[{"publication_identifier":{"isbn":["9798400704161"],"issn":["1548-6109"]},"citation":{"mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2024, pp. 403–14, doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>.","ista":"Kolmogorov V. 2024. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 403–414.","ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In: <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2024:403-414. doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>","chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 403–14. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>.","ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut,” in <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Nantes, France, 2024, pp. 403–414.","short":"V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414.","apa":"Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 403–414). Nantes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>"},"file_date_updated":"2024-07-16T06:38:08Z","file":[{"file_name":"2024_SPAA_Kolmogorov.pdf","checksum":"6ca18ac8508719dbd5d5735f4c991af2","date_created":"2024-07-16T06:38:08Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2024-07-16T06:38:08Z","file_size":1116166,"relation":"main_file","file_id":"17245","creator":"dernst"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"page":"403-414","ddc":["510"],"publication":"Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures","scopus_import":"1","day":"17","abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm.\r\nWe present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors.\r\nWe also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}],"supplementarymaterial":"no","researchdata_availability":"no","external_id":{"arxiv":["2307.00115"],"isi":["001253331900044"]},"conference":{"location":"Nantes, France","start_date":"2024-06-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2024-06-21"},"date_created":"2024-07-14T22:01:11Z","publication_status":"published","OA_place":"publisher","month":"06","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","department":[{"_id":"VlKo"}],"fulldoi":"https://doi.org/10.1145/3626183.3659969","das_tickbox":"0","arxiv":1,"related_material":{"record":[{"status":"public","id":"21007","relation":"extended_version"}]},"date_published":"2024-06-17T00:00:00Z","type":"conference","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","date_updated":"2026-10-21T13:45:27Z","title":"A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut","doi":"10.1145/3626183.3659969","_id":"17236","isi":1},{"das_tickbox":"1","fulldoi":"https://doi.org/10.1186/s12915-024-01956-4","date_published":"2024-08-02T00:00:00Z","type":"journal_article","pmid":1,"date_created":"2024-08-11T22:01:11Z","article_number":"157","external_id":{"pmid":["39090637"],"isi":["001282893200001"]},"dataavailabilitystatement":"All data generated or analyzed during this study are included in this published article and its supplementary information files. Drosophila stocks used and/or analyzed during the current study are available from the corresponding author on reasonable request.","department":[{"_id":"XiFe"}],"month":"08","article_processing_charge":"Yes","publication_status":"published","doi":"10.1186/s12915-024-01956-4","date_updated":"2026-10-21T13:47:19Z","year":"2024","title":"Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut","quality_controlled":"1","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","isi":1,"_id":"17408","publisher":"Springer Nature","intvolume":"        22","oa":1,"author":[{"orcid":"0000-0003-1671-9434","id":"608df3e6-e2ab-11ed-8890-c9318cec7da4","first_name":"Hiroki","full_name":"Nagai, Hiroki","last_name":"Nagai"},{"first_name":"Yuya","full_name":"Adachi, Yuya","last_name":"Adachi"},{"first_name":"Tenki","full_name":"Nakasugi, Tenki","last_name":"Nakasugi"},{"first_name":"Ema","full_name":"Takigawa, Ema","last_name":"Takigawa"},{"last_name":"Ui","full_name":"Ui, Junichiro","first_name":"Junichiro"},{"first_name":"Takashi","last_name":"Makino","full_name":"Makino, Takashi"},{"full_name":"Miura, Masayuki","last_name":"Miura","first_name":"Masayuki"},{"first_name":"Yu Ichiro","full_name":"Nakajima, Yu Ichiro","last_name":"Nakajima"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank I. Miguel-Aliaga, N. Shinoda, M. Furuse, Y. Izumi, BDSC, Kyoto Stock Center, Drosophila Genomics Resource Center (DGRC), and Developmental Studies Hybridoma Bank (DSHB) for fly stocks and reagents.\r\nThis work was supported by JSPS/MEXT KAKENHI (grant numbers JP22J01430 to H.N., JP21H04774, JP23H04766, JP24H00567 to M.M., and JP17H06332, JP22H02762, JP23K18134, JP23H04696 to Y.N.), AMED-Aging (JP21gm5010001 to M.M.), AMED-PRIME (JP22gm6110025 to Y.N.), and Sadako O. Hirai Ban Award for Young Researchers (H.N.)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"mla":"NAGAI, HIROKI, et al. “Highly Regenerative Species-Specific Genes Improve Age-Associated Features in the Adult Drosophila Midgut.” <i>BMC Biology</i>, vol. 22, 157, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s12915-024-01956-4\">10.1186/s12915-024-01956-4</a>.","ista":"NAGAI H, Adachi Y, Nakasugi T, Takigawa E, Ui J, Makino T, Miura M, Nakajima YI. 2024. Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. BMC Biology. 22, 157.","ama":"NAGAI H, Adachi Y, Nakasugi T, et al. Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. <i>BMC Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1186/s12915-024-01956-4\">10.1186/s12915-024-01956-4</a>","ieee":"H. NAGAI <i>et al.</i>, “Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut,” <i>BMC Biology</i>, vol. 22. Springer Nature, 2024.","chicago":"NAGAI, HIROKI, Yuya Adachi, Tenki Nakasugi, Ema Takigawa, Junichiro Ui, Takashi Makino, Masayuki Miura, and Yu Ichiro Nakajima. “Highly Regenerative Species-Specific Genes Improve Age-Associated Features in the Adult Drosophila Midgut.” <i>BMC Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s12915-024-01956-4\">https://doi.org/10.1186/s12915-024-01956-4</a>.","short":"H. NAGAI, Y. Adachi, T. Nakasugi, E. Takigawa, J. Ui, T. Makino, M. Miura, Y.I. Nakajima, BMC Biology 22 (2024).","apa":"NAGAI, H., Adachi, Y., Nakasugi, T., Takigawa, E., Ui, J., Makino, T., … Nakajima, Y. I. (2024). Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-024-01956-4\">https://doi.org/10.1186/s12915-024-01956-4</a>"},"publication_identifier":{"eissn":["1741-7007"]},"file":[{"file_size":3345718,"relation":"main_file","file_id":"17417","creator":"dernst","access_level":"open_access","success":1,"date_updated":"2024-08-12T08:14:44Z","content_type":"application/pdf","file_name":"2024_BMCBio_Nagai.pdf","checksum":"318759626ec83b13f909c82904393ef1","date_created":"2024-08-12T08:14:44Z"}],"file_date_updated":"2024-08-12T08:14:44Z","supplementarymaterial":"yes","volume":22,"abstract":[{"lang":"eng","text":"Background: The remarkable regenerative abilities observed in planarians and cnidarians are closely linked to the active proliferation of adult stem cells and the precise differentiation of their progeny, both of which typically deteriorate during aging in low regenerative animals. While regeneration-specific genes conserved in highly regenerative organisms may confer regenerative abilities and long-term maintenance of tissue homeostasis, it remains unclear whether introducing these regenerative genes into low regenerative animals can improve their regeneration and aging processes.\r\n\r\nResults: Here, we ectopically express highly regenerative species-specific JmjC domain-encoding genes (HRJDs) in Drosophila, a widely used low regenerative model organism. Surprisingly, HRJD expression impedes tissue regeneration in the developing wing disc but extends organismal lifespan when expressed in the intestinal stem cell lineages of the adult midgut under non-regenerative conditions. Notably, HRJDs enhance the proliferative activity of intestinal stem cells while maintaining their differentiation fidelity, ameliorating age-related decline in gut barrier functions.\r\n\r\nConclusions: These findings together suggest that the introduction of highly regenerative species-specific genes can improve stem cell functions and promote a healthy lifespan when expressed in aging animals."}],"day":"02","article_type":"original","scopus_import":"1","researchdata_availability":"upon request","publication":"BMC Biology","ddc":["570"]},{"fulldoi":"https://doi.org/10.3847/2041-8213/ad6c34","das_tickbox":"0","type":"journal_article","date_published":"2024-09-12T00:00:00Z","DOAJ_listed":"1","article_number":"L9","external_id":{"isi":["001310592900001"]},"date_created":"2024-09-22T22:01:42Z","publication_status":"published","department":[{"_id":"YlGo"}],"month":"09","article_processing_charge":"Yes","status":"public","quality_controlled":"1","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.3847/2041-8213/ad6c34","year":"2024","title":"Tidal disruption events from stripped stars","date_updated":"2026-10-21T13:50:17Z","isi":1,"_id":"18111","oa":1,"author":[{"full_name":"Mockler, Brenna","last_name":"Mockler","first_name":"Brenna"},{"first_name":"Monica","last_name":"Gallegos-Garcia","full_name":"Gallegos-Garcia, Monica"},{"orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg"},{"first_name":"Jon M.","last_name":"Miller","full_name":"Miller, Jon M."