[{"file_date_updated":"2024-06-20T11:52:22Z","type":"dissertation","oa":1,"doi":"10.15479/at:ista:17133","has_accepted_license":"1","keyword":["Quantum information","Qubits","Superconducting devices"],"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"citation":{"mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"article_processing_charge":"No","supervisor":[{"full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"day":"11","date_published":"2024-06-11T00:00:00Z","OA_place":"publisher","abstract":[{"lang":"eng","text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing."}],"page":"161","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"year":"2024","date_created":"2024-06-11T18:20:05Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13227"},{"status":"public","id":"9928","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8755","status":"public"}]},"oa_version":"Published Version","_id":"17133","language":[{"iso":"eng"}],"title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","status":"public","file":[{"file_name":"Thesis_main_final.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"17137","creator":"fhassani","date_updated":"2024-06-20T11:52:22Z","date_created":"2024-06-12T07:53:19Z","checksum":"258c353d47fa37ea63ea43b1e10a34a0","file_size":28370759},{"creator":"fhassani","file_id":"17138","content_type":"text/x-tex","access_level":"closed","relation":"source_file","file_name":"Thesis_main.tex","file_size":445735,"checksum":"deffa5d0db88093f74812fa71520d5e1","date_created":"2024-06-12T07:54:27Z","date_updated":"2024-06-12T07:54:27Z"}],"ddc":["530"],"date_updated":"2026-04-15T06:43:02Z","publication_status":"published","month":"06","author":[{"last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","first_name":"Farid"}]},{"language":[{"iso":"eng"}],"_id":"18135","status":"public","file":[{"checksum":"c7bc3b31e430d57c65393051ca439575","file_size":3648831,"date_updated":"2024-09-26T13:11:24Z","date_created":"2024-09-26T13:11:24Z","success":1,"file_id":"18147","creator":"alaurits","file_name":"Lauritsen-thesis-final.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access"},{"file_name":"Lauritsen-thesis-source.zip","access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","creator":"alaurits","file_id":"18148","date_updated":"2024-09-26T13:12:55Z","date_created":"2024-09-26T13:12:55Z","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","file_size":1625888}],"title":"Energies of dilute Fermi gases and universalities in BCS theory","publication_status":"published","date_updated":"2026-04-16T08:17:55Z","ddc":["515","539"],"author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288"}],"month":"09","page":"353","ec_funded":1,"abstract":[{"lang":"eng","text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$."}],"year":"2024","project":[{"grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"related_material":{"record":[{"id":"11732","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14542","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18107","status":"public"},{"relation":"part_of_dissertation","id":"17240","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14931"}]},"date_created":"2024-09-24T10:56:25Z","oa_version":"Published Version","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"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.","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.","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>."},"alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"day":"23","OA_place":"publisher","date_published":"2024-09-23T00:00:00Z","type":"dissertation","file_date_updated":"2024-09-26T13:12:55Z","doi":"10.15479/at:ista:18135","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","corr_author":"1"},{"day":"18","OA_place":"publisher","date_published":"2024-09-18T00:00:00Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"citation":{"short":"O. Sagi, Hybrid Circuits on Planar Germanium, Institute of Science and Technology Austria, 2024.","ama":"Sagi O. Hybrid circuits on planar Germanium. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18076\">10.15479/at:ista:18076</a>","ista":"Sagi O. 2024. Hybrid circuits on planar Germanium. Institute of Science and Technology Austria.","chicago":"Sagi, Oliver. “Hybrid Circuits on Planar Germanium.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18076\">https://doi.org/10.15479/at:ista:18076</a>.","ieee":"O. Sagi, “Hybrid circuits on planar Germanium,” Institute of Science and Technology Austria, 2024.","apa":"Sagi, O. (2024). <i>Hybrid circuits on planar Germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18076\">https://doi.org/10.15479/at:ista:18076</a>","mla":"Sagi, Oliver. <i>Hybrid Circuits on Planar Germanium</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18076\">10.15479/at:ista:18076</a>."