[{"department":[{"_id":"KrCh"}],"author":[{"id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","orcid":"0009-0001-5009-4987","full_name":"Hübner, Valentin","last_name":"Hübner"},{"first_name":"Maria","full_name":"Kleshnina, Maria","last_name":"Kleshnina"}],"citation":{"apa":"Hübner, V., &#38; Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.10639167\">https://doi.org/10.5281/ZENODO.10639167</a>","chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.10639167\">https://doi.org/10.5281/ZENODO.10639167</a>.","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.10639167\">10.5281/ZENODO.10639167</a>","mla":"Hübner, Valentin, and Maria Kleshnina. <i>Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.10639167\">10.5281/ZENODO.10639167</a>.","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.10639167\">10.5281/ZENODO.10639167</a>.","short":"V. Hübner, M. Kleshnina, (2024)."},"related_material":{"record":[{"id":"15083","relation":"used_in_publication","status":"public"}]},"fulldoi":"https://doi.org/10.5281/ZENODO.10639167","corr_author":"1","_id":"15108","main_file_link":[{"open_access":"1","url":"https://10.5281/zenodo.10639167"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","date_updated":"2026-10-15T10:10:25Z","oa":1,"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","date_published":"2024-02-09T00:00:00Z","status":"public","ddc":["000"],"type":"research_data_reference","doi":"10.5281/ZENODO.10639167","month":"02","date_created":"2024-03-12T13:02:58Z","publisher":"Zenodo","year":"2024","article_processing_charge":"No","abstract":[{"text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below.","lang":"eng"}]},{"publication_identifier":{"issn":["2791-4585"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","has_accepted_license":"1","day":"02","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/at:ista:15352","corr_author":"1","alternative_title":["ISTA Master's Thesis"],"author":[{"last_name":"Murmann","full_name":"Murmann, Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5","first_name":"Julie Stefanie"}],"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. "}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","year":"2024","month":"05","file_date_updated":"2025-05-02T22:30:04Z","type":"dissertation","publication_status":"published","status":"public","date_published":"2024-05-02T00:00:00Z","supervisor":[{"first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","last_name":"Siegert"}],"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","oa":1,"date_updated":"2026-04-07T13:05:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"15352","page":"54","citation":{"ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>"},"file":[{"access_level":"open_access","date_created":"2024-05-02T12:26:13Z","content_type":"application/pdf","file_name":"Murmann_Thesis_final_2024_2.pdf","relation":"main_file","file_size":5936142,"file_id":"15354","date_updated":"2025-05-02T22:30:04Z","checksum":"095817a6c944954ac3f277e547031a33","embargo":"2025-05-02","creator":"cchlebak"},{"creator":"cchlebak","checksum":"43b632255372973a437ac87739cfd4db","embargo_to":"open_access","date_updated":"2025-05-02T22:30:04Z","file_size":20645510,"file_id":"15355","relation":"source_file","content_type":"application/x-zip-compressed","file_name":"Murmann_Thesis_final_2024.zip","date_created":"2024-05-02T12:37:56Z","access_level":"closed"}],"date_created":"2024-05-02T08:31:38Z","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15352","ddc":["570"],"degree_awarded":"MS"},{"date_published":"2024-02-20T00:00:00Z","status":"public","publication_status":"published","type":"journal_article","file_date_updated":"2024-03-12T13:42:42Z","month":"02","year":"2024","article_processing_charge":"Yes (in subscription journal)","publisher":"National Academy of Sciences","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n            <jats:sup>2+</jats:sup>\r\n            -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"13173","relation":"research_data"},{"id":"19271","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/"}]},"author":[{"full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","first_name":"Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0863-4481","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","last_name":"Önal","full_name":"Önal, Hüseyin C"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","first_name":"Carolina","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane"},{"full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roy","full_name":"Roy, Utsa","first_name":"Utsa","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"first_name":"Tetsushi","last_name":"Sadakata","full_name":"Sadakata, Tetsushi"},{"first_name":"Makoto","last_name":"Sanbo","full_name":"Sanbo, Makoto"},{"full_name":"Hirabayashi, Masumi","last_name":"Hirabayashi","first_name":"Masumi"},{"first_name":"JeongSeop","full_name":"Rhee, JeongSeop","last_name":"Rhee"},{"full_name":"Brose, Nils","last_name":"Brose","first_name":"Nils"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"department":[{"_id":"RySh"},{"_id":"PeJo"}],"article_type":"original","corr_author":"1","fulldoi":"https://doi.org/10.1073/pnas.2301449121","ec_funded":1,"OA_place":"publisher","has_accepted_license":"1","day":"20","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":"       121","isi":1,"ddc":["570"],"doi":"10.1073/pnas.2301449121","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2024-03-05T09:23:55Z","acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","issue":"8","article_number":"e2301449121","pmid":1,"external_id":{"pmid":["38346189"],"isi":["001208567300006"]},"citation":{"mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>.","ieee":"P. Koppensteiner <i>et al.</i>, “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 8. National Academy of Sciences, 2024.","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2301449121\">https://doi.org/10.1073/pnas.2301449121</a>.