},{"full_name":"Ramirez-Ruiz, Enrico","last_name":"Ramirez-Ruiz","first_name":"Enrico"}],"publisher":"IOP Publishing","intvolume":"       973","issue":"1","acknowledgement":"This work was performed in part at Aspen Center for Physics, which is supported by National Science Foundation grant PHY-2210452. We thank the participants and organizers of the summer Aspen 2023 workshop on “Stellar Interactions and the Transients They Cause” for fruitful discussions. B.M. is grateful for support from the Carnegie Theoretical Astrophysics\r\nCenter. M.G.-G. is grateful for the support from Northwestern University’s Presidential Fellowship. E.R.-R. thanks the Heising-Simons Foundation, NSF (AST-2150255 and AST2307710), Swift (80NSSC21K1409, 80NSSC19K1391), and Chandra (22-0142) for support. ","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"eissn":["2041-8213"],"issn":["2041-8205"]},"citation":{"ista":"Mockler B, Gallegos-Garcia M, Götberg YLL, Miller JM, Ramirez-Ruiz E. 2024. Tidal disruption events from stripped stars. Astrophysical Journal Letters. 973(1), L9.","mla":"Mockler, Brenna, et al. “Tidal Disruption Events from Stripped Stars.” <i>Astrophysical Journal Letters</i>, vol. 973, no. 1, L9, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">10.3847/2041-8213/ad6c34</a>.","ama":"Mockler B, Gallegos-Garcia M, Götberg YLL, Miller JM, Ramirez-Ruiz E. Tidal disruption events from stripped stars. <i>Astrophysical Journal Letters</i>. 2024;973(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">10.3847/2041-8213/ad6c34</a>","chicago":"Mockler, Brenna, Monica Gallegos-Garcia, Ylva Louise Linsdotter Götberg, Jon M. Miller, and Enrico Ramirez-Ruiz. “Tidal Disruption Events from Stripped Stars.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">https://doi.org/10.3847/2041-8213/ad6c34</a>.","ieee":"B. Mockler, M. Gallegos-Garcia, Y. L. L. Götberg, J. M. Miller, and E. Ramirez-Ruiz, “Tidal disruption events from stripped stars,” <i>Astrophysical Journal Letters</i>, vol. 973, no. 1. IOP Publishing, 2024.","apa":"Mockler, B., Gallegos-Garcia, M., Götberg, Y. L. L., Miller, J. M., &#38; Ramirez-Ruiz, E. (2024). Tidal disruption events from stripped stars. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">https://doi.org/10.3847/2041-8213/ad6c34</a>","short":"B. Mockler, M. Gallegos-Garcia, Y.L.L. Götberg, J.M. Miller, E. Ramirez-Ruiz, Astrophysical Journal Letters 973 (2024)."},"file_date_updated":"2024-09-30T08:54:26Z","file":[{"file_name":"2024_AstrophysicalJourn_Mockler.pdf","checksum":"050ddf873244839825714cca42b5d857","date_created":"2024-09-30T08:54:26Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2024-09-30T08:54:26Z","file_size":844227,"file_id":"18161","relation":"main_file","creator":"dernst"}],"day":"12","article_type":"original","scopus_import":"1","supplementarymaterial":"no","volume":973,"abstract":[{"text":"Observations of tidal disruption events (TDEs) show signs of nitrogen enrichment reminiscent of other astrophysical sources such as active galactic nuclei and star-forming galaxies. Given that TDEs probe the gas from a single star, it is possible to test whether the observed enrichment is consistent with expectations from the CNO cycle by looking at the observed nitrogen/carbon (N/C) abundance ratios. Given that ≈20% of solar-mass stars (and an even larger fraction of more massive stars) live in close binaries, it is worthwhile to also consider what TDEs from stars influenced by binary evolution would look like. We show here that TDEs from stars stripped of their hydrogen-rich (and nitrogen-poor) envelopes through previous binary-induced mass loss can produce much higher observable N/C enhancements than even TDEs from massive stars. Additionally, we predict that the time dependence of the N/C abundance ratio in the mass fallback rate of stripped stars will follow the inverse behavior of main-sequence stars, enabling a more accurate characterization of the disrupted star.","lang":"eng"}],"researchdata_availability":"no","publication":"Astrophysical Journal Letters","ddc":["520"]},{"oa":1,"author":[{"last_name":"Lorenc","full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan"},{"first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"}],"corr_author":"1","APC_amount":"2982,14 EUR","publisher":"American Physical Society","intvolume":"         6","_id":"14886","quality_controlled":"1","has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1103/PhysRevResearch.6.013042","title":"Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect","date_updated":"2026-10-21T13:52:11Z","year":"2024","publication_status":"published","OA_type":"gold","department":[{"_id":"ZhAl"}],"article_processing_charge":"Yes","month":"01","OA_place":"publisher","article_number":"013042","date_created":"2024-01-28T23:01:42Z","type":"journal_article","date_published":"2024-01-11T00:00:00Z","DOAJ_listed":"1","fulldoi":"https://doi.org/10.1103/PhysRevResearch.6.013042","das_tickbox":"0","publication":"Physical Review Research","ddc":["530"],"researchdata_availability":"no","article_type":"original","day":"11","scopus_import":"1","volume":6,"supplementarymaterial":"yes","abstract":[{"lang":"eng","text":"It is a basic principle that an effect cannot come before the cause. Dispersive relations that follow from this fundamental fact have proven to be an indispensable tool in physics and engineering. They are most powerful in the domain of linear response where they are known as Kramers-Kronig relations. However, when it comes to nonlinear phenomena the implications of causality are much less explored, apart from several notable exceptions. Here in this paper we demonstrate how to apply the dispersive formalism to analyze the ultrafast nonlinear response in the context of the paradigmatic nonlinear Kerr effect. We find that the requirement of causality introduces a noticeable effect even under assumption that Kerr effect is mediated by quasi-instantaneous off-resonant electronic hyperpolarizability. We confirm this by experimentally measuring the time-resolved Kerr dynamics in GaAs by means of a hybrid pump-probe Mach-Zehnder interferometer and demonstrate the presence of an intrinsic lagging between amplitude and phase responses as predicted by dispersive analysis. Our results describe a general property of the time-resolved nonlinear processes thereby highlighting the importance of accounting for dispersive effects in the nonlinear optical processes involving ultrashort pulses."}],"file_date_updated":"2024-01-31T11:59:30Z","file":[{"file_size":2863627,"file_id":"14918","relation":"main_file","creator":"dernst","access_level":"open_access","success":1,"date_updated":"2024-01-31T11:59:30Z","content_type":"application/pdf","file_name":"2024_PhysicalReviewResearch_Lorenc.pdf","checksum":"42d58f93ae74e7f2c4de058ef75ff8b2","date_created":"2024-01-31T11:59:30Z"}],"publication_identifier":{"eissn":["2643-1564"]},"citation":{"ieee":"D. Lorenc and Z. Alpichshev, “Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.013042\">https://doi.org/10.1103/PhysRevResearch.6.013042</a>.","apa":"Lorenc, D., &#38; Alpichshev, Z. (2024). Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.013042\">https://doi.org/10.1103/PhysRevResearch.6.013042</a>","short":"D. Lorenc, Z. Alpichshev, Physical Review Research 6 (2024).","ista":"Lorenc D, Alpichshev Z. 2024. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. 6(1), 013042.","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” <i>Physical Review Research</i>, vol. 6, no. 1, 013042, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.013042\">10.1103/PhysRevResearch.6.013042</a>.","ama":"Lorenc D, Alpichshev Z. