--- OA_place: publisher OA_type: hybrid _id: '17236' abstract: - lang: eng 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." article_processing_charge: Yes (via OA deal) arxiv: 1 author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2024:403-414. doi:10.1145/3626183.3659969' apa: 'Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 403–414). Nantes, France: Association for Computing Machinery. https://doi.org/10.1145/3626183.3659969' chicago: Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” In Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, 403–14. Association for Computing Machinery, 2024. https://doi.org/10.1145/3626183.3659969. ieee: V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut,” in Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Nantes, France, 2024, pp. 403–414. 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.' mla: Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–14, doi:10.1145/3626183.3659969. short: V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414. conference: end_date: 2024-06-21 location: Nantes, France name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' start_date: 2024-06-17 corr_author: '1' das_tickbox: '0' date_created: 2024-07-14T22:01:11Z date_published: 2024-06-17T00:00:00Z date_updated: 2026-10-21T13:45:27Z day: '17' ddc: - '510' department: - _id: VlKo doi: 10.1145/3626183.3659969 external_id: arxiv: - '2307.00115' isi: - '001253331900044' file: - access_level: open_access checksum: 6ca18ac8508719dbd5d5735f4c991af2 content_type: application/pdf creator: dernst date_created: 2024-07-16T06:38:08Z date_updated: 2024-07-16T06:38:08Z file_id: '17245' file_name: 2024_SPAA_Kolmogorov.pdf file_size: 1116166 relation: main_file success: 1 file_date_updated: 2024-07-16T06:38:08Z fulldoi: https://doi.org/10.1145/3626183.3659969 has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 403-414 publication: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures publication_identifier: isbn: - '9798400704161' issn: - 1548-6109 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '21007' relation: extended_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '17408' 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." 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.)" article_number: '157' article_processing_charge: Yes article_type: original author: - first_name: Hiroki full_name: Nagai, Hiroki id: 608df3e6-e2ab-11ed-8890-c9318cec7da4 last_name: Nagai orcid: 0000-0003-1671-9434 - 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 - first_name: Junichiro full_name: Ui, Junichiro last_name: Ui - first_name: Takashi full_name: Makino, Takashi last_name: Makino - first_name: Masayuki full_name: Miura, Masayuki last_name: Miura - first_name: Yu Ichiro full_name: Nakajima, Yu Ichiro last_name: Nakajima citation: ama: NAGAI H, Adachi Y, Nakasugi T, et al. Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. BMC Biology. 2024;22. doi:10.1186/s12915-024-01956-4 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. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-024-01956-4 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.” BMC Biology. Springer Nature, 2024. https://doi.org/10.1186/s12915-024-01956-4. ieee: H. NAGAI et al., “Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut,” BMC Biology, vol. 22. Springer Nature, 2024. 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. mla: NAGAI, HIROKI, et al. “Highly Regenerative Species-Specific Genes Improve Age-Associated Features in the Adult Drosophila Midgut.” BMC Biology, vol. 22, 157, Springer Nature, 2024, doi:10.1186/s12915-024-01956-4. short: H. NAGAI, Y. Adachi, T. Nakasugi, E. Takigawa, J. Ui, T. Makino, M. Miura, Y.I. Nakajima, BMC Biology 22 (2024). das_tickbox: '1' 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. date_created: 2024-08-11T22:01:11Z date_published: 2024-08-02T00:00:00Z date_updated: 2026-10-21T13:47:19Z day: '02' ddc: - '570' department: - _id: XiFe doi: 10.1186/s12915-024-01956-4 external_id: isi: - '001282893200001' pmid: - '39090637' file: - access_level: open_access checksum: 318759626ec83b13f909c82904393ef1 content_type: application/pdf creator: dernst date_created: 2024-08-12T08:14:44Z date_updated: 2024-08-12T08:14:44Z file_id: '17417' file_name: 2024_BMCBio_Nagai.pdf file_size: 3345718 relation: main_file success: 1 file_date_updated: 2024-08-12T08:14:44Z fulldoi: https://doi.org/10.1186/s12915-024-01956-4 has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Biology publication_identifier: eissn: - 1741-7007 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 22 year: '2024' ... --- DOAJ_listed: '1' _id: '18111' abstract: - lang: eng 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. 