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","file_date_updated":"2024-09-19T09:20:33Z","type":"dissertation","doi":"10.15479/at:ista:18076","oa":1,"date_updated":"2026-04-16T12:20:39Z","publication_status":"published","ddc":["539"],"author":[{"first_name":"Oliver","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi"}],"month":"09","language":[{"iso":"eng"}],"_id":"18076","title":"Hybrid circuits on planar Germanium","file":[{"date_updated":"2024-09-18T14:13:01Z","date_created":"2024-09-18T14:13:01Z","success":1,"checksum":"d01d0e2846c2f3ac5bb14d321554a4cd","file_size":86679095,"file_name":"OliverSagi_Thesis_pdfa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"osagi","file_id":"18093"},{"file_id":"18094","creator":"osagi","file_name":"Thesis_OliverSagi.zip","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"local","checksum":"0543f473d509ee545f4ed3a56f742f4b","file_size":172098524,"date_updated":"2024-09-19T09:20:33Z","date_created":"2024-09-18T14:14:02Z"}],"status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17202"}]},"date_created":"2024-09-16T12:58:36Z","oa_version":"Published Version","page":"111","abstract":[{"lang":"eng","text":"The new era of Ge has opened up new possibilities in quantum computing. The maturity of Ge\r\nspin qubits is unquestioned, while hybrid semiconductor-superconductor Ge circuits are on track\r\nto enter the game. Gate-tunable transmons (gatemons) employing semiconductor Josephson\r\njunctions have recently emerged as building blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor from the Ge quantum well. The Josephson junction is then integrated\r\ninto an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults, combined with the recent advances in the spin qubit field, pave the way towards novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material."}],"ec_funded":1,"project":[{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"year":"2024"},{"publication_status":"published","date_updated":"2026-04-07T13:03:22Z","ddc":["570"],"author":[{"full_name":"Raices, Julia","first_name":"Julia","last_name":"Raices","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87"}],"month":"07","language":[{"iso":"eng"}],"_id":"17206","status":"public","file":[{"file_id":"17223","creator":"cchlebak","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"ThesisRaices2024_postDefense.docx","file_size":13788479,"checksum":"d5e9234bde8667b005a8cfe18bb467d3","embargo_to":"open_access","date_created":"2024-07-11T07:18:01Z","date_updated":"2025-01-11T23:30:04Z"},{"file_size":5580296,"checksum":"f5ed0139aa3e11ce58369f0915647c5c","date_created":"2024-07-11T07:22:32Z","date_updated":"2025-01-11T23:30:04Z","file_id":"17224","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","embargo":"2025-01-11","access_level":"open_access","file_name":"ThesisRaices2024_nosignature.pdf"}],"title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","date_created":"2024-07-05T14:15:29Z","oa_version":"Published Version","page":"82","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. "}],"ec_funded":1,"year":"2024","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"day":"05","OA_place":"publisher","date_published":"2024-07-05T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"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.","ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>","chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","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>","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.","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.","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>."},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"license":"https://creativecommons.org/licenses/by-sa/4.0/","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"dissertation","file_date_updated":"2025-01-11T23:30:04Z","doi":"10.15479/at:ista:17206","oa":1},{"language":[{"iso":"eng"}],"_id":"18101","title":"Structural characterization of spumavirus capsid assemblies","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"PhD_thesis_DPorley_final_20240919.docx","creator":"dporley","file_id":"18149","embargo_to":"open_access","date_created":"2024-09-26T13:40:33Z","date_updated":"2025-03-25T23:30:03Z","file_size":14213128,"checksum":"3b8b0bacfe61112f3852744f3170e468"},{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2025-03-25","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","file_id":"18150","creator":"dporley","date_created":"2024-09-26T13:41:39Z","date_updated":"2025-03-25T23:30:03Z","checksum":"6c3a652a8eede874118e11d66a63652f","file_size":18583031}],"status":"public","date_updated":"2026-04-07T13:21:01Z","publication_status":"published","ddc":["570"],"month":"09","author":[{"full_name":"Porley, Dario J","first_name":"Dario J","last_name":"Porley","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87"}],"page":"131","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."}],"ec_funded":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","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"}],"year":"2024","date_created":"2024-09-20T10:21:03Z","oa_version":"Published Version","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"citation":{"ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","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>","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>.