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.013042\">10.1103/PhysRevResearch.6.013042</a>"},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","issue":"1","acknowledgement":"The work was supported by the Institute of Science and Technology Austria (ISTA). We thank Prof. John M. Dudley, Dr. Ugur Sezer, and Dr. Artem Volosniev for valuable discussions.","language":[{"iso":"eng"}]},{"external_id":{"isi":["001268807700002"],"pmid":["38987431"]},"dataavailabilitystatement":"The omics data at SO, S2, S3, DAP0, DAP2, DAP6 stages are reported for the first time in this paper and the raw sequence data have been deposited in the Genome Sequence Archive of the National Genomics Data Center, China National Center of Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (CRA014372). Other omics data were downloaded from the previous report under project number CRA008877 and PRJCA008382 (Lin et al., 2024; Zhao et al., 2023).","date_created":"2024-07-21T22:01:02Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2023.12.19.572364","open_access":"1"}],"month":"10","OA_place":"repository","article_processing_charge":"No","department":[{"_id":"XiFe"}],"OA_type":"green","fulldoi":"https://doi.org/10.1007/s11427-024-2664-0","das_tickbox":"1","pmid":1,"type":"journal_article","date_published":"2024-10-01T00:00:00Z","author":[{"first_name":"Xuemei","full_name":"Liu, Xuemei","last_name":"Liu"},{"first_name":"Min","full_name":"Deng, Min","last_name":"Deng"},{"first_name":"Bingxin","last_name":"Shi","full_name":"Shi, Bingxin"},{"first_name":"Kehui","full_name":"Zhu, Kehui","last_name":"Zhu"},{"last_name":"Chen","full_name":"Chen, Jinchao","first_name":"Jinchao"},{"first_name":"Shujuan","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","full_name":"Xu, Shujuan","last_name":"Xu"},{"first_name":"Xiaomin","last_name":"Bie","full_name":"Bie, Xiaomin"},{"first_name":"Xiansheng","full_name":"Zhang, Xiansheng","last_name":"Zhang"},{"first_name":"Xuelei","last_name":"Lin","full_name":"Lin, Xuelei"},{"first_name":"Jun","last_name":"Xiao","full_name":"Xiao, Jun"}],"oa":1,"intvolume":"        67","publisher":"Springer Nature","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","year":"2024","date_updated":"2026-10-21T13:50:04Z","title":"Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat","doi":"10.1007/s11427-024-2664-0","isi":1,"_id":"17285","publication_identifier":{"issn":["1674-7305"],"eissn":["1869-1889"]},"citation":{"ama":"Liu X, Deng M, Shi B, et al. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. <i>Science China Life Sciences</i>. 2024;67:2251-2266. doi:<a href=\"https://doi.org/10.1007/s11427-024-2664-0\">10.1007/s11427-024-2664-0</a>","ista":"Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J. 2024. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. Science China Life Sciences. 67, 2251–2266.","mla":"Liu, Xuemei, et al. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.” <i>Science China Life Sciences</i>, vol. 67, Springer Nature, 2024, pp. 2251–66, doi:<a href=\"https://doi.org/10.1007/s11427-024-2664-0\">10.1007/s11427-024-2664-0</a>.","apa":"Liu, X., Deng, M., Shi, B., Zhu, K., Chen, J., Xu, S., … Xiao, J. (2024). Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. <i>Science China Life Sciences</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11427-024-2664-0\">https://doi.org/10.1007/s11427-024-2664-0</a>","short":"X. Liu, M. Deng, B. Shi, K. Zhu, J. Chen, S. Xu, X. Bie, X. Zhang, X. Lin, J. Xiao, Science China Life Sciences 67 (2024) 2251–2266.","chicago":"Liu, Xuemei, Min Deng, Bingxin Shi, Kehui Zhu, Jinchao Chen, Shujuan Xu, Xiaomin Bie, Xiansheng Zhang, Xuelei Lin, and Jun Xiao. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.” <i>Science China Life Sciences</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s11427-024-2664-0\">https://doi.org/10.1007/s11427-024-2664-0</a>.","ieee":"X. Liu <i>et al.</i>, “Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat,” <i>Science China Life Sciences</i>, vol. 67. Springer Nature, pp. 2251–2266, 2024."},"acknowledgement":"We thank Prof. Kang Chong from Institute of Botany, the Chinese Academy of Science for valuable comments, Dr. Haoran Li for the help with western blot of H3K36me3 in Tasdg8-cr lines. This research was supported by National Natural Science Foundation (31970529), Beijing Natural Science Foundation Outstanding Youth Project (JQ23026), National Key Research and Development Program of China (2021YFD1201500), and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).","language":[{"iso":"eng"}],"oa_version":"Preprint","page":"2251-2266","publication":"Science China Life Sciences","scopus_import":"1","day":"01","article_type":"original","abstract":[{"text":"Winter plants rely on vernalization, a crucial process for adapting to cold conditions and ensuring successful reproduction. However, understanding the role of histone modifications in guiding the vernalization process in winter wheat remains limited. In this study, we investigated the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the field. Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS), components of the writer complex for H3K27me3 and H3K36me3, respectively, affected flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure memory in the absence of H3K36me3. During embryo development, VRN1 was silenced with the removal of active histone modifications in both winter and spring wheat, with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87, a component of H3K27me3 “writer” complex, did not influence the silence of VRN1 during embryo development, but rather attenuated the cold exposure requirement of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of flowering. This study unveils distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and resetting in winter wheat.","lang":"eng"}],"supplementarymaterial":"yes","volume":67,"researchdata_availability":"yes"},{"citation":{"apa":"Lorenc, D., Zhumekenov, A., Bakr, O. M., &#38; Alpichshev, Z. (2024). No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">https://doi.org/10.1103/PhysRevMaterials.8.085403</a>","short":"D. Lorenc, A. Zhumekenov, O.M. Bakr, Z. Alpichshev, Physical Review Materials 8 (2024).","ieee":"D. Lorenc, A. Zhumekenov, O. M. Bakr, and Z. Alpichshev, “No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry,” <i>Physical Review Materials</i>, vol. 8, no. 8. American Physical Society, 2024.","chicago":"Lorenc, Dusan, Ayan Zhumekenov, Osman M. Bakr, and Zhanybek Alpichshev. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” <i>Physical Review Materials</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">https://doi.org/10.1103/PhysRevMaterials.8.085403</a>.","ama":"Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. <i>Physical Review Materials</i>. 2024;8(8). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">10.1103/PhysRevMaterials.8.085403</a>","ista":"Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. 2024. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. 8(8), 085403.","mla":"Lorenc, Dusan, et al. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” <i>Physical Review Materials</i>, vol. 8, no. 8, 085403, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">10.1103/PhysRevMaterials.8.085403</a>."},"publication_identifier":{"eissn":["2475-9953"]},"oa_version":"None","language":[{"iso":"eng"}],"acknowledgement":"We gratefully acknowledge the assistance of Prof. John\r\nDudley.","issue":"8","publication":"Physical Review Materials","researchdata_availability":"no","abstract":[{"lang":"eng","text":"Lead halide perovskites have recently been reported to demonstrate an exceptionally high nonlinear (Kerr) refractive index n2 of up to 10−8cm2/W in CH3⁢NH3⁢PbBr3. Other researchers, however, observe different, substantially more conservative numbers. In order to resolve this disagreement, the nonlinear Kerr index of a bulk sample of lead halide perovskite was measured directly by means of an interferometer. This approach has many advantages as compared to the more standard z-scan technique. In particular, this method allows studying the induced changes to the refractive index in a time-resolved manner, thus enabling to separate the different contributions to 𝑛2. The extracted 𝑛2 values for CsPbBr3 and MAPbBr3 at 𝜆≈1µ⁢m are 𝑛2=+2.1×10−14cm2/W and 𝑛2=+6×10−15cm2/W, respectively. Hence, these values are substantially lower than what has been indicated in most of the previous reports, implying the latter one should be regarded with great care."}],"supplementarymaterial":"yes","volume":8,"scopus_import":"1","article_type":"original","day":"23","month":"08","article_processing_charge":"No","department":[{"_id":"ZhAl"}],"publication_status":"published","date_created":"2024-09-01T22:01:08Z","external_id":{"isi":["001299497800001"]},"article_number":"085403","date_published":"2024-08-23T00:00:00Z","type":"journal_article","das_tickbox":"0","fulldoi":"https://doi.org/10.1103/PhysRevMaterials.8.085403","intvolume":"         8","publisher":"American Physical Society","corr_author":"1","author":[{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","full_name":"Lorenc, Dusan","last_name":"Lorenc"},{"first_name":"Ayan","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan"},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"}],"_id":"17476","isi":1,"title":"No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry","date_updated":"2026-10-21T13:51:39Z","year":"2024","doi":"10.1103/PhysRevMaterials.8.085403","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1"},{"intvolume":"       690","publisher":"EDP Sciences","oa":1,"author":[{"first_name":"Irene","full_name":"Shivaei, Irene","last_name":"Shivaei"},{"first_name":"Stacey","full_name":"Alberts, Stacey","last_name":"Alberts"},{"full_name":"Florian, Michael","last_name":"Florian","first_name":"Michael"},{"last_name":"Rieke","full_name":"Rieke, George","first_name":"George"},{"last_name":"Wuyts","full_name":"Wuyts, Stijn","first_name":"Stijn"},{"first_name":"Sarah","last_name":"Bodansky","full_name":"Bodansky, Sarah"},{"first_name":"Andrew J.","last_name":"Bunker","full_name":"Bunker, Andrew J."