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. " article_number: L9 article_processing_charge: Yes article_type: original author: - first_name: Brenna full_name: Mockler, Brenna last_name: Mockler - first_name: Monica full_name: Gallegos-Garcia, Monica last_name: Gallegos-Garcia - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: Jon M. full_name: Miller, Jon M. last_name: Miller - first_name: Enrico full_name: Ramirez-Ruiz, Enrico last_name: Ramirez-Ruiz citation: ama: Mockler B, Gallegos-Garcia M, Götberg YLL, Miller JM, Ramirez-Ruiz E. Tidal disruption events from stripped stars. Astrophysical Journal Letters. 2024;973(1). doi:10.3847/2041-8213/ad6c34 apa: Mockler, B., Gallegos-Garcia, M., Götberg, Y. L. L., Miller, J. M., & Ramirez-Ruiz, E. (2024). Tidal disruption events from stripped stars. Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad6c34 chicago: Mockler, Brenna, Monica Gallegos-Garcia, Ylva Louise Linsdotter Götberg, Jon M. Miller, and Enrico Ramirez-Ruiz. “Tidal Disruption Events from Stripped Stars.” Astrophysical Journal Letters. IOP Publishing, 2024. https://doi.org/10.3847/2041-8213/ad6c34. ieee: B. Mockler, M. Gallegos-Garcia, Y. L. L. Götberg, J. M. Miller, and E. Ramirez-Ruiz, “Tidal disruption events from stripped stars,” Astrophysical Journal Letters, vol. 973, no. 1. IOP Publishing, 2024. 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.” Astrophysical Journal Letters, vol. 973, no. 1, L9, IOP Publishing, 2024, doi:10.3847/2041-8213/ad6c34. short: B. Mockler, M. Gallegos-Garcia, Y.L.L. Götberg, J.M. Miller, E. Ramirez-Ruiz, Astrophysical Journal Letters 973 (2024). das_tickbox: '0' date_created: 2024-09-22T22:01:42Z date_published: 2024-09-12T00:00:00Z date_updated: 2026-10-21T13:50:17Z day: '12' ddc: - '520' department: - _id: YlGo doi: 10.3847/2041-8213/ad6c34 external_id: isi: - '001310592900001' file: - access_level: open_access checksum: 050ddf873244839825714cca42b5d857 content_type: application/pdf creator: dernst date_created: 2024-09-30T08:54:26Z date_updated: 2024-09-30T08:54:26Z file_id: '18161' file_name: 2024_AstrophysicalJourn_Mockler.pdf file_size: 844227 relation: main_file success: 1 file_date_updated: 2024-09-30T08:54:26Z fulldoi: https://doi.org/10.3847/2041-8213/ad6c34 has_accepted_license: '1' intvolume: ' 973' isi: 1 issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Astrophysical Journal Letters publication_identifier: eissn: - 2041-8213 issn: - 2041-8205 publication_status: published publisher: IOP Publishing quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Tidal disruption events from stripped stars tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 973 year: '2024' ... --- APC_amount: 2982,14 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '14886' 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. 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. article_number: '013042' article_processing_charge: Yes article_type: original author: - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: 'Lorenc D, Alpichshev Z. Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013042' apa: 'Lorenc, D., & Alpichshev, Z. (2024). Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013042' chicago: 'Lorenc, Dusan, and Zhanybek Alpichshev. “Dispersive Effects in Ultrafast Nonlinear Phenomena: The Case of Optical Kerr Effect.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013042.' ieee: 'D. Lorenc and Z. Alpichshev, “Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect,” Physical Review Research, vol. 6, no. 1. American Physical Society, 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.” Physical Review Research, vol. 6, no. 1, 013042, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013042.' short: D. Lorenc, Z. Alpichshev, Physical Review Research 6 (2024). corr_author: '1' das_tickbox: '0' date_created: 2024-01-28T23:01:42Z date_published: 2024-01-11T00:00:00Z date_updated: 2026-10-21T13:52:11Z day: '11' ddc: - '530' department: - _id: ZhAl doi: 10.1103/PhysRevResearch.6.013042 file: - access_level: open_access checksum: 42d58f93ae74e7f2c4de058ef75ff8b2 content_type: application/pdf creator: dernst date_created: 2024-01-31T11:59:30Z date_updated: 2024-01-31T11:59:30Z file_id: '14918' file_name: 2024_PhysicalReviewResearch_Lorenc.pdf file_size: 2863627 relation: main_file success: 1 file_date_updated: 2024-01-31T11:59:30Z fulldoi: https://doi.org/10.1103/PhysRevResearch.6.013042 has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Physical Review Research publication_identifier: eissn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'Dispersive effects in ultrafast nonlinear phenomena: The case of optical Kerr effect' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2024' ... --- OA_place: repository OA_type: green _id: '17285' abstract: - lang: eng 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. 