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","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>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"day":"26","OA_place":"publisher","date_published":"2024-09-26T00:00:00Z","file_date_updated":"2025-03-25T23:30:03Z","type":"dissertation","doi":"10.15479/at:ista:18101","oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"corr_author":"1"},{"page":"232","abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"year":"2024","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11420"},{"status":"public","relation":"part_of_dissertation","id":"17469"},{"status":"public","relation":"part_of_dissertation","id":"14459"},{"id":"9198","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-08-28T15:14:25Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17465","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2024-10-04","file_name":"thesis_a2b.pdf","file_id":"17482","creator":"ashevche","date_created":"2024-09-02T09:23:32Z","date_updated":"2024-10-05T22:30:05Z","checksum":"da6dd3166078934577f6af93d27000e2","file_size":4468610},{"date_updated":"2024-10-05T22:30:05Z","date_created":"2024-09-02T09:23:46Z","embargo_to":"open_access","checksum":"76a39ef252239560923cdda4ce0a31a4","file_size":15930999,"file_name":"Thesis Alex - ISTA.zip","access_level":"closed","content_type":"application/zip","relation":"source_file","creator":"ashevche","file_id":"17483"}],"status":"public","title":"High-dimensional limits in artificial neural networks","publication_status":"published","date_updated":"2025-04-25T10:32:06Z","ddc":["519"],"author":[{"full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"}],"month":"08","type":"dissertation","file_date_updated":"2024-10-05T22:30:05Z","doi":"10.15479/at:ista:17465","oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>"},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"29","OA_place":"repository","date_published":"2024-08-29T00:00:00Z"},{"oa_version":"Published Version","related_material":{"record":[{"id":"542","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"date_created":"2024-06-07T16:14:13Z","year":"2024","project":[{"grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"ec_funded":1,"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."}],"page":"105","month":"06","author":[{"last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","first_name":"Réka K","full_name":"Kelemen, Réka K"}],"ddc":["576"],"publication_status":"published","date_updated":"2026-04-07T13:21:37Z","status":"public","file":[{"file_id":"17121","creator":"rkelemen","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"thesis.zip","checksum":"fab59146e3b3dc2e5d214576984a2a63","file_size":180557931,"date_created":"2024-06-07T16:09:17Z","embargo_to":"open_access","date_updated":"2025-01-10T23:30:10Z"},{"checksum":"91cc4c25a792239e8a7688e8aec7c62a","file_size":19405484,"date_updated":"2025-01-10T23:30:10Z","date_created":"2024-07-10T08:00:20Z","creator":"rkelemen","file_id":"17213","file_name":"thesis_to_archive.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2025-01-10","relation":"main_file"}],"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","_id":"17119","language":[{"iso":"eng"}],"corr_author":"1","has_accepted_license":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"oa":1,"doi":"10.15479/at:ista:17119","type":"dissertation","file_date_updated":"2025-01-10T23:30:10Z","date_published":"2024-06-20T00:00:00Z","OA_place":"publisher","day":"20","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"article_processing_charge":"No","supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"citation":{"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>","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.","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>.","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.","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>.","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>","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria."},"degree_awarded":"PhD"},{"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"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>","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","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>.","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>.","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."},"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","supervisor":[{"last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","first_name":"Carrie A"}],"publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"day":"29","OA_place":"publisher","date_published":"2024-10-29T00:00:00Z","type":"dissertation","file_date_updated":"2025-10-29T23:30:02Z","doi":"10.15479/at:ista:18477","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"corr_author":"1","language":[{"iso":"eng"}],"_id":"18477","file":[{"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"20241029_PhD_thesis_BKaczmarek.docx","file_id":"18485","creator":"bkaczmar","date_created":"2024-10-29T11:56:36Z","embargo_to":"open_access","date_updated":"2025-10-29T23:30:02Z","file_size":23136626,"checksum":"2053294ea4d770c495e4cc501e2a218b"},{"creator":"bkaczmar","file_id":"18486","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","content_type":"application/pdf","access_level":"open_access","embargo":"2025-10-29","relation":"main_file","file_size":11707360,"checksum":"8ce857a4cd44b776791eaf180ac9dbb3","date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-29T11:56:44Z"}],"status":"public","title":"Biochemical and structural insights into ADAR1 RNA editing","publication_status":"published","date_updated":"2026-04-07T13:23:59Z","ddc":["572"],"author":[{"full_name":"Kaczmarek, Beata M","first_name":"Beata M","last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"}],"month":"10","page":"124","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."