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(8). doi:<a href=\"https://doi.org/10.1073/pnas.2301449121\">10.1073/pnas.2301449121</a>"},"file":[{"creator":"dernst","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","success":1,"date_updated":"2024-03-12T13:42:42Z","file_size":13648221,"file_id":"15110","relation":"main_file","content_type":"application/pdf","file_name":"2024_PNAS_Koppensteiner.pdf","date_created":"2024-03-12T13:42:42Z","access_level":"open_access"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":121,"_id":"15084","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"scopus_import":"1","date_updated":"2026-10-15T22:30:38Z","OA_type":"hybrid","title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","oa":1,"APC_amount":"5887,8 EUR"},{"oa":1,"title":"The genetic basis of a recent transition to live-bearing in marine snails","OA_type":"green","scopus_import":"1","date_updated":"2026-10-15T22:30:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241","open_access":"1"}],"_id":"14796","volume":383,"page":"114-119","publication":"Science","citation":{"ieee":"S. Stankowski <i>et al.</i>, “The genetic basis of a recent transition to live-bearing in marine snails,” <i>Science</i>, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. 2024;383(6678):114-119. doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>"},"pmid":1,"external_id":{"isi":["001138156400003"],"pmid":["38175895"]},"issue":"6678","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","date_created":"2024-01-14T23:00:56Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1126/science.adi2982","intvolume":"       383","isi":1,"publication_identifier":{"eissn":["1095-9203"]},"oa_version":"Submitted Version","day":"05","OA_place":"repository","corr_author":"1","fulldoi":"https://doi.org/10.1126/science.adi2982","article_type":"original","related_material":{"record":[{"id":"14812","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"22905"},{"status":"public","id":"20694","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release","description":"News on ISTA Website"}]},"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka","first_name":"Zuzanna B."},{"full_name":"Garlovsky, Martin D.","last_name":"Garlovsky","first_name":"Martin D."},{"last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"full_name":"Shipilina, Daria","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"},{"last_name":"Lifchitz","full_name":"Lifchitz, Hila","first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Erica","full_name":"Leder, Erica","last_name":"Leder"},{"last_name":"Reeve","full_name":"Reeve, James","first_name":"James"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"abstract":[{"lang":"eng","text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step."}],"year":"2024","article_processing_charge":"No","publisher":"American Association for the Advancement of Science","month":"01","type":"journal_article","publication_status":"published","status":"public","date_published":"2024-01-05T00:00:00Z"},{"month":"07","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"}],"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. "}],"year":"2024","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"status":"public","date_published":"2024-07-05T00:00:00Z","file_date_updated":"2025-01-11T23:30:04Z","doi_confirm":"1","type":"dissertation","has_accepted_license":"1","day":"05","das_tickbox":"0","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"researchdata_availability":"no","author":[{"full_name":"Raices, Julia","last_name":"Raices","first_name":"Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeVi"},{"_id":"GradSch"}],"ec_funded":1,"OA_place":"publisher","corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:17206","date_created":"2024-07-05T14:15:29Z","ddc":["570"],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:17206","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","oa":1,"license":"https://creativecommons.org/licenses/by-sa/4.0/","acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2026-09-24T11:19:04Z","file":[{"embargo_to":"open_access","checksum":"d5e9234bde8667b005a8cfe18bb467d3","creator":"cchlebak","access_level":"closed","date_created":"2024-07-11T07:18:01Z","file_name":"ThesisRaices2024_postDefense.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"17223","file_size":13788479,"date_updated":"2025-01-11T23:30:04Z"},{"date_created":"2024-07-11T07:22:32Z","access_level":"open_access","file_size":5580296,"file_id":"17224","file_name":"ThesisRaices2024_nosignature.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-11T23:30:04Z","embargo":"2025-01-11","checksum":"f5ed0139aa3e11ce58369f0915647c5c","creator":"cchlebak"}],"citation":{"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>","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>.","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>","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.","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>.","ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","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."},"_id":"17206","page":"82"},{"intvolume":"        59","isi":1,"ddc":["570"],"doi":"10.1016/j.devcel.2024.04.021","language":[{"iso":"eng"}],"quality_controlled":"1","acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","date_created":"2024-06-16T22:01:07Z","issue":"15","pmid":1,"external_id":{"pmid":["38776925"],"isi":["001289684800001"]},"citation":{"apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>.","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. 2024;59(15):1940-1953.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>.","ieee":"T. Krammer <i>et al.</i>, “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” <i>Developmental Cell</i>, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10."