},{"first_name":"Alex J.","full_name":"Cameron, Alex J.","last_name":"Cameron"},{"first_name":"Mirko","full_name":"Curti, Mirko","last_name":"Curti"},{"last_name":"Da'Eugenio","full_name":"Da'Eugenio, Francesco","first_name":"Francesco"},{"full_name":"Dudzevičiūte, Ugne","last_name":"Dudzevičiūte","first_name":"Ugne"},{"full_name":"Ji, Zhiyuan","last_name":"Ji","first_name":"Zhiyuan"},{"first_name":"Benjamin D.","full_name":"Johnson, Benjamin D.","last_name":"Johnson"},{"full_name":"Kramarenko, Ivan","last_name":"Kramarenko","orcid":"0000-0001-5346-6048","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","first_name":"Ivan"},{"full_name":"Lyu, Jianwei","last_name":"Lyu","first_name":"Jianwei"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"first_name":"Jane","last_name":"Morrison","full_name":"Morrison, Jane"},{"last_name":"Naidu","full_name":"Naidu, Rohan","first_name":"Rohan"},{"full_name":"Pérez-González, Pablo G.","last_name":"Pérez-González","first_name":"Pablo G."},{"last_name":"Reddy","full_name":"Reddy, Naveen","first_name":"Naveen"},{"full_name":"Robertson, Brant","last_name":"Robertson","first_name":"Brant"},{"last_name":"Sun","full_name":"Sun, Yang","first_name":"Yang"},{"full_name":"Tacchella, Sandro","last_name":"Tacchella","first_name":"Sandro"},{"full_name":"Whitaker, Katherine","last_name":"Whitaker","first_name":"Katherine"},{"full_name":"Williams, Christina C.","last_name":"Williams","first_name":"Christina C."},{"last_name":"Willmer","full_name":"Willmer, Christopher N.A.","first_name":"Christopher N.A."},{"first_name":"Joris","last_name":"Witstok","full_name":"Witstok, Joris"},{"first_name":"Mengyuan","full_name":"Xiao, Mengyuan","last_name":"Xiao"},{"last_name":"Zhu","full_name":"Zhu, Yongda","first_name":"Yongda"}],"_id":"18448","isi":1,"date_updated":"2026-10-21T14:03:27Z","title":"A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI","year":"2024","doi":"10.1051/0004-6361/202449579","quality_controlled":"1","has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","department":[{"_id":"JoMa"}],"publication_status":"published","date_created":"2024-10-20T22:02:06Z","dataavailabilitystatement":"Full table is published in an online repository: https://zenodo.org/records/12671075","external_id":{"isi":["001381135700006"],"arxiv":["2402.07989"]},"article_number":"A89","type":"journal_article","date_published":"2024-10-01T00:00:00Z","arxiv":1,"das_tickbox":"1","fulldoi":"https://doi.org/10.1051/0004-6361/202449579","publication":"Astronomy & Astrophysics","ddc":["520"],"researchdata_availability":"yes","abstract":[{"text":"Aims. This paper utilises the James Webb Space Telescope (JWST) Mid-Infrared Instrument (MIRI) to extend the observational studies of dust and polycyclic aromatic hydrocarbon (PAH) emission to a new mass and star formation rate (SFR) parameter space beyond our local Universe. The combination of fully sampled spectral energy distributions (SEDs) with multiple mid-infrared (mid-IR) bands and the unprecedented sensitivity of MIRI allows us to investigate dust obscuration and PAH behaviour from z = 0.7 up to z = 2 in typical main-sequence galaxies. Our focus is on constraining the evolution of PAH strength and the dust-obscured luminosity fraction before and during cosmic noon, the epoch of peak star formation activity in the Universe.\r\n\r\nMethods. In this study, we utilise MIRI multi-band imaging data from the SMILES survey (5 to 25 μm), complemented with NIRCam photometry from the JADES survey (1 to 5 μm), available HST photometry (0.4 to 0.9 μm), and spectroscopic redshifts from the FRESCO and JADES surveys in GOODS-S for 443 star-forming (without dominant active galactic nucleus (AGN)) galaxies at z = 0.7 − 2.0. This redshift range was chosen to ensure that the MIRI data cover mid-IR dust emission. Our methodology involved employing ultraviolet (UV) to IR energy balance SED fitting to robustly constrain the fraction of dust mass in PAHs and dust-obscured luminosity. Additionally, we inferred dust sizes from MIRI 15 μm imaging data, enhancing our understanding of the physical characteristics of dust within these galaxies.\r\n\r\nResults. We find a strong correlation between the fraction of dust in PAHs (PAH fraction, qPAH) with stellar mass. Moreover, the sub-sample with robust qPAH measurements (N = 216) shows a similar behaviour between qPAH and gas-phase metallicity to that at z ∼ 0, suggesting a universal relation: qPAH is constant (∼3.4%) above a metallicity of Z ∼ 0.5 Z⊙ and decreases to < 1% at metallicities ≲0.3 Z⊙. This indicates that metallicity is a good indicator of the interstellar medium properties that affect the balance between the formation and destruction of PAHs. The lack of a redshift evolution from z ∼ 0 − 2 also implies that above Z ∼ 0.5 Z⊙ the PAH emission effectively traces obscured luminosity and the previous locally calibrated PAH-SFR calibrations remain applicable in this metallicity regime. We observe a strong correlation between the obscured UV luminosity fraction (ratio of obscured to total luminosity) and stellar mass. Above the stellar mass of M* > 5 × 109 M⊙, on average, more than half of the emitted luminosity is obscured, while there exists a non-negligible population of lower-mass galaxies with > 50% obscured fractions. At a fixed mass, the obscured fraction correlates with SFR surface density. This is a result of higher dust covering fractions in galaxies with more compact star-forming regions. Similarly, galaxies with high IRX (IR to UV luminosity) at a given mass or UV continuum slope (β) tend to have higher ΣSFR and shallower attenuation curves, owing to their higher effective dust optical depths and more compact star-forming regions.","lang":"eng"}],"volume":690,"supplementarymaterial":"yes","scopus_import":"1","article_type":"original","day":"01","file":[{"file_name":"2024_AstronomyAstrophysics_Shivaei.pdf","checksum":"f399be98968b9ca5611c832a9b1eee2b","date_created":"2024-10-21T11:52:29Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2024-10-21T11:52:29Z","file_size":10777358,"file_id":"18458","relation":"main_file","creator":"dernst"}],"file_date_updated":"2024-10-21T11:52:29Z","citation":{"ista":"Shivaei I, Alberts S, Florian M, Rieke G, Wuyts S, Bodansky S, Bunker AJ, Cameron AJ, Curti M, Da’Eugenio F, Dudzevičiūte U, Ji Z, Johnson BD, Kramarenko I, Lyu J, Matthee JJ, Morrison J, Naidu R, Pérez-González PG, Reddy N, Robertson B, Sun Y, Tacchella S, Whitaker K, Williams CC, Willmer CNA, Witstok J, Xiao M, Zhu Y. 2024. A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI. Astronomy &#38; Astrophysics. 690, A89.","mla":"Shivaei, Irene, et al. “A New Census of Dust and Polycyclic Aromatic Hydrocarbons at z = 0.7-2 with JWST MIRI.” <i>Astronomy &#38; Astrophysics</i>, vol. 690, A89, EDP Sciences, 2024, doi:<a href=\"https://doi.org/10.1051/0004-6361/202449579\">10.1051/0004-6361/202449579</a>.","ama":"Shivaei I, Alberts S, Florian M, et al. A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI. <i>Astronomy &#38; Astrophysics</i>. 2024;690. doi:<a href=\"https://doi.org/10.1051/0004-6361/202449579\">10.1051/0004-6361/202449579</a>","ieee":"I. Shivaei <i>et al.</i>, “A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI,” <i>Astronomy &#38; Astrophysics</i>, vol. 690. EDP Sciences, 2024.","chicago":"Shivaei, Irene, Stacey Alberts, Michael Florian, George Rieke, Stijn Wuyts, Sarah Bodansky, Andrew J. Bunker, et al. “A New Census of Dust and Polycyclic Aromatic Hydrocarbons at z = 0.7-2 with JWST MIRI.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2024. <a href=\"https://doi.org/10.1051/0004-6361/202449579\">https://doi.org/10.1051/0004-6361/202449579</a>.","apa":"Shivaei, I., Alberts, S., Florian, M., Rieke, G., Wuyts, S., Bodansky, S., … Zhu, Y. (2024). A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202449579\">https://doi.org/10.1051/0004-6361/202449579</a>","short":"I. Shivaei, S. Alberts, M. Florian, G. Rieke, S. Wuyts, S. Bodansky, A.J. Bunker, A.J. Cameron, M. Curti, F. Da’Eugenio, U. Dudzevičiūte, Z. Ji, B.D. Johnson, I. Kramarenko, J. Lyu, J.J. Matthee, J. Morrison, R. Naidu, P.G. Pérez-González, N. Reddy, B. Robertson, Y. Sun, S. Tacchella, K. Whitaker, C.C. Williams, C.N.A. Willmer, J. Witstok, M. Xiao, Y. Zhu, Astronomy &#38; Astrophysics 690 (2024)."