}],"year":"2024","date_created":"2024-10-27T07:35:13Z","oa_version":"Published Version"},{"doi":"10.15479/at:ista:17319","oa":1,"type":"dissertation","file_date_updated":"2025-01-26T23:30:04Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"corr_author":"1","has_accepted_license":"1","supervisor":[{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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.","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>.","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>","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.","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>."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"LeSa"},{"_id":"GradSch"}],"OA_place":"publisher","date_published":"2024-07-26T00:00:00Z","day":"26","year":"2024","page":"224","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","date_created":"2024-07-26T09:05:55Z","status":"public","file":[{"date_updated":"2025-01-26T23:30:04Z","date_created":"2024-07-26T13:14:24Z","checksum":"95517e697ea6a87e267e649cad560989","file_size":24639084,"file_name":"Thesis_Kristina_Lukic.pdf","embargo":"2025-01-26","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","file_id":"17320"},{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Kristina_Lukic.docx","file_id":"17321","creator":"cchlebak","embargo_to":"open_access","date_created":"2024-07-26T13:14:50Z","date_updated":"2025-01-26T23:30:04Z","file_size":96334272,"checksum":"74325746a9a05078fb9935dbf2aef752"}],"title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","language":[{"iso":"eng"}],"_id":"17319","author":[{"id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","last_name":"Lukic","full_name":"Lukic, Kristina","first_name":"Kristina","orcid":"0000-0003-1581-881X"}],"month":"07","publication_status":"published","date_updated":"2026-04-07T13:20:44Z","ddc":["580"]},{"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"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>.","ista":"Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria.","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>","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>.","ieee":"L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024.","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>","short":"L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","supervisor":[{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"publication_identifier":{"issn":["2663-337X"]},"day":"31","OA_place":"publisher","date_published":"2024-07-31T00:00:00Z","type":"dissertation","file_date_updated":"2025-01-31T23:30:03Z","doi":"10.15479/at:ista:17346","oa":1,"keyword":["Memory","Hippocampus","Consolidation"],"has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"_id":"17346","file":[{"file_name":"PhD_Thesis_Lars_Bollmann.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2025-01-31","relation":"main_file","creator":"lbollman","file_id":"17359","date_updated":"2025-01-31T23:30:03Z","date_created":"2024-07-31T18:37:19Z","checksum":"12c76297cc27449da80c60d79127770d","file_size":12920169},{"file_id":"17360","creator":"lbollman","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Latex_source.zip","checksum":"19a0265079dec8038830ad6e35c5106e","file_size":27568807,"date_created":"2024-07-31T18:38:39Z","embargo_to":"open_access","date_updated":"2025-01-31T23:30:03Z"}],"status":"public","title":"Stability and change in the memory system during rest","publication_status":"published","date_updated":"2026-04-07T13:21:20Z","ddc":["573"],"author":[{"full_name":"Bollmann, Lars","first_name":"Lars","last_name":"Bollmann","id":"47AD3038-F248-11E8-B48F-1D18A9856A87"}],"month":"07","page":"103","abstract":[{"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.","lang":"eng"}],"year":"2024","date_created":"2024-07-29T15:08:42Z","oa_version":"Published Version"},{"publication_status":"published","date_updated":"2026-04-07T13:21:56Z","ddc":["570"],"author":[{"first_name":"Heloisa","orcid":"0009-0004-2973-278X","full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","last_name":"Chiossi"}],"month":"01","language":[{"iso":"eng"}],"_id":"14821","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"PhD_Thesis_190124.docx","creator":"hchiossi","file_id":"14838","date_created":"2024-01-19T11:04:05Z","embargo_to":"open_access","date_updated":"2025-01-19T23:30:04Z","checksum":"d3fa3de1abd5af5204c13e9d55375615","file_size":8656268},{"file_id":"14839","creator":"hchiossi","file_name":"PhD_Thesis_190124.