},"file":[{"checksum":"fefdea9c02862b4bb74de49b65ce638a","creator":"dernst","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2024_DevelopmentalCell_Krammer.pdf","file_size":6249076,"file_id":"18841","date_updated":"2025-01-13T10:59:12Z","access_level":"open_access","date_created":"2025-01-13T10:59:12Z"}],"publication":"Developmental Cell","page":"1940-1953.e10","_id":"17148","volume":59,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_updated":"2026-10-15T22:31:13Z","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","OA_type":"hybrid","oa":1,"dataavailabilitystatement":"RNA-seq data generated in this study have been deposited at GEO under accession codes GSE221187 (FOXA2+ versus FOXA2- cells at Day 5, Figure 3), GSE236543 (FOXA2+ versus FOXA2- cells after BMP perturbations, Figure 4), and GSE260579 (RNA-seq of FOXA2- versus FOXA2+ low, medium, high cells, Figure S4) and RNA-seq analyses are provided in Table S2.","status":"public","date_published":"2024-08-01T00:00:00Z","publication_status":"published","type":"journal_article","file_date_updated":"2025-01-13T10:59:12Z","month":"08","article_processing_charge":"Yes (in subscription journal)","year":"2024","publisher":"Elsevier","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"abstract":[{"text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.","lang":"eng"}],"researchdata_availability":"yes","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"author":[{"full_name":"Krammer, Teresa","last_name":"Krammer","first_name":"Teresa"},{"first_name":"Hannah T.","last_name":"Stuart","full_name":"Stuart, Hannah T."},{"first_name":"Elena","full_name":"Gromberg, Elena","last_name":"Gromberg"},{"full_name":"Ishihara, Keisuke","last_name":"Ishihara","first_name":"Keisuke"},{"first_name":"Dillon","last_name":"Cislo","full_name":"Cislo, Dillon"},{"first_name":"Manuela","last_name":"Melchionda","full_name":"Melchionda, Manuela"},{"first_name":"Fernando","last_name":"Becerril Perez","full_name":"Becerril Perez, Fernando"},{"first_name":"Jingkui","last_name":"Wang","full_name":"Wang, Jingkui"},{"full_name":"Costantini, Elena","last_name":"Costantini","first_name":"Elena"},{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","last_name":"Rus"},{"full_name":"Arbanas, Laura","last_name":"Arbanas","first_name":"Laura"},{"last_name":"Hörmann","full_name":"Hörmann, Alexandra","first_name":"Alexandra"},{"last_name":"Neumüller","full_name":"Neumüller, Ralph A.","first_name":"Ralph A."},{"last_name":"Elvassore","full_name":"Elvassore, Nicola","first_name":"Nicola"},{"first_name":"Eric","last_name":"Siggia","full_name":"Siggia, Eric"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"first_name":"Elly M.","last_name":"Tanaka","full_name":"Tanaka, Elly M."}],"department":[{"_id":"AnKi"}],"article_type":"original","fulldoi":"https://doi.org/10.1016/j.devcel.2024.04.021","OA_place":"publisher","das_tickbox":"1","has_accepted_license":"1","day":"01","supplementarymaterial":"yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]}},{"year":"2024","article_processing_charge":"Yes","publisher":"Elsevier","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011"}],"abstract":[{"text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1","lang":"eng"}],"month":"12","type":"journal_article","file_date_updated":"2024-12-03T10:53:23Z","dataavailabilitystatement":"This study did not generate datasets or code.","date_published":"2024-12-20T00:00:00Z","status":"public","publication_status":"published","supplementarymaterial":"no","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"eissn":["2666-1667"]},"das_tickbox":"1","has_accepted_license":"1","day":"20","corr_author":"1","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103187","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"researchdata_availability":"no","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"author":[{"first_name":"Stefanie","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie","last_name":"Rus"},{"last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kulig, Monika Aleksandra","last_name":"Kulig","first_name":"Monika Aleksandra","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7"},{"full_name":"Minchington, Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","issue":"4","article_number":"103187","pmid":1,"external_id":{"pmid":["39602310"]},"quality_controlled":"1","date_created":"2024-12-01T23:01:53Z","acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","doi":"10.1016/j.xpro.2024.103187","language":[{"iso":"eng"}],"intvolume":"         5","ddc":["570"],"scopus_import":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"date_updated":"2026-10-15T22:31:13Z","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","OA_type":"gold","oa":1,"APC_amount":"804 EUR","DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18601","volume":5,"file":[{"success":1,"checksum":"0c61a6f9978608a103865905e06f4581","creator":"dernst","access_level":"open_access","date_created":"2024-12-03T10:53:23Z","content_type":"application/pdf","relation":"main_file","file_name":"2024_STARProtoc_Lehr.pdf","file_size":4989169,"file_id":"18610","date_updated":"2024-12-03T10:53:23Z"}],"citation":{"ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024.","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>.","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>"},"publication":"STAR Protocols"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","date_updated":"2026-10-15T22:31:15Z","oa":1,"OA_type":"gold","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","APC_amount":"3145,39 EUR","DOAJ_listed":"1","file":[{"date_updated":"2024-09-11T07:54:12Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_PloSGenetics_Elkrewi.pdf","file_id":"18056","file_size":8962687,"access_level":"open_access","date_created":"2024-09-11T07:54:12Z","creator":"dernst","checksum":"f5d96b9af57126fc1063e951440477d6","success":1}],"citation":{"apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024)."