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). article_processing_charge: No article_type: original author: - first_name: Xuemei full_name: Liu, Xuemei last_name: Liu - first_name: Min full_name: Deng, Min last_name: Deng - first_name: Bingxin full_name: Shi, Bingxin last_name: Shi - first_name: Kehui full_name: Zhu, Kehui last_name: Zhu - first_name: Jinchao full_name: Chen, Jinchao last_name: Chen - first_name: Shujuan full_name: Xu, Shujuan id: 9724dd9d-f591-11ee-bd51-e97ed0652286 last_name: Xu - first_name: Xiaomin full_name: Bie, Xiaomin last_name: Bie - first_name: Xiansheng full_name: Zhang, Xiansheng last_name: Zhang - first_name: Xuelei full_name: Lin, Xuelei last_name: Lin - first_name: Jun full_name: Xiao, Jun last_name: Xiao 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. Science China Life Sciences. 2024;67:2251-2266. doi:10.1007/s11427-024-2664-0 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. Science China Life Sciences. Springer Nature. https://doi.org/10.1007/s11427-024-2664-0 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.” Science China Life Sciences. Springer Nature, 2024. https://doi.org/10.1007/s11427-024-2664-0. ieee: X. Liu et al., “Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat,” Science China Life Sciences, vol. 67. Springer Nature, pp. 2251–2266, 2024. 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.” Science China Life Sciences, vol. 67, Springer Nature, 2024, pp. 2251–66, doi:10.1007/s11427-024-2664-0. 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. das_tickbox: '1' 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 date_published: 2024-10-01T00:00:00Z date_updated: 2026-10-21T13:50:04Z day: '01' department: - _id: XiFe doi: 10.1007/s11427-024-2664-0 external_id: isi: - '001268807700002' pmid: - '38987431' fulldoi: https://doi.org/10.1007/s11427-024-2664-0 intvolume: ' 67' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.12.19.572364 month: '10' oa: 1 oa_version: Preprint page: 2251-2266 pmid: 1 publication: Science China Life Sciences publication_identifier: eissn: - 1869-1889 issn: - 1674-7305 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 67 year: '2024' ... --- _id: '17476' 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 \U0001D45B2. The extracted \U0001D45B2 values for CsPbBr3 and MAPbBr3 at \U0001D706≈1µ⁢m are \U0001D45B2=+2.1×10−14cm2/W and \U0001D45B2=+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." acknowledgement: "We gratefully acknowledge the assistance of Prof. John\r\nDudley." article_number: '085403' article_processing_charge: No article_type: original author: - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Ayan full_name: Zhumekenov, Ayan last_name: Zhumekenov - first_name: Osman M. full_name: Bakr, Osman M. last_name: Bakr - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: 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. Physical Review Materials. 2024;8(8). doi:10.1103/PhysRevMaterials.8.085403' apa: 'Lorenc, D., Zhumekenov, A., Bakr, O. M., & 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. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.8.085403' 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.” Physical Review Materials. American Physical Society, 2024. https://doi.org/10.1103/PhysRevMaterials.8.085403.' 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,” Physical Review Materials, vol. 8, no. 8. American Physical Society, 2024.' 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.” Physical Review Materials, vol. 8, no. 8, 085403, American Physical Society, 2024, doi:10.1103/PhysRevMaterials.8.085403.' short: D. Lorenc, A. Zhumekenov, O.M. Bakr, Z. Alpichshev, Physical Review Materials 8 (2024). corr_author: '1' das_tickbox: '0' date_created: 2024-09-01T22:01:08Z date_published: 2024-08-23T00:00:00Z date_updated: 2026-10-21T13:51:39Z day: '23' department: - _id: ZhAl doi: 10.1103/PhysRevMaterials.8.085403 external_id: isi: - '001299497800001' fulldoi: https://doi.org/10.1103/PhysRevMaterials.8.085403 intvolume: ' 8' isi: 1 issue: '8' language: - iso: eng month: '08' oa_version: None publication: Physical Review Materials publication_identifier: eissn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18448' abstract: - lang: eng 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." 