raices, Julia"}],"day":"05","ddc":["570"],"date_updated":"2026-04-07T13:03:22Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria"},{"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Porley, Dario J","last_name":"Porley","first_name":"Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T13:21:01Z","ddc":["570"],"day":"26","OA_place":"publisher","article_processing_charge":"No","file":[{"embargo_to":"open_access","creator":"dporley","date_created":"2024-09-26T13:40:33Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-03-25T23:30:03Z","checksum":"3b8b0bacfe61112f3852744f3170e468","access_level":"closed","file_name":"PhD_thesis_DPorley_final_20240919.docx","file_size":14213128,"relation":"source_file","file_id":"18149"},{"relation":"main_file","file_id":"18150","file_size":18583031,"file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","embargo":"2025-03-25","checksum":"6c3a652a8eede874118e11d66a63652f","access_level":"open_access","date_updated":"2025-03-25T23:30:03Z","date_created":"2024-09-26T13:41:39Z","content_type":"application/pdf","creator":"dporley"}],"supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"date_created":"2024-09-20T10:21:03Z","file_date_updated":"2025-03-25T23:30:03Z","status":"public","oa":1,"year":"2024","doi":"10.15479/at:ista:18101","page":"131","type":"dissertation","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"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."}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","grant_number":"25762"}],"month":"09","date_published":"2024-09-26T00:00:00Z","ec_funded":1,"_id":"18101","publication_status":"published","citation":{"ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","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>","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>","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","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>.","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>.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria."},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa_version":"Published Version","has_accepted_license":"1","title":"Structural characterization of spumavirus capsid assemblies","corr_author":"1"},{"article_processing_charge":"No","file":[{"date_updated":"2025-01-26T23:30:04Z","checksum":"95517e697ea6a87e267e649cad560989","access_level":"open_access","creator":"cchlebak","date_created":"2024-07-26T13:14:24Z","content_type":"application/pdf","embargo":"2025-01-26","file_name":"Thesis_Kristina_Lukic.pdf","file_size":24639084,"file_id":"17320","relation":"main_file"},{"file_name":"Thesis_Kristina_Lukic.docx","creator":"cchlebak","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-07-26T13:14:50Z","date_updated":"2025-01-26T23:30:04Z","access_level":"closed","checksum":"74325746a9a05078fb9935dbf2aef752","relation":"source_file","file_id":"17321","file_size":96334272}],"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"26","date_updated":"2026-04-07T13:20:44Z","ddc":["580"],"author":[{"full_name":"Lukic, Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","first_name":"Kristina","orcid":"0000-0003-1581-881X","last_name":"Lukic"}],"doi":"10.15479/at:ista:17319","status":"public","year":"2024","oa":1,"degree_awarded":"PhD","page":"224","type":"dissertation","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"file_date_updated":"2025-01-26T23:30:04Z","date_created":"2024-07-26T09:05:55Z","_id":"17319","publication_status":"published","date_published":"2024-07-26T00:00:00Z","month":"07","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor."}],"oa_version":"Published Version","title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","corr_author":"1","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"citation":{"short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.","apa":"Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>","ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>.","mla":"Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>."},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}]},{"has_accepted_license":"1","corr_author":"1","title":"Stability and change in the memory system during rest","oa_version":"Published Version","citation":{"mla":"Bollmann, Lars. <i>Stability and Change in the Memory System during Rest</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>.","chicago":"Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>.","ista":"Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria.","ama":"Bollmann L. Stability and change in the memory system during rest. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>","ieee":"L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024.","apa":"Bollmann, L. (2024). <i>Stability and change in the memory system during rest</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>","short":"L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","_id":"17346","abstract":[{"lang":"eng","text":"Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas."}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"date_published":"2024-07-31T00:00:00Z","month":"07","type":"dissertation","page":"103","degree_awarded":"PhD","year":"2024","oa":1,"status":"public","doi":"10.15479/at:ista:17346","date_created":"2024-07-29T15:08:42Z","keyword":["Memory","Hippocampus","Consolidation"],"file_date_updated":"2025-01-31T23:30:03Z","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"language":[{"iso":"eng"}],"OA_place":"publisher","file":[{"file_name":"PhD_Thesis_Lars_Bollmann.pdf","embargo":"2025-01-31","access_level":"open_access","checksum":"12c76297cc27449da80c60d79127770d","date_updated":"2025-01-31T23:30:03Z","content_type":"application/pdf","date_created":"2024-07-31T18:37:19Z","creator":"lbollman","relation":"main_file","file_id":"17359","file_size":12920169},{"access_level":"closed","checksum":"19a0265079dec8038830ad6e35c5106e","date_updated":"2025-01-31T23:30:03Z","date_created":"2024-07-31T18:38:39Z","content_type":"application/zip","embargo_to":"open_access","creator":"lbollman","file_name":"Latex_source.zip","file_size":27568807,"file_id":"17360","relation":"source_file"}],"article_processing_charge":"No","author":[{"full_name":"Bollmann, Lars","first_name":"Lars","last_name":"Bollmann","id":"47AD3038-F248-11E8-B48F-1D18A9856A87"}],"ddc":["573"],"date_updated":"2026-04-07T13:21:20Z","day":"31","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria"}]