},"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"acknowledgement":"IS thanks the members of the JWST/MIRI instrument team for their exceptional efforts and for providing an outstanding experience during the commissioning period of JWST, which fostered numerous fruitful discussions and significantly enhanced the quality of data reduction in this study. IS also thanks Karin Sandstrom and Joel Leja for their insightful discussions during the scientific development of this work. Additionally, IS acknowledges the contribution of Andras Gáspar to the construction of the F560W PSF utilised in this research. This work was supported in part by NASA grant NNX13AD82G. Part of this research has been funded by Atraccíon de Talento Grant No. 2022-T1/TIC-20472 of the Comunidad de Madrid, Spain. AJB and AC acknowledges funding from the ‘FirstGalaxies’ Advanced Grant from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 789056). The work of CCW is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. PGP-G acknowledges support from grant PID2022-139567NB-I00 funded by Spanish Ministerio de Ciencia e Innovación CIN/AEI/10.13039/501100011033, FEDER Una manera de hacer Europa. SA acknowledges support from the JWST Mid-Infrared Instrument (MIRI) Science Team Lead, grant 80NSSC18K0555, from NASA Goddard Space Flight Center to the University of Arizona. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program PID 1207, 1080, 1081, 1895, 1220, 1286, 1287, 1963. Based on observations made with the NASA/ESA Hubble Space Telescope, and obtained from the Hubble Legacy Archive, which is a collaboration between the Space Telescope Science Institute (STScI/NASA), the Space Telescope European Coordinating Facility (ST-ECF/ESAC/ESA) and the Canadian Astronomy Data Centre (CADC/NRC/CSA)."},{"publisher":"American Physical Society","intvolume":"         6","author":[{"full_name":"Savchenko, M. L.","last_name":"Savchenko","first_name":"M. L."},{"first_name":"J.","full_name":"Gospodarič, J.","last_name":"Gospodarič"},{"last_name":"Shuvaev","full_name":"Shuvaev, A.","first_name":"A."},{"first_name":"I. A.","last_name":"Dmitriev","full_name":"Dmitriev, I. A."},{"id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","first_name":"Vlad","orcid":"0000-0002-1648-0999","last_name":"Dziom","full_name":"Dziom, Vlad"},{"last_name":"Dobretsova","full_name":"Dobretsova, A. A.","first_name":"A. A."},{"first_name":"N. N.","full_name":"Mikhailov, N. N.","last_name":"Mikhailov"},{"first_name":"Z. D.","full_name":"Kvon, Z. D.","last_name":"Kvon"},{"last_name":"Pimenov","full_name":"Pimenov, A.","first_name":"A."}],"oa":1,"doi":"10.1103/PhysRevResearch.6.L022027","year":"2024","date_updated":"2026-10-21T13:52:32Z","title":"Optical Shubnikov-de Haas oscillations in two-dimensional electron systems","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","status":"public","_id":"15406","date_created":"2024-05-19T22:01:12Z","article_number":"L022027","external_id":{"arxiv":["2402.05879"]},"department":[{"_id":"ZhAl"}],"month":"04","article_processing_charge":"Yes","publication_status":"published","das_tickbox":"0","fulldoi":"https://doi.org/10.1103/PhysRevResearch.6.L022027","date_published":"2024-04-01T00:00:00Z","type":"journal_article","DOAJ_listed":"1","arxiv":1,"ddc":["530"],"publication":"Physical Review Research","volume":6,"supplementarymaterial":"yes","abstract":[{"text":"We report on dynamic Shubnikov–de Haas (SdH) oscillations that are measured in the optical response, subterahertz transmittance of two-dimensional systems, and reveal two distinct types of oscillation nodes: “universal” nodes at integer ratios of radiation and cyclotron frequencies and “tunable” nodes at positions sensitive to all parameters of the structure. The nodes in both real and imaginary parts of the measured complex transmittance are analyzed using a dynamic version of the static Lifshitz-Kosevich formula. These results demonstrate that the node structure of the dynamic SdH oscillations provides an all-optical access to quantization- and interaction-induced renormalization effects, in addition to parameters one can obtain from the static SdH oscillations.","lang":"eng"}],"article_type":"letter_note","day":"01","scopus_import":"1","researchdata_availability":"no","citation":{"ama":"Savchenko ML, Gospodarič J, Shuvaev A, et al. Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. <i>Physical Review Research</i>. 2024;6(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">10.1103/PhysRevResearch.6.L022027</a>","mla":"Savchenko, M. L., et al. “Optical Shubnikov-de Haas Oscillations in Two-Dimensional Electron Systems.” <i>Physical Review Research</i>, vol. 6, no. 2, L022027, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">10.1103/PhysRevResearch.6.L022027</a>.","ista":"Savchenko ML, Gospodarič J, Shuvaev A, Dmitriev IA, Dziom V, Dobretsova AA, Mikhailov NN, Kvon ZD, Pimenov A. 2024. Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. Physical Review Research. 6(2), L022027.","short":"M.L. Savchenko, J. Gospodarič, A. Shuvaev, I.A. Dmitriev, V. Dziom, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, A. Pimenov, Physical Review Research 6 (2024).","apa":"Savchenko, M. L., Gospodarič, J., Shuvaev, A., Dmitriev, I. A., Dziom, V., Dobretsova, A. A., … Pimenov, A. (2024). Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">https://doi.org/10.1103/PhysRevResearch.6.L022027</a>","chicago":"Savchenko, M. L., J. Gospodarič, A. Shuvaev, I. A. Dmitriev, Vlad Dziom, A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, and A. Pimenov. “Optical Shubnikov-de Haas Oscillations in Two-Dimensional Electron Systems.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022027\">https://doi.org/10.1103/PhysRevResearch.6.L022027</a>.","ieee":"M. L. Savchenko <i>et al.</i>, “Optical Shubnikov-de Haas oscillations in two-dimensional electron systems,” <i>Physical Review Research</i>, vol. 6, no. 2. American Physical Society, 2024."},"publication_identifier":{"eissn":["2643-1564"]},"file":[{"file_name":"2024_PhysicalReviewResearch_Savchenko.pdf","checksum":"78c8c3cf1bda766e3de0db45f143a367","date_created":"2024-05-22T06:39:35Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2024-05-22T06:39:35Z","file_size":1697856,"file_id":"15412","relation":"main_file","creator":"dernst"}],"file_date_updated":"2024-05-22T06:39:35Z","language":[{"iso":"eng"}],"issue":"2","acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/I3456,10.55776/I5539]. I.A.D. acknowledges the financial support of the German Research Foundation (DM 1/6-1). The quantum well growth and transport measurements were supported by RSF 23-72-30003. For open access purposes, the authors have applied a CC BY public copyright license to any authoraccepted manuscript version arising from this submission.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"researchdata_availability":"no","abstract":[{"text":"This research is aimed to solve the tweet/user geolocation prediction task and provide a flexible methodology for the geo-tagging of textual big data. The suggested approach implements neural networks for natural language processing (NLP) to estimate the location as coordinate pairs (longitude, latitude) and two-dimensional Gaussian Mixture Models (GMMs). The scope of proposed models has been finetuned on a Twitter dataset using pretrained Bidirectional Encoder Representations from Transformers (BERT) as base models. Performance metrics show a median error of fewer than 30 km on a worldwide-level, and fewer than 15 km on the US-level datasets for the models trained and evaluated on text features of tweets' content and metadata context. Our source code and data are available at https://github.com/K4TEL/geo-twitter.git.","lang":"eng"}],"supplementarymaterial":"no","scopus_import":"1","day":"26","article_type":"original","publication":"Journal of Spatial Information Science","ddc":["500"],"license":"https://creativecommons.org/licenses/by/3.0/","page":"69-99","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"language":[{"iso":"eng"}],"acknowledgement":"The authors acknowledge the Institute of Science and Technology (ISTA) for their material support and for granting access to the Twitter database archive, which was essential for the research.","issue":"29","file":[{"relation":"main_file","file_id":"18857","file_size":7250655,"creator":"dernst","success":1,"access_level":"open_access","date_updated":"2025-01-20T08:41:10Z","content_type":"application/pdf","checksum":"b82413f00398ffb5168e8e747571a98d","file_name":"2024_JourSpatialInfoScience_Lutsai.pdf","date_created":"2025-01-20T08:41:10Z"}],"file_date_updated":"2025-01-20T08:41:10Z","citation":{"mla":"Lutsai, Kateryna, and Christoph Lampert. “Predicting the Geolocation of Tweets Using Transformer Models on Customized Data.” <i>Journal of Spatial Information Science</i>, no. 29, University of Maine, 2024, pp. 69–99, doi:<a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">10.5311/JOSIS.2024.29.295</a>.","ista":"Lutsai K, Lampert C. 2024. Predicting the geolocation of tweets using transformer models on customized data. Journal of Spatial Information Science. (29), 69–99.","ama":"Lutsai K, Lampert C. Predicting the geolocation of tweets using transformer models on customized data. <i>Journal of Spatial Information Science</i>. 