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2025-01-19","file_size":6567275,"checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","date_updated":"2025-01-19T23:30:04Z","date_created":"2024-01-19T11:03:59Z"}],"status":"public","title":"Adaptive hierarchical representations in the hippocampus","date_created":"2024-01-16T14:25:21Z","oa_version":"Published Version","page":"89","ec_funded":1,"abstract":[{"lang":"eng","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."}],"year":"2024","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"day":"19","OA_place":"publisher","date_published":"2024-01-19T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"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>.","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>","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>.","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>"},"article_processing_charge":"No","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","corr_author":"1","type":"dissertation","file_date_updated":"2025-01-19T23:30:04Z","doi":"10.15479/at:ista:14821","oa":1},{"project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge"},{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235"},{"name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"year":"2024","page":"164","abstract":[{"text":"State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate\r\nfor qubits due to their long coherence, tunability, control, and readout. However, their natural\r\ncoupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.\r\nLong-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a\r\ncoherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of\r\nhigh-impedance resonators to compensate for this has gained significant attention in the past\r\ndecade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not\r\nexceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The\r\nlarge kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude\r\nenhancement. However, fully exploiting the potential of disordered or granular superconductors\r\nis challenging as their impedances close to the superconductor-to-insulator transition are\r\ndifficult to control reproducibly. We report on the realization of a wireless ohmmeter which\r\nallows in situ resistance measurements during film deposition and, therefore, indirect control\r\nof the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators\r\nwith characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due\r\nto the large sheet kinetic inductance of up to 3 nH □−1\r\n. By integrating an 8 kW resonator\r\nwith a germanium double QD, we demonstrate a strong charge-photon coupling with the\r\nhighest rate reported, 566 MHz. The demonstrated method and grAl properties make these\r\nresonators suitable for boosting the spin-photon coupling strength, a crucial requirement for\r\nfast, high-fidelity, long-distance two-qubit gates.\r\n","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"18144","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-09-23T17:25:43Z","title":"Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors","file":[{"date_updated":"2025-05-23T22:30:09Z","embargo_to":"open_access","date_created":"2024-09-23T17:15:09Z","checksum":"dc15958f6400b5bdaa28bf58fc7a4056","file_size":156207943,"file_name":"janik_thesis.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","creator":"mjanik","file_id":"18130"},{"date_created":"2024-09-23T17:15:30Z","date_updated":"2025-05-23T22:30:09Z","file_size":96195684,"checksum":"74737aee285dc1f491643327350efe9c","content_type":"application/pdf","embargo":"2025-05-23","access_level":"open_access","relation":"main_file","file_name":"janik_thesis_pdfa.pdf","creator":"mjanik","file_id":"18131"}],"status":"public","language":[{"iso":"eng"}],"_id":"18129","author":[{"full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","first_name":"Marian","last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87"}],"month":"09","date_updated":"2026-04-07T13:23:25Z","publication_status":"published","ddc":["539"],"doi":"10.15479/at:ista:18129","oa":1,"file_date_updated":"2025-05-23T22:30:09Z","type":"dissertation","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","supervisor":[{"orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>","short":"M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024.","mla":"Janik, Marian. <i>Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>.","ieee":"M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024.","apa":"Janik, M. (2024). <i>Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>","chicago":"Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>.","ista":"Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2024-09-24T00:00:00Z","day":"24"},{"ddc":["570"],"publication_status":"published","date_updated":"2026-04-07T13:24:22Z","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"month":"03","_id":"15101","language":[{"iso":"eng"}],"file":[{"file_size":11271363,"checksum":"db4947474ffa271e66c254b6fe876a55","date_created":"2024-03-11T14:10:58Z","embargo_to":"open_access","date_updated":"2024-04-02T22:30:03Z","creator":"jchen","file_id":"15104","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Jingjing CHEN.docx"},{"creator":"jchen","file_id":"15105","file_name":"Thesis_Jingjing CHEN_merged.