},"publication":"PLoS Genetics","volume":20,"_id":"17890","quality_controlled":"1","acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","date_created":"2024-09-08T22:01:11Z","article_number":"e1011376","issue":"8","pmid":1,"external_id":{"pmid":["39213449"],"isi":["001304090200001"]},"intvolume":"        20","isi":1,"ddc":["570"],"doi":"10.1371/journal.pgen.1011376","language":[{"iso":"eng"}],"das_tickbox":"1","has_accepted_license":"1","day":"30","supplementarymaterial":"yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"related_material":{"link":[{"url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project","relation":"software"}],"record":[{"relation":"research_data","id":"17362","status":"public"},{"relation":"dissertation_contains","id":"19386","status":"public"}]},"researchdata_availability":"yes","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"department":[{"_id":"BeVi"}],"article_type":"original","corr_author":"1","fulldoi":"https://doi.org/10.1371/journal.pgen.1011376","OA_place":"publisher","month":"08","year":"2024","article_processing_charge":"Yes","publisher":"Public Library of Science","project":[{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"abstract":[{"lang":"eng","text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group."}],"dataavailabilitystatement":"The scripts used in the analysis can be accessed on the GitHub page: https://github.com/Melkrewi/Artemia-snRNAseq Project. The raw data are available on the NCBI short read archive (BioProject number PRJNA1128544). The Seurat objects produced in the analysis, the loom files generated by Velocyto, the reciprocal best hits used for the SAMap analysis, and the module tables and their GO enrichment results are available for download on ISTA Research Explorer (ISTA REx) using the following link: https://doi.org/10.15479/AT: ISTA:17362. The single nucleus atlas can be viewed with this link on the UCSC Cell Browser: https://brine-shrimp-repro.cells.ucsc.edu","status":"public","date_published":"2024-08-30T00:00:00Z","publication_status":"published","type":"journal_article","file_date_updated":"2024-09-11T07:54:12Z"},{"year":"2024","article_processing_charge":"Yes","publisher":"National Academy of Sciences","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"abstract":[{"text":"As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.","lang":"eng"}],"month":"10","type":"journal_article","file_date_updated":"2024-11-11T09:31:00Z","dataavailabilitystatement":"Previously published data were used for this work (34).\r\n34 F. W. Albert, J. S. Bloom, J. Siegel, L. Day, L. Kruglyak, Genetics of trans-regulatory variation in gene expression. eLife 7, e35471 (2018).","status":"public","date_published":"2024-10-29T00:00:00Z","publication_status":"published","supplementarymaterial":"yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"das_tickbox":"1","has_accepted_license":"1","day":"29","corr_author":"1","fulldoi":"https://doi.org/10.1073/pnas.2402340121","OA_place":"publisher","researchdata_availability":"not applicable","related_material":{"record":[{"relation":"dissertation_contains","id":"20357","status":"public"}]},"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"author":[{"first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova"},{"last_name":"Hledik","full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"article_type":"original","issue":"44","article_number":"e2402340121","pmid":1,"external_id":{"isi":["001349462600001"],"pmid":["39441639"]},"quality_controlled":"1","acknowledgement":"N.R.acknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew R. Robinson for fruitful discussions.","date_created":"2024-11-10T23:01:59Z","doi":"10.1073/pnas.2402340121","language":[{"iso":"eng"}],"intvolume":"       121","isi":1,"ddc":["570"],"scopus_import":"1","date_updated":"2026-10-15T22:31:18Z","oa":1,"OA_type":"hybrid","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","APC_amount":"3062,93 EUR","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18525","volume":121,"file":[{"date_updated":"2024-11-11T09:31:00Z","content_type":"application/pdf","file_name":"2024_PNAS_Ruzickova.pdf","relation":"main_file","file_id":"18536","file_size":25529709,"access_level":"open_access","date_created":"2024-11-11T09:31:00Z","creator":"dernst","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","success":1}],"citation":{"chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>.","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>","apa":"Ruzickova, N., Hledik, M., &#38; Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>","ista":"Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2402340121.","short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>.","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024."},"publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"date_created":"2024-09-08T10:23:25Z","degree_awarded":"PhD","ddc":["539"],"doi":"10.15479/at:ista:17881","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:12:07Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"title":"Thermal effects in one dimensional Josephson chains","oa":1,"file":[{"access_level":"open_access","date_created":"2024-09-12T10:46:04Z","date_updated":"2025-03-13T23:30:04Z","relation":"main_file","content_type":"application/pdf","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","file_id":"18059","file_size":10297052,"creator":"smukhopa","embargo":"2025-03-13","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c"},{"embargo_to":"open_access","creator":"smukhopa","checksum":"e352667482701dd18a9a0e7418aef465","date_created":"2024-09-12T10:50:58Z","access_level":"closed","date_updated":"2025-03-13T23:30:04Z","file_id":"18060","file_size":29178634,"file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","content_type":"application/zip","relation":"source_file"}],"citation":{"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>.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","short":"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.","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>","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>","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>."