2024;(29):69-99. doi:<a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">10.5311/JOSIS.2024.29.295</a>","chicago":"Lutsai, Kateryna, and Christoph Lampert. “Predicting the Geolocation of Tweets Using Transformer Models on Customized Data.” <i>Journal of Spatial Information Science</i>. University of Maine, 2024. <a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">https://doi.org/10.5311/JOSIS.2024.29.295</a>.","ieee":"K. Lutsai and C. Lampert, “Predicting the geolocation of tweets using transformer models on customized data,” <i>Journal of Spatial Information Science</i>, no. 29. University of Maine, pp. 69–99, 2024.","short":"K. Lutsai, C. Lampert, Journal of Spatial Information Science (2024) 69–99.","apa":"Lutsai, K., &#38; Lampert, C. (2024). Predicting the geolocation of tweets using transformer models on customized data. <i>Journal of Spatial Information Science</i>. University of Maine. <a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">https://doi.org/10.5311/JOSIS.2024.29.295</a>"},"publication_identifier":{"eissn":["1948-660X"]},"_id":"18856","date_updated":"2026-10-21T14:07:54Z","year":"2024","title":"Predicting the geolocation of tweets using transformer models on customized data","doi":"10.5311/JOSIS.2024.29.295","has_accepted_license":"1","quality_controlled":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"University of Maine","author":[{"first_name":"Kateryna","full_name":"Lutsai, Kateryna","last_name":"Lutsai"},{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"corr_author":"1","oa":1,"DOAJ_listed":"1","type":"journal_article","date_published":"2024-12-26T00:00:00Z","related_material":{"link":[{"url":"https://github.com/K4TEL/geo-twitter.git","relation":"software"}]},"das_tickbox":"0","fulldoi":"https://doi.org/10.5311/JOSIS.2024.29.295","month":"12","article_processing_charge":"Yes","OA_place":"publisher","department":[{"_id":"ChLa"}],"OA_type":"gold","publication_status":"published","date_created":"2025-01-19T23:01:53Z"},{"degree_awarded":"PhD","_id":"17206","year":"2024","date_updated":"2026-09-24T11:19:04Z","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.15479/at:ista:17206","has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"last_name":"Raices","full_name":"Raices, Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"}],"corr_author":"1","type":"dissertation","date_published":"2024-07-05T00:00:00Z","das_tickbox":"0","fulldoi":"https://doi.org/10.15479/at:ista:17206","month":"07","OA_place":"publisher","article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"publication_status":"published","supervisor":[{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"date_created":"2024-07-05T14:15:29Z","researchdata_availability":"no","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. ","lang":"eng"}],"supplementarymaterial":"no","alternative_title":["ISTA Thesis"],"day":"05","doi_confirm":"1","ec_funded":1,"ddc":["570"],"license":"https://creativecommons.org/licenses/by-sa/4.0/","page":"82","oa_version":"Published Version","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"language":[{"iso":"eng"}],"file":[{"embargo_to":"open_access","creator":"cchlebak","file_id":"17223","relation":"source_file","file_size":13788479,"date_updated":"2025-01-11T23:30:04Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-07-11T07:18:01Z","checksum":"d5e9234bde8667b005a8cfe18bb467d3","file_name":"ThesisRaices2024_postDefense.docx"},{"file_name":"ThesisRaices2024_nosignature.pdf","checksum":"f5ed0139aa3e11ce58369f0915647c5c","date_created":"2024-07-11T07:22:32Z","embargo":"2025-01-11","content_type":"application/pdf","access_level":"open_access","date_updated":"2025-01-11T23:30:04Z","file_size":5580296,"file_id":"17224","relation":"main_file","creator":"cchlebak"}],"file_date_updated":"2025-01-11T23:30:04Z","citation":{"chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","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.","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.","apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>.","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.","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>"},"publication_identifier":{"issn":["2663-337X"]}},{"publication_status":"published","OA_place":"publisher","month":"08","article_processing_charge":"Yes","OA_type":"gold","department":[{"_id":"BeVi"}],"external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"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","article_number":"e1011376","date_created":"2024-09-08T22:01:11Z","pmid":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project"}],"record":[{"status":"public","relation":"research_data","id":"17362"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"DOAJ_listed":"1","type":"journal_article","date_published":"2024-08-30T00:00:00Z","fulldoi":"https://doi.org/10.1371/journal.pgen.1011376","das_tickbox":"1","oa":1,"corr_author":"1","author":[{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"APC_amount":"3145,39 EUR","publisher":"Public Library of Science","intvolume":"        20","isi":1,"_id":"17890","status":"public","quality_controlled":"1","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","date_updated":"2026-11-09T23:31:00Z","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1371/journal.pgen.1011376","file_date_updated":"2024-09-11T07:54:12Z","file":[{"date_created":"2024-09-11T07:54:12Z","checksum":"f5d96b9af57126fc1063e951440477d6","file_name":"2024_PloSGenetics_Elkrewi.pdf","content_type":"application/pdf","date_updated":"2024-09-11T07:54:12Z","success":1,"access_level":"open_access","creator":"dernst","file_id":"18056","relation":"main_file","file_size":8962687}],"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"citation":{"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.","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>.","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>","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>.","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.","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>","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024)."},"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"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. ","issue":"8","language":[{"iso":"eng"}],"publication":"PLoS Genetics","ddc":["570"],"project":[{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"researchdata_availability":"yes","scopus_import":"1","article_type":"original","day":"30","abstract":[{"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.","lang":"eng"}],"supplementarymaterial":"yes","volume":20},{"language":[{"iso":"eng"}],"oa_version":"Published Version","publication_identifier":{"isbn":["978-3-99078-041-1"],"issn":["2663-337X"]},"citation":{"ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>"},"file_date_updated":"2025-03-25T23:30:03Z","file":[{"date_updated":"2025-03-25T23:30:03Z","access_level":"closed","embargo_to":"open_access","creator":"dporley","relation":"source_file","file_id":"18149","file_size":14213128,"date_created":"2024-09-26T13:40:33Z","checksum":"3b8b0bacfe61112f3852744f3170e468","file_name":"PhD_thesis_DPorley_final_20240919.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","embargo":"2025-03-25","date_created":"2024-09-26T13:41:39Z","checksum":"6c3a652a8eede874118e11d66a63652f","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","creator":"dporley","file_id":"18150","relation":"main_file","file_size":18583031,"date_updated":"2025-03-25T23:30:03Z","access_level":"open_access"}],"day":"26","supplementarymaterial":"unclear","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies."}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"25762","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A"}],"researchdata_availability":"unclear","page":"131","ddc":["570"],"ec_funded":1,"doi_confirm":"1","fulldoi":"https://doi.org/10.15479/at:ista:18101","date_published":"2024-09-26T00:00:00Z","type":"dissertation","date_created":"2024-09-20T10:21:03Z","supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"month":"09","OA_place":"publisher","article_processing_charge":"No","has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.15479/at:ista:18101","title":"Structural characterization of spumavirus capsid assemblies","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"date_updated":"2026-10-02T11:20:53Z","year":"2024","degree_awarded":"PhD","_id":"18101","corr_author":"1","author":[{"full_name":"Porley, Dario J","last_name":"Porley","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","first_name":"Dario J"}],"oa":1,"publisher":"Institute of Science and Technology Austria"},{"related_material":{"record":[{"status":"public","id":"20357","relation":"dissertation_contains"}]},"pmid":1,"date_published":"2024-10-29T00:00:00Z","type":"journal_article","fulldoi":"https://doi.org/10.1073/pnas.2402340121","das_tickbox":"1","publication_status":"published","OA_type":"hybrid","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"month":"10","OA_place":"publisher","article_processing_charge":"Yes","article_number":"e2402340121","external_id":{"pmid":["39441639"],"isi":["001349462600001"]},"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).","date_created":"2024-11-10T23:01:59Z","_id":"18525","isi":1,"status":"public","has_accepted_license":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1073/pnas.2402340121","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","date_updated":"2026-11-09T23:31:02Z","year":"2024","author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia","last_name":"Ruzickova","full_name":"Ruzickova, Natalia"},{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"oa":1,"APC_amount":"3062,93 EUR","corr_author":"1","intvolume":"       121","publisher":"National Academy of Sciences","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","issue":"44","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.","language":[{"iso":"eng"}],"file_date_updated":"2024-11-11T09:31:00Z","file":[{"checksum":"d930e2ccf9ec900c7d7509a78cfb3564","file_name":"2024_PNAS_Ruzickova.pdf","date_created":"2024-11-11T09:31:00Z","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2024-11-11T09:31:00Z","relation":"main_file","file_id":"18536","file_size":25529709,"creator":"dernst"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"citation":{"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.","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>.","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>","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.","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>.","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>","short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"project":[{"name":"Collective behaviour of cells in pancreatic Islets of Langerhans","_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"}],"researchdata_availability":"not applicable","day":"29","article_type":"original","scopus_import":"1","supplementarymaterial":"yes","volume":121,"abstract":[{"lang":"eng","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."}],"ddc":["570"],"publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"date_created":"2024-09-08T10:23:25Z","supervisor":[{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"}],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"article_processing_charge":"No","month":"09","OA_place":"publisher","publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:17881","date_published":"2024-09-10T00:00:00Z","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","id":"14032","status":"public"},{"id":"18057","relation":"part_of_dissertation","status":"public"}]},"publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham"}],"corr_author":"1","doi":"10.15479/at:ista:17881","year":"2024","title":"Thermal effects in one dimensional Josephson chains","date_updated":"2026-10-02T11:12:07Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17881","degree_awarded":"PhD","citation":{"ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","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>.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","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>","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>.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"file":[{"file_size":10297052,"file_id":"18059","relation":"main_file","creator":"smukhopa","access_level":"open_access","date_updated":"2025-03-13T23:30:04Z","embargo":"2025-03-13","content_type":"application/pdf","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","date_created":"2024-09-12T10:46:04Z"},{"content_type":"application/zip","date_created":"2024-09-12T10:50:58Z","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","checksum":"e352667482701dd18a9a0e7418aef465","creator":"smukhopa","embargo_to":"open_access","file_size":29178634,"relation":"source_file","file_id":"18060","date_updated":"2025-03-13T23:30:04Z","access_level":"closed"}],"file_date_updated":"2025-03-13T23:30:04Z","language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["539"],"page":"82","doi_confirm":"1","supplementarymaterial":"unclear","alternative_title":["ISTA Thesis"],"abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"day":"10","researchdata_availability":"unclear","project":[{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}]},{"publication":"Genome Biology and Evolution","ddc":["570"],"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"}],"supplementarymaterial":"yes","volume":16,"scopus_import":"1","article_type":"original","day":"20","researchdata_availability":"yes","citation":{"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.","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>.","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>","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","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.","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>.","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>"},"publication_identifier":{"eissn":["1759-6653"]},"file":[{"relation":"main_file","file_id":"15029","file_size":5213306,"creator":"dernst","success":1,"access_level":"open_access","date_updated":"2024-02-26T09:54:59Z","content_type":"application/pdf","checksum":"106a40f10443b2e7ba66749844ebbdf1","file_name":"2024_GBE_Bett.pdf","date_created":"2024-02-26T09:54:59Z"}],"file_date_updated":"2024-02-26T09:54:59Z","language":[{"iso":"eng"}],"issue":"1","oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"intvolume":"        16","publisher":"Oxford University Press","oa":1,"corr_author":"1","author":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","last_name":"Bett"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"date_updated":"2026-11-09T23:31:02Z","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","year":"2024","doi":"10.1093/gbe/evae006","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","has_accepted_license":"1","_id":"15009","isi":1,"date_created":"2024-02-18T23:01:02Z","external_id":{"pmid":["38245839"],"isi":["001153952800001"]},"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.","article_number":"evae006","article_processing_charge":"Yes","OA_place":"publisher","month":"01","OA_type":"gold","department":[{"_id":"BeVi"}],"publication_status":"published","das_tickbox":"1","fulldoi":"https://doi.org/10.1093/gbe/evae006","DOAJ_listed":"1","date_published":"2024-01-20T00:00:00Z","type":"journal_article","pmid":1,"related_material":{"record":[{"relation":"research_data","id":"14705","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19386"},{"id":"20449","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"20444","status":"deleted"}]}},{"citation":{"ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","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>.","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>","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>.","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>. .","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>","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.)."},"oa_version":"Preprint","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","language":[{"iso":"eng"}],"ec_funded":1,"publication":"arXiv","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"researchdata_availability":"no","day":"14","supplementarymaterial":"no","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"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.07829"}],"publication_status":"draft","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"article_processing_charge":"No","OA_place":"repository","month":"08","article_number":"2408.07829","external_id":{"arxiv":["2408.07829"]},"date_created":"2024-09-11T09:25:22Z","related_material":{"record":[{"relation":"later_version","id":"20324","status":"public"},{"id":"17881","relation":"dissertation_contains","status":"public"}]},"arxiv":1,"type":"preprint","date_published":"2024-08-14T00:00:00Z","fulldoi":"https://doi.org/10.48550/arXiv.2408.07829","das_tickbox":"0","oa":1,"corr_author":"1","author":[{"last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham","orcid":"0000-0001-5263-5559"},{"full_name":"Lancheros Naranjo, Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","first_name":"Diego A"},{"last_name":"Senior","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","orcid":"0000-0002-0672-9295"},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"_id":"18057","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","doi":"10.48550/arXiv.2408.07829","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_updated":"2026-11-09T23:31:01Z","title":"Dual relaxation oscillations in a Josephson junction array","year":"2024"},{"file":[{"content_type":"application/zip","date_created":"2024-06-07T16:09:17Z","file_name":"thesis.zip","checksum":"fab59146e3b3dc2e5d214576984a2a63","embargo_to":"open_access","creator":"rkelemen","file_size":180557931,"file_id":"17121","relation":"source_file","date_updated":"2025-01-10T23:30:10Z","access_level":"closed"},{"relation":"main_file","file_id":"17213","file_size":19405484,"creator":"rkelemen","access_level":"open_access","date_updated":"2025-01-10T23:30:10Z","embargo":"2025-01-10","content_type":"application/pdf","checksum":"91cc4c25a792239e8a7688e8aec7c62a","file_name":"thesis_to_archive.pdf","date_created":"2024-07-10T08:00:20Z"}],"file_date_updated":"2025-01-10T23:30:10Z","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"citation":{"ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","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>","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.","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>.","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."