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2024-04-01","relation":"main_file","file_size":16627311,"checksum":"a5eeae8b5702cd540f5d03469bc33dde","date_updated":"2024-04-02T22:30:03Z","date_created":"2024-03-11T14:11:06Z"}],"status":"public","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14843"}]},"date_created":"2024-03-11T10:09:54Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"page":"84","year":"2024","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383"}],"day":"11","date_published":"2024-03-11T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"citation":{"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.","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.","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>","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>.","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."},"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"type":"dissertation","file_date_updated":"2024-04-02T22:30:03Z","oa":1,"doi":"10.15479/at:ista:15101"},{"oa_version":"Published Version","date_created":"2024-09-08T10:23:25Z","related_material":{"record":[{"status":"public","id":"14032","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"18057"}]},"year":"2024","project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692"}],"abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"page":"82","author":[{"last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","first_name":"Soham"}],"month":"09","ddc":["539"],"publication_status":"published","date_updated":"2026-04-07T13:04:06Z","file":[{"file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","relation":"main_file","embargo":"2025-03-13","access_level":"open_access","content_type":"application/pdf","file_id":"18059","creator":"smukhopa","date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-12T10:46:04Z","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","file_size":10297052},{"file_size":29178634,"checksum":"e352667482701dd18a9a0e7418aef465","date_updated":"2025-03-13T23:30:04Z","embargo_to":"open_access","date_created":"2024-09-12T10:50:58Z","file_id":"18060","creator":"smukhopa","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","relation":"source_file","content_type":"application/zip","access_level":"closed"}],"status":"public","title":"Thermal effects in one dimensional Josephson chains","_id":"17881","language":[{"iso":"eng"}],"corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"has_accepted_license":"1","oa":1,"doi":"10.15479/at:ista:17881","type":"dissertation","file_date_updated":"2025-03-13T23:30:04Z","date_published":"2024-09-10T00:00:00Z","OA_place":"publisher","day":"10","publication_identifier":{"isbn":["978-3-99078-043-5"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","first_name":"Andrew P"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"degree_awarded":"PhD"},{"article_processing_charge":"No","supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","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>","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>.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","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>.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","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>"},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"OA_place":"publisher","date_published":"2024-11-11T00:00:00Z","day":"11","doi":"10.15479/at:ista:18531","oa":1,"type":"dissertation","file_date_updated":"2025-05-11T22:30:04Z","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"tmp":{"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)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","keyword":["Sex chromosomes","evolution","selection","sheltering"],"has_accepted_license":"1","status":"public","file":[{"file_name":"AMrnjavac_thesis_library.docx","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18551","creator":"amrnjava","title":"Early stages of sex chromosome evolution","date_updated":"2025-05-11T22:30:04Z","embargo_to":"open_access","date_created":"2024-11-13T12:15:28Z","checksum":"3e48b163c22114ef5d5371f758668289","file_size":26870629},{"file_size":4228766,"checksum":"3ead60c1b678e7dcf018043aef3b5db2","date_updated":"2025-05-11T22:30:04Z","date_created":"2024-11-13T12:15:54Z","creator":"amrnjava","title":"Early stages of sex chromosome evolution","file_id":"18552","file_name":"AMrnjavac_thesis_library.pdf","embargo":"2025-05-11","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"title":"Early stages of sex chromosome evolution","OA_embargo":"6","language":[{"iso":"eng"}],"_id":"18531","month":"11","author":[{"last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea","first_name":"Andrea"}],"publication_status":"published","date_updated":"2026-04-07T13:22:45Z","ddc":["576"],"year":"2024","page":"181","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"12521","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18549"}]},"date_created":"2024-11-11T08:40:45Z"},{"ddc":["572","530"],"date_updated":"2026-04-07T13:22:29Z","publication_status":"published","author":[{"first_name":"Miguel","full_name":"Santana de Freitas Amaral, Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"}],"month":"12","_id":"18661","language":[{"iso":"eng"}],"title":"Archaeal membranes : In silico modelling and design","status":"public","file":[{"file_size":19161387,"checksum":"eca06497a29078558395455c890a32d9","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:27:01Z","embargo_to":"open_access","file_id":"18671","creator":"mamaral","file_name":"2024_msfa_thesis.zip","relation":"source_file","access_level":"closed","content_type":"application/zip"},{"file_name":"2024_msfa_thesis.