},"page":"82","_id":"17881","month":"09","publisher":"Institute of Science and Technology Austria","year":"2024","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"}],"status":"public","date_published":"2024-09-10T00:00:00Z","supervisor":[{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","type":"dissertation","doi_confirm":"1","file_date_updated":"2025-03-13T23:30:04Z","has_accepted_license":"1","day":"10","oa_version":"Published Version","supplementarymaterial":"unclear","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"author":[{"last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"}],"related_material":{"record":[{"id":"14032","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18057"}]},"researchdata_availability":"unclear","alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:17881","corr_author":"1","OA_place":"publisher"},{"dataavailabilitystatement":"The assembly pipeline and the scripts used in the analysis can be accessed on the gitpage (https://github.com/Melkrewi/Artemia_franciscana_genome/). The raw data are available on the National Center for Biotechnology Information (NCBI) short-read archive (BioProject number PRJNA1017357). The final assembly, the annotation, and the supplementary data sets are available on (https://doi.org/10.15479/AT:ISTA:14705). All genomic and transcriptomic samples used for this study and the steps of the analysis they were used in are described in supplementary table S3, Supplementary Material online.","status":"public","date_published":"2024-01-20T00:00:00Z","publication_status":"published","type":"journal_article","file_date_updated":"2024-02-26T09:54:59Z","month":"01","year":"2024","article_processing_charge":"Yes","publisher":"Oxford University Press","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"researchdata_availability":"yes","related_material":{"record":[{"status":"public","relation":"research_data","id":"14705"},{"status":"public","id":"19386","relation":"dissertation_contains"},{"status":"public","id":"20449","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"20444","status":"deleted"}]},"department":[{"_id":"BeVi"}],"author":[{"last_name":"Bett","full_name":"Bett, Vincent K","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"article_type":"original","corr_author":"1","fulldoi":"https://doi.org/10.1093/gbe/evae006","OA_place":"publisher","das_tickbox":"1","has_accepted_license":"1","day":"20","supplementarymaterial":"yes","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1759-6653"]},"intvolume":"        16","isi":1,"ddc":["570"],"doi":"10.1093/gbe/evae006","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2024-02-18T23:01:02Z","article_number":"evae006","issue":"1","pmid":1,"external_id":{"isi":["001153952800001"],"pmid":["38245839"]},"citation":{"chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. 2024;16(1). doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>","apa":"Bett, V. K., Macon, A., Vicoso, B., &#38; Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” <i>Genome Biology and Evolution</i>, vol. 16, no. 1. Oxford University Press, 2024.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>."},"file":[{"success":1,"checksum":"106a40f10443b2e7ba66749844ebbdf1","creator":"dernst","access_level":"open_access","date_created":"2024-02-26T09:54:59Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_GBE_Bett.pdf","file_size":5213306,"file_id":"15029","date_updated":"2024-02-26T09:54:59Z"}],"publication":"Genome Biology and Evolution","_id":"15009","volume":16,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_updated":"2026-10-15T22:31:17Z","OA_type":"gold","oa":1,"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","DOAJ_listed":"1"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.07829"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_updated":"2026-10-15T22:31:16Z","title":"Dual relaxation oscillations in a Josephson junction array","oa":1,"citation":{"ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. .","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>.","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>","apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>"},"arxiv":1,"publication":"arXiv","_id":"18057","date_created":"2024-09-11T09:25:22Z","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","article_number":"2408.07829","external_id":{"arxiv":["2408.07829"]},"doi":"10.48550/arXiv.2408.07829","language":[{"iso":"eng"}],"das_tickbox":"0","day":"14","supplementarymaterial":"no","oa_version":"Preprint","related_material":{"record":[{"id":"20324","relation":"later_version","status":"public"},{"status":"public","id":"17881","relation":"dissertation_contains"}]},"researchdata_availability":"no","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"author":[{"full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","first_name":"Soham","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"first_name":"Diego A","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","full_name":"Lancheros Naranjo, Diego A","last_name":"Lancheros Naranjo"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295","first_name":"Jorden L","last_name":"Senior","full_name":"Senior, Jorden L"},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363"}],"corr_author":"1","fulldoi":"https://doi.org/10.48550/arXiv.2408.07829","OA_place":"repository","ec_funded":1,"month":"08","article_processing_charge":"No","year":"2024","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"abstract":[{"text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations.","lang":"eng"}],"status":"public","date_published":"2024-08-14T00:00:00Z","publication_status":"draft","type":"preprint"},{"corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:18531","OA_place":"publisher","OA_embargo":"6","researchdata_availability":"unclear","related_material":{"record":[{"status":"public","id":"12521","relation":"part_of_dissertation"},{"id":"18549","relation":"part_of_dissertation","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"author":[{"last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"}],"alternative_title":["ISTA