},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa_version":"Published Version","language":[{"iso":"eng"}],"doi_confirm":"1","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ddc":["576"],"page":"105","researchdata_availability":"unclear","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"alternative_title":["ISTA Thesis"],"supplementarymaterial":"unclear","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."}],"day":"20","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"OA_place":"publisher","article_processing_charge":"No","month":"06","publication_status":"published","supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"date_created":"2024-06-07T16:14:13Z","type":"dissertation","date_published":"2024-06-20T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"542","status":"public"},{"id":"10767","relation":"part_of_dissertation","status":"public"}]},"fulldoi":"https://doi.org/10.15479/at:ista:17119","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Kelemen","full_name":"Kelemen, Réka K","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281"}],"corr_author":"1","oa":1,"_id":"17119","degree_awarded":"PhD","doi":"10.15479/at:ista:17119","date_updated":"2026-10-02T11:14:33Z","year":"2024","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","has_accepted_license":"1"},{"publisher":"Institute of Science and Technology Austria","author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac"}],"oa":1,"corr_author":"1","title":"Early stages of sex chromosome evolution","year":"2024","date_updated":"2026-10-02T11:14:08Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"doi":"10.15479/at:ista:18531","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","degree_awarded":"PhD","_id":"18531","date_created":"2024-11-11T08:40:45Z","supervisor":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"OA_embargo":"6","OA_place":"publisher","article_processing_charge":"No","month":"11","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:18531","type":"dissertation","date_published":"2024-11-11T00:00:00Z","related_material":{"record":[{"status":"public","id":"12521","relation":"part_of_dissertation"},{"id":"18549","relation":"part_of_dissertation","status":"public"}]},"ddc":["576"],"page":"181","doi_confirm":"1","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"}],"alternative_title":["ISTA Thesis"],"supplementarymaterial":"unclear","day":"11","researchdata_availability":"unclear","citation":{"ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","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>.","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>","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","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>.","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>","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024."},"keyword":["Sex chromosomes","evolution","selection","sheltering"],"publication_identifier":{"issn":["2663-337X"]},"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"3e48b163c22114ef5d5371f758668289","file_name":"AMrnjavac_thesis_library.docx","date_created":"2024-11-13T12:15:28Z","file_id":"18551","relation":"source_file","file_size":26870629,"creator":"amrnjava","embargo_to":"open_access","access_level":"closed","title":"Early stages of sex chromosome evolution","date_updated":"2025-05-11T22:30:04Z"},{"file_size":4228766,"file_id":"18552","relation":"main_file","creator":"amrnjava","access_level":"open_access","date_updated":"2025-05-11T22:30:04Z","title":"Early stages of sex chromosome evolution","embargo":"2025-05-11","content_type":"application/pdf","file_name":"AMrnjavac_thesis_library.pdf","checksum":"3ead60c1b678e7dcf018043aef3b5db2","date_created":"2024-11-13T12:15:54Z"}],"file_date_updated":"2025-05-11T22:30:04Z","language":[{"iso":"eng"}],"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"}},{"researchdata_availability":"unclear","abstract":[{"lang":"eng","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"}],"alternative_title":["ISTA Thesis"],"supplementarymaterial":"unclear","day":"17","doi_confirm":"1","ddc":["572","530"],"page":"57","oa_version":"Published Version","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"language":[{"iso":"eng"}],"file":[{"creator":"mamaral","embargo_to":"open_access","file_id":"18671","relation":"source_file","file_size":19161387,"date_updated":"2025-06-18T22:30:03Z","access_level":"closed","content_type":"application/zip","date_created":"2024-12-18T12:27:01Z","checksum":"eca06497a29078558395455c890a32d9","file_name":"2024_msfa_thesis.zip"},{"creator":"mamaral","file_size":16530084,"relation":"main_file","file_id":"18672","date_updated":"2025-06-18T22:30:03Z","access_level":"open_access","content_type":"application/pdf","embargo":"2025-06-18","date_created":"2024-12-18T12:26:30Z","file_name":"2024_msfa_thesis.pdf","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00"}],"file_date_updated":"2025-06-18T22:30:03Z","citation":{"ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.","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>.","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>","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.","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>.","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>","short":"M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024."},"publication_identifier":{"isbn":["978-3-99078-046-6"],"issn":["2663-337X"]},"degree_awarded":"PhD","_id":"18661","year":"2024","title":"Archaeal membranes: In silico modelling and design","date_updated":"2026-10-02T11:12:49Z","doi":"10.15479/at:ista:18661","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","publisher":"Institute of Science and Technology Austria","corr_author":"1","oa":1,"author":[{"last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel"}],"date_published":"2024-12-17T00:00:00Z","type":"dissertation","related_material":{"record":[{"status":"public","id":"18670","relation":"part_of_dissertation"}]},"fulldoi":"https://doi.org/10.15479/at:ista:18661","article_processing_charge":"No","month":"12","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"publication_status":"published","supervisor":[{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"}],"date_created":"2024-12-16T10:53:39Z"},{"publication":"bioRxiv","day":"04","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"}],"supplementarymaterial":"yes","researchdata_availability":"no","citation":{"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>.","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","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>","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>.","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>.","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>"},"language":[{"iso":"eng"}],"oa_version":"Preprint","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa":1,"corr_author":"1","author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","date_updated":"2026-11-09T23:31:03Z","title":"Evidence of a Slower-Z effect in Schistosoma japonicum","year":"2024","doi":"10.1101/2024.07.02.601697","_id":"18549","external_id":{"biorxivid":["10.1101/2024.07.02.601697"]},"date_created":"2024-11-13T09:12:08Z","main_file_link":[{"url":"https://doi.org/10.1101/2024.07.02.601697","open_access":"1"}],"publication_status":"draft","article_processing_charge":"No","month":"07","OA_place":"repository","department":[{"_id":"BeVi"}],"fulldoi":"https://doi.org/10.1101/2024.07.02.601697","das_tickbox":"0","biorxivid":1,"related_material":{"record":[{"id":"19370","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18531"}]},"date_published":"2024-07-04T00:00:00Z","type":"preprint"}]