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2025-06-18","relation":"main_file","creator":"mamaral","file_id":"18672","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:26:30Z","file_size":16530084,"checksum":"2dc30ea46c5daf48d07e4cccb3c3de00"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18670"}]},"date_created":"2024-12-16T10:53:39Z","oa_version":"Published Version","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"}],"page":"57","year":"2024","day":"17","date_published":"2024-12-17T00:00:00Z","OA_place":"publisher","alternative_title":["ISTA Thesis"],"citation":{"ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.","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>","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>.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.","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>.","short":"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>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"supervisor":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"article_processing_charge":"No","has_accepted_license":"1","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"corr_author":"1","file_date_updated":"2025-06-18T22:30:03Z","type":"dissertation","oa":1,"doi":"10.15479/at:ista:18661"},{"language":[{"iso":"eng"}],"_id":"18104","title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","status":"public","file":[{"file_size":10778238,"checksum":"7969263451b2356bfa0924725aa9de10","date_created":"2024-09-20T12:07:48Z","date_updated":"2025-05-20T22:30:05Z","file_id":"18105","creator":"cchlebak","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2025-05-20","file_name":"PhD_DPuglia_Final.pdf"},{"file_name":"PhD_DPuglia_Thesis.zip","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"18106","creator":"cchlebak","date_updated":"2025-05-20T22:30:05Z","embargo_to":"open_access","date_created":"2024-09-20T12:13:09Z","checksum":"98dfe7675775e30efffa03f7ff7c091b","file_size":385419748}],"date_updated":"2026-04-07T13:22:10Z","publication_status":"published","ddc":["530"],"author":[{"last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","orcid":"0000-0003-1144-2763","first_name":"Denise"}],"month":"09","page":"63","abstract":[{"text":"We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n","lang":"eng"}],"project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"}],"year":"2024","date_created":"2024-09-20T12:13:30Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"18143","status":"public"}]},"oa_version":"Published Version","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"citation":{"mla":"Puglia, Denise. <i>Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18104\">10.15479/at:ista:18104</a>.","ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","apa":"Puglia, D. (2024). <i>Everyday electromechanics: Capacitive strong coupling to mechanical motion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18104\">https://doi.org/10.15479/at:ista:18104</a>","chicago":"Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18104\">https://doi.org/10.15479/at:ista:18104</a>.","ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18104\">10.15479/at:ista:18104</a>","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","first_name":"Andrew P"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"20","OA_place":"publisher","date_published":"2024-09-20T00:00:00Z","file_date_updated":"2025-05-20T22:30:05Z","type":"dissertation","doi":"10.15479/at:ista:18104","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","has_accepted_license":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1"},{"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"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>","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","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>.","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>","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","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>.","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","date_published":"2024-12-11T00:00:00Z","OA_place":"publisher","day":"11","oa":1,"doi":"10.15479/at:ista:18642","type":"dissertation","file_date_updated":"2025-06-12T22:30:02Z","corr_author":"1","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.","has_accepted_license":"1","file":[{"date_created":"2024-12-11T11:59:54Z","date_updated":"2025-06-12T22:30:02Z","checksum":"d45e4d170f9a70a1f69b44b99bd058e4","file_size":12845009,"content_type":"application/pdf","embargo":"2025-06-12","access_level":"open_access","relation":"main_file","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","creator":"nmachnik","file_id":"18649"},{"creator":"nmachnik","file_id":"18650","file_name":"thesis.