Thesis"],"supplementarymaterial":"unclear","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","day":"11","type":"dissertation","file_date_updated":"2025-05-11T22:30:04Z","doi_confirm":"1","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"status":"public","date_published":"2024-11-11T00:00:00Z","publication_status":"published","year":"2024","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","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"}],"month":"11","page":"181","_id":"18531","file":[{"creator":"amrnjava","checksum":"3e48b163c22114ef5d5371f758668289","embargo_to":"open_access","date_updated":"2025-05-11T22:30:04Z","title":"Early stages of sex chromosome evolution","file_id":"18551","file_size":26870629,"file_name":"AMrnjavac_thesis_library.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_created":"2024-11-13T12:15:28Z","access_level":"closed"},{"date_updated":"2025-05-11T22:30:04Z","content_type":"application/pdf","relation":"main_file","file_name":"AMrnjavac_thesis_library.pdf","file_id":"18552","title":"Early stages of sex chromosome evolution","file_size":4228766,"access_level":"open_access","date_created":"2024-11-13T12:15:54Z","creator":"amrnjava","checksum":"3ead60c1b678e7dcf018043aef3b5db2","embargo":"2025-05-11"}],"citation":{"apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria."},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"date_updated":"2026-10-02T11:14:08Z","oa":1,"title":"Early stages of sex chromosome evolution","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.15479/at:ista:18531","language":[{"iso":"eng"}],"degree_awarded":"PhD","ddc":["576"],"date_created":"2024-11-11T08:40:45Z","keyword":["Sex chromosomes","evolution","selection","sheltering"]},{"page":"57","_id":"18661","citation":{"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>.","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>","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>.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.","short":"M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024."},"file":[{"embargo_to":"open_access","checksum":"eca06497a29078558395455c890a32d9","creator":"mamaral","date_created":"2024-12-18T12:27:01Z","access_level":"closed","file_id":"18671","file_size":19161387,"relation":"source_file","file_name":"2024_msfa_thesis.zip","content_type":"application/zip","date_updated":"2025-06-18T22:30:03Z"},{"relation":"main_file","file_name":"2024_msfa_thesis.pdf","content_type":"application/pdf","file_id":"18672","file_size":16530084,"date_updated":"2025-06-18T22:30:03Z","access_level":"open_access","date_created":"2024-12-18T12:26:30Z","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","embargo":"2025-06-18","creator":"mamaral"}],"date_updated":"2026-10-02T11:12:49Z","oa":1,"title":"Archaeal membranes: In silico modelling and design","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.15479/at:ista:18661","language":[{"iso":"eng"}],"ddc":["572","530"],"degree_awarded":"PhD","date_created":"2024-12-16T10:53:39Z","fulldoi":"https://doi.org/10.15479/at:ista:18661","corr_author":"1","OA_place":"publisher","author":[{"first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel"}],"department":[{"_id":"GradSch"},{"_id":"AnSa"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18670","status":"public"}]},"researchdata_availability":"unclear","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"supplementarymaterial":"unclear","publication_identifier":{"isbn":["978-3-99078-046-6"],"issn":["2663-337X"]},"has_accepted_license":"1","day":"17","type":"dissertation","doi_confirm":"1","file_date_updated":"2025-06-18T22:30:03Z","status":"public","date_published":"2024-12-17T00:00:00Z","supervisor":[{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","year":"2024","article_processing_charge":"No","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"}],"month":"12"},{"ddc":["530"],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:18104","date_created":"2024-09-20T12:13:30Z","file":[{"access_level":"open_access","date_created":"2024-09-20T12:07:48Z","date_updated":"2025-05-20T22:30:05Z","content_type":"application/pdf","file_name":"PhD_DPuglia_Final.pdf","relation":"main_file","file_id":"18105","file_size":10778238,"creator":"cchlebak","checksum":"7969263451b2356bfa0924725aa9de10","embargo":"2025-05-20"},{"access_level":"closed","date_created":"2024-09-20T12:13:09Z","date_updated":"2025-05-20T22:30:05Z","relation":"source_file","content_type":"application/x-zip-compressed","file_name":"PhD_DPuglia_Thesis.zip","file_id":"18106","file_size":385419748,"embargo_to":"open_access","creator":"cchlebak","checksum":"98dfe7675775e30efffa03f7ff7c091b"}],"citation":{"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>","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>","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.","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>.","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.","ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria."},"_id":"18104","page":"63","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","license":"https://creativecommons.org/licenses/by-nc/4.0/","title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","oa":1,"date_updated":"2026-10-02T11:12:28Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication_status":"published","date_published":"2024-09-20T00:00:00Z","status":"public","supervisor":[{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"doi_confirm":"1","file_date_updated":"2025-05-20T22:30:05Z","type":"dissertation","month":"09","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":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"grant_number":"26088","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging"}],"publisher":"Institute of Science and Technology Austria","year":"2024","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0003-1144-2763","first_name":"Denise","last_name":"Puglia","full_name":"Puglia, Denise"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18143","status":"public"}]},"researchdata_availability":"unclear","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/at:ista:18104","corr_author":"1","day":"20","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"supplementarymaterial":"unclear"},{"type":"preprint","date_published":"2024-08-24T00:00:00Z","status":"public","publication_status":"draft","article_processing_charge":"No","year":"2024","project":[{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"},{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"abstract":[{"lang":"eng","text":"Strong optomechanical coupling -- a regime where mechanical motion is damped\r\nby environmental radiation -- has traditionally required demanding experimental\r\ningredients such as superconducting resonators, high-quality optical cavities,\r\nor large magnetic fields. Here we demonstrate a room temperature, cavity-free,\r\nall-electric device reaching this regime at radio frequencies, enabled by a\r\nmechanically compliant parallel-plate capacitor with a nanoscale plate\r\nseparation and an aspect ratio exceeding 1,000. The device has four orders of\r\nmagnitude lower insertion loss than a comparable commercial quartz crystal, and\r\nachieves a position imprecision rivaling an optical interferometer. With the\r\nhelp of a back-action isolation scheme, we observe radiative cooling of\r\nmechanical motion by a remote cryogenic load. This work provides a\r\ntechnologically accessible route to high-precision sensing, transduction, and\r\nsignal processing."}],"month":"08","corr_author":"1","fulldoi":"https://doi.org/10.48550/arXiv.2407.15314","OA_place":"repository","related_material":{"record":[{"id":"19026","relation":"later_version","status":"public"},{"status":"public","id":"18104","relation":"dissertation_contains"}]},"author":[{"last_name":"Puglia","full_name":"Puglia, Denise","first_name":"Denise","orcid":"0000-0003-1144-2763","id":"4D495994-AE37-11E9-AC72-31CAE5697425"},{"last_name":"Odessey","full_name":"Odessey, Rachel H","first_name":"Rachel H","id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd"},{"full_name":"Burns, Peter S.","last_name":"Burns","first_name":"Peter S."},{"first_name":"Niklas","last_name":"Luhmann","full_name":"Luhmann, Niklas"},{"first_name":"Silvan","last_name":"Schmid","full_name":"Schmid, Silvan"},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"department":[{"_id":"AnHi"}],"oa_version":"Preprint","day":"24","doi":"10.48550/arXiv.2407.15314","language":[{"iso":"eng"}],"article_number":"2407.15314","external_id":{"arxiv":["2407.15314"]},"date_created":"2024-09-26T06:58:27Z","_id":"18143","citation":{"short":"D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, ArXiv (n.d.).","ista":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical  motion. arXiv, 2407.15314.","ieee":"D. Puglia, R. H. Odessey, P. S. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical  motion,” <i>arXiv</i>. .","mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” <i>ArXiv</i>, 2407.15314, doi:<a href=\"https://doi.org/10.48550/arXiv.2407.15314\">10.48550/arXiv.2407.15314</a>.","ama":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical  motion. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2407.15314\">10.48550/arXiv.2407.15314</a>","chicago":"Puglia, Denise, Rachel H Odessey, Peter S. Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2407.15314\">https://doi.org/10.48550/arXiv.2407.15314</a>.","apa":"Puglia, D., Odessey, R. H., Burns, P. S., Luhmann, N., Schmid, S., &#38; Higginbotham, A. P. (n.d.). Room temperature, cavity-free capacitive strong coupling to mechanical  motion. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2407.15314\">https://doi.org/10.48550/arXiv.2407.15314</a>"},"arxiv":1,"publication":"arXiv","date_updated":"2026-10-15T22:31:20Z","oa":1,"title":"Room temperature, cavity-free capacitive strong coupling to mechanical  motion","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.15314","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"07","article_processing_charge":"No","year":"2024","abstract":[{"text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n","lang":"eng"}],"status":"public","date_published":"2024-07-04T00:00:00Z","publication_status":"draft","type":"preprint","das_tickbox":"0","day":"04","oa_version":"Preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"supplementarymaterial":"yes","department":[{"_id":"BeVi"}],"author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"researchdata_availability":"no","related_material":{"record":[{"relation":"later_version","id":"19370","status":"public"},{"status":"public","id":"18531","relation":"dissertation_contains"}]},"fulldoi":"https://doi.org/10.1101/2024.07.02.601697","corr_author":"1","OA_place":"repository","biorxivid":1,"date_created":"2024-11-13T09:12:08Z","external_id":{"biorxivid":["10.1101/2024.07.02.601697"]},"doi":"10.1101/2024.07.02.601697","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.07.02.601697","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-15T22:31:18Z","title":"Evidence of a Slower-Z effect in Schistosoma japonicum","oa":1,"citation":{"ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>.","apa":"Mrnjavac, A., &#38; Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, <a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>."},"publication":"bioRxiv","_id":"18549"},{"doi":"10.1101/2024.10.18.619072","language":[{"iso":"eng"}],"date_created":"2024-12-18T10:07:45Z","acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","_id":"18670","citation":{"ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>","chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>.","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., &#38; Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.18.619072\">https://doi.org/10.1101/2024.10.18.619072</a>","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.).","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” <i>bioRxiv</i>. .","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.18.619072\">10.1101/2024.10.18.619072</a>."},"publication":"bioRxiv","date_updated":"2026-10-15T22:31:19Z","title":"Stability vs flexibility: Reshaping archaeal membranes in silico","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2024.10.18.619072","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"preprint","date_published":"2024-11-27T00:00:00Z","status":"public","publication_status":"draft","article_processing_charge":"No","year":"2024","project":[{"grant_number":"802960","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties."}],"month":"11","corr_author":"1","fulldoi":"https://doi.org/10.1101/2024.10.18.619072","OA_place":"repository","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"18661","status":"public"}]},"author":[{"id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel"},{"full_name":"Frey, Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","orcid":"0000-0001-8501-6017","first_name":"Felix F"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić"}],"department":[{"_id":"AnSa"}],"oa_version":"Preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"day":"27"},{"title":"High-dimensional limits in artificial neural networks","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2026-10-02T11:20:32Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17465","page":"232","citation":{"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>.","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>","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>","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","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>.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024."},"file":[{"relation":"main_file","content_type":"application/pdf","file_name":"thesis_a2b.pdf","file_id":"17482","file_size":4468610,"date_updated":"2024-10-05T22:30:05Z","access_level":"open_access","date_created":"2024-09-02T09:23:32Z","embargo":"2024-10-04","checksum":"da6dd3166078934577f6af93d27000e2","creator":"ashevche"},{"file_name":"Thesis Alex - ISTA.zip","relation":"source_file","content_type":"application/zip","file_size":15930999,"file_id":"17483","date_updated":"2024-10-05T22:30:05Z","access_level":"closed","date_created":"2024-09-02T09:23:46Z","checksum":"76a39ef252239560923cdda4ce0a31a4","creator":"ashevche","embargo_to":"open_access"}],"date_created":"2024-08-28T15:14:25Z","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:17465","degree_awarded":"PhD","ddc":["519"],"publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"no","oa_version":"Published Version","day":"29","has_accepted_license":"1","das_tickbox":"0","OA_place":"repository","corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:17465","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11420","status":"public"},{"status":"public","id":"14459","relation":"part_of_dissertation"},{"id":"9198","relation":"part_of_dissertation","status":"public"},{"id":"17469","relation":"part_of_dissertation","status":"public"}]},"researchdata_availability":"no","author":[{"full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"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"}],"abstract":[{"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","lang":"eng"}],"year":"2024","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","month":"08","file_date_updated":"2024-10-05T22:30:05Z","doi_confirm":"1","type":"dissertation","publication_status":"published","supervisor":[{"last_name":"Mondelli","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_published":"2024-08-29T00:00:00Z"},{"doi":"10.15479/at:ista:17119","language":[{"iso":"eng"}],"degree_awarded":"PhD","ddc":["576"],"date_created":"2024-06-07T16:14:13Z","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"page":"105","_id":"17119","file":[{"date_updated":"2025-01-10T23:30:10Z","file_id":"17121","file_size":180557931,"file_name":"thesis.zip","content_type":"application/zip","relation":"source_file","date_created":"2024-06-07T16:09:17Z","access_level":"closed","creator":"rkelemen","checksum":"fab59146e3b3dc2e5d214576984a2a63","embargo_to":"open_access"},{"access_level":"open_access","date_created":"2024-07-10T08:00:20Z","content_type":"application/pdf","file_name":"thesis_to_archive.pdf","relation":"main_file","file_id":"17213","file_size":19405484,"date_updated":"2025-01-10T23:30:10Z","checksum":"91cc4c25a792239e8a7688e8aec7c62a","embargo":"2025-01-10","creator":"rkelemen"}],"citation":{"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.","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>.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","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>.","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>"},"date_updated":"2026-10-02T11:14:33Z","oa":1,"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"dissertation","file_date_updated":"2025-01-10T23:30:10Z","doi_confirm":"1","supervisor":[{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"date_published":"2024-06-20T00:00:00Z","status":"public","publication_status":"published","year":"2024","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"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."}],"month":"06","corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:17119","ec_funded":1,"OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"542"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"researchdata_availability":"unclear","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"author":[{"last_name":"Kelemen","full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","orcid":"0000-0002-8489-9281"}],"alternative_title":["ISTA Thesis"],"supplementarymaterial":"unclear","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"has_accepted_license":"1","day":"20"}]