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","file_size":14189810,"date_updated":"2025-06-12T22:30:02Z","date_created":"2024-12-11T11:59:34Z","embargo_to":"open_access"}],"status":"public","title":"Algorithms for causal learning and comparative analysis for genomic data","_id":"18642","language":[{"iso":"eng"}],"author":[{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","full_name":"Machnik, Nick N","first_name":"Nick N","orcid":"0000-0001-6617-9742"}],"month":"12","ddc":["576"],"publication_status":"published","date_updated":"2026-04-07T13:23:06Z","year":"2024","project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"abstract":[{"lang":"eng","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"}],"page":"138","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18648"},{"status":"public","relation":"part_of_dissertation","id":"8707"}]},"date_created":"2024-12-10T13:49:15Z"},{"date_updated":"2026-04-07T13:24:48Z","publication_status":"published","ddc":["573"],"month":"11","author":[{"last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Divyansh","orcid":"0000-0001-7400-6665","first_name":"Divyansh"}],"language":[{"iso":"eng"}],"OA_embargo":"12","_id":"18574","title":"Visual adaptations to natural statistics","status":"public","file":[{"file_size":75512262,"checksum":"ebb000d361c36b22ed6e639a931c6b7c","date_created":"2024-11-25T14:44:03Z","embargo_to":"open_access","date_updated":"2025-11-11T23:30:02Z","creator":"dgupta","file_id":"18589","access_level":"closed","content_type":"application/zip","relation":"source_file","file_name":"PhD Thesis - Divyansh Gupta.zip"},{"date_created":"2024-11-26T11:43:19Z","date_updated":"2025-11-11T23:30:02Z","file_size":6412619,"checksum":"1282401eb71598bc311058b0fcefc6a1","access_level":"open_access","embargo":"2025-11-11","content_type":"application/pdf","relation":"main_file","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","creator":"dgupta","file_id":"18591"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12349"},{"id":"12370","relation":"research_data","status":"public"}]},"date_created":"2024-11-20T21:30:44Z","oa_version":"Published Version","page":"86","ec_funded":1,"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"}],"project":[{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"year":"2024","day":"22","OA_place":"publisher","date_published":"2024-11-22T00:00:00Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"citation":{"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.","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>.","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>","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>.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-050-3"],"issn":["2663-337X"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","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.","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"file_date_updated":"2025-11-11T23:30:02Z","type":"dissertation","doi":"10.15479/at:ista:18574","oa":1},{"date_published":"2024-10-28T00:00:00Z","OA_place":"publisher","day":"28","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-044-2"]},"article_processing_charge":"No","supervisor":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"citation":{"short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","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>","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>","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>.","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","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>."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"corr_author":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"doi":"10.15479/at:ista:18471","file_date_updated":"2025-05-05T22:30:04Z","type":"dissertation","author":[{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas"}],"month":"10","ddc":["570"],"date_updated":"2026-04-14T08:34:37Z","publication_status":"published","title":"Visualizing the neuronal transcriptional landscape with tissue context","file":[{"checksum":"6d7c7725d040d8debc070dcb35ac965d","file_size":183077763,"embargo_to":"open_access","date_created":"2024-10-26T22:29:06Z","date_updated":"2025-05-05T22:30:04Z","file_id":"18475","creator":"nagudelo","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx"},{"file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","relation":"main_file","embargo":"2025-05-05","access_level":"open_access","content_type":"application/pdf","file_id":"18476","creator":"nagudelo","date_updated":"2025-05-05T22:30:04Z","date_created":"2024-10-26T23:13:33Z","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","file_size":47027710}],"status":"public","_id":"18471","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2024-10-26T20:02:42Z","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"year":"2024","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. "}],"ec_funded":1,"page":"97"}]