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). article_number: A89 article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Irene full_name: Shivaei, Irene last_name: Shivaei - first_name: Stacey full_name: Alberts, Stacey last_name: Alberts - first_name: Michael full_name: Florian, Michael last_name: Florian - first_name: George full_name: Rieke, George last_name: Rieke - first_name: Stijn full_name: Wuyts, Stijn last_name: Wuyts - first_name: Sarah full_name: Bodansky, Sarah last_name: Bodansky - first_name: Andrew J. full_name: Bunker, Andrew J. last_name: Bunker - first_name: Alex J. full_name: Cameron, Alex J. last_name: Cameron - first_name: Mirko full_name: Curti, Mirko last_name: Curti - first_name: Francesco full_name: Da'Eugenio, Francesco last_name: Da'Eugenio - first_name: Ugne full_name: Dudzevičiūte, Ugne last_name: Dudzevičiūte - first_name: Zhiyuan full_name: Ji, Zhiyuan last_name: Ji - first_name: Benjamin D. full_name: Johnson, Benjamin D. last_name: Johnson - first_name: Ivan full_name: Kramarenko, Ivan id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4 last_name: Kramarenko orcid: 0000-0001-5346-6048 - first_name: Jianwei full_name: Lyu, Jianwei last_name: Lyu - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Jane full_name: Morrison, Jane last_name: Morrison - first_name: Rohan full_name: Naidu, Rohan last_name: Naidu - first_name: Pablo G. full_name: Pérez-González, Pablo G. last_name: Pérez-González - first_name: Naveen full_name: Reddy, Naveen last_name: Reddy - first_name: Brant full_name: Robertson, Brant last_name: Robertson - first_name: Yang full_name: Sun, Yang last_name: Sun - first_name: Sandro full_name: Tacchella, Sandro last_name: Tacchella - first_name: Katherine full_name: Whitaker, Katherine last_name: Whitaker - first_name: Christina C. full_name: Williams, Christina C. last_name: Williams - first_name: Christopher N.A. full_name: Willmer, Christopher N.A. last_name: Willmer - first_name: Joris full_name: Witstok, Joris last_name: Witstok - first_name: Mengyuan full_name: Xiao, Mengyuan last_name: Xiao - first_name: Yongda full_name: Zhu, Yongda last_name: Zhu citation: 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. Astronomy & Astrophysics. 2024;690. doi:10.1051/0004-6361/202449579 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. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202449579 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.” Astronomy & Astrophysics. EDP Sciences, 2024. https://doi.org/10.1051/0004-6361/202449579. ieee: I. Shivaei et al., “A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI,” Astronomy & Astrophysics, vol. 690. EDP Sciences, 2024. 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 & 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.” Astronomy & Astrophysics, vol. 690, A89, EDP Sciences, 2024, doi:10.1051/0004-6361/202449579. 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 & Astrophysics 690 (2024). das_tickbox: '1' dataavailabilitystatement: 'Full table is published in an online repository: https://zenodo.org/records/12671075' date_created: 2024-10-20T22:02:06Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-10-21T14:03:27Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.1051/0004-6361/202449579 external_id: arxiv: - '2402.07989' isi: - '001381135700006' file: - access_level: open_access checksum: f399be98968b9ca5611c832a9b1eee2b content_type: application/pdf creator: dernst date_created: 2024-10-21T11:52:29Z date_updated: 2024-10-21T11:52:29Z file_id: '18458' file_name: 2024_AstronomyAstrophysics_Shivaei.pdf file_size: 10777358 relation: main_file success: 1 file_date_updated: 2024-10-21T11:52:29Z fulldoi: https://doi.org/10.1051/0004-6361/202449579 has_accepted_license: '1' intvolume: ' 690' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with JWST MIRI tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 690 year: '2024' ... --- DOAJ_listed: '1' _id: '15406' abstract: - lang: eng 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.' 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. article_number: L022027 article_processing_charge: Yes article_type: letter_note arxiv: 1 author: - first_name: M. L. full_name: Savchenko, M. L. last_name: Savchenko - first_name: J. full_name: Gospodarič, J. last_name: Gospodarič - first_name: A. full_name: Shuvaev, A. last_name: Shuvaev - first_name: I. A. full_name: Dmitriev, I. A. last_name: Dmitriev - first_name: Vlad full_name: Dziom, Vlad id: 6A9A37C2-8C5C-11E9-AE53-F2FDE5697425 last_name: Dziom orcid: 0000-0002-1648-0999 - first_name: A. A. full_name: Dobretsova, A. A. last_name: Dobretsova - first_name: N. N. full_name: Mikhailov, N. N. last_name: Mikhailov - first_name: Z. D. full_name: Kvon, Z. D. last_name: Kvon - first_name: A. full_name: Pimenov, A. last_name: Pimenov citation: ama: Savchenko ML, Gospodarič J, Shuvaev A, et al. Optical Shubnikov-de Haas oscillations in two-dimensional electron systems. Physical Review Research. 2024;6(2). doi:10.1103/PhysRevResearch.6.L022027 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. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.L022027 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.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.L022027. ieee: M. L. Savchenko et al., “Optical Shubnikov-de Haas oscillations in two-dimensional electron systems,” Physical Review Research, vol. 6, no. 2. American Physical Society, 2024. 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. mla: Savchenko, M. L., et al. “Optical Shubnikov-de Haas Oscillations in Two-Dimensional Electron Systems.” Physical Review Research, vol. 6, no. 2, L022027, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.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). das_tickbox: '0' date_created: 2024-05-19T22:01:12Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-10-21T13:52:32Z day: '01' ddc: - '530' department: - _id: ZhAl doi: 10.1103/PhysRevResearch.6.L022027 external_id: arxiv: - '2402.05879' file: - access_level: open_access checksum: 78c8c3cf1bda766e3de0db45f143a367 content_type: application/pdf creator: dernst date_created: 2024-05-22T06:39:35Z date_updated: 2024-05-22T06:39:35Z file_id: '15412' file_name: 2024_PhysicalReviewResearch_Savchenko.pdf file_size: 1697856 relation: main_file success: 1 file_date_updated: 2024-05-22T06:39:35Z fulldoi: https://doi.org/10.1103/PhysRevResearch.6.L022027 has_accepted_license: '1' intvolume: ' 6' issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Physical Review Research publication_identifier: eissn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Optical Shubnikov-de Haas oscillations in two-dimensional electron systems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18856' abstract: - lang: eng 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. 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. article_processing_charge: Yes article_type: original author: - first_name: Kateryna full_name: Lutsai, Kateryna last_name: Lutsai - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Lutsai K, Lampert C. Predicting the geolocation of tweets using transformer models on customized data. Journal of Spatial Information Science. 2024;(29):69-99. doi:10.5311/JOSIS.2024.29.295 apa: Lutsai, K., & Lampert, C. (2024). Predicting the geolocation of tweets using transformer models on customized data. Journal of Spatial Information Science. University of Maine. https://doi.org/10.5311/JOSIS.2024.29.295 chicago: Lutsai, Kateryna, and Christoph Lampert. “Predicting the Geolocation of Tweets Using Transformer Models on Customized Data.” Journal of Spatial Information Science. University of Maine, 2024. https://doi.org/10.5311/JOSIS.2024.29.295. ieee: K. Lutsai and C. Lampert, “Predicting the geolocation of tweets using transformer models on customized data,” Journal of Spatial Information Science, no. 29. University of Maine, pp. 69–99, 2024. 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. mla: Lutsai, Kateryna, and Christoph Lampert. “Predicting the Geolocation of Tweets Using Transformer Models on Customized Data.” Journal of Spatial Information Science, no. 29, University of Maine, 2024, pp. 69–99, doi:10.5311/JOSIS.2024.29.295. short: K. Lutsai, C. Lampert, Journal of Spatial Information Science (2024) 69–99. corr_author: '1' das_tickbox: '0' date_created: 2025-01-19T23:01:53Z date_published: 2024-12-26T00:00:00Z date_updated: 2026-10-21T14:07:54Z day: '26' ddc: - '500' department: - _id: ChLa doi: 10.5311/JOSIS.2024.29.295 file: - access_level: open_access checksum: b82413f00398ffb5168e8e747571a98d content_type: application/pdf creator: dernst date_created: 2025-01-20T08:41:10Z date_updated: 2025-01-20T08:41:10Z file_id: '18857' file_name: 2024_JourSpatialInfoScience_Lutsai.pdf file_size: 7250655 relation: main_file success: 1 file_date_updated: 2025-01-20T08:41:10Z fulldoi: https://doi.org/10.5311/JOSIS.2024.29.295 has_accepted_license: '1' issue: '29' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '12' oa: 1 oa_version: Published Version page: 69-99 publication: Journal of Spatial Information Science publication_identifier: eissn: - 1948-660X publication_status: published publisher: University of Maine quality_controlled: '1' related_material: link: - relation: software url: https://github.com/K4TEL/geo-twitter.git researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Predicting the geolocation of tweets using transformer models on customized data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '17206' abstract: - lang: eng text: "Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. " acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia full_name: Raices, Julia id: 3EE67F22-F248-11E8-B48F-1D18A9856A87 last_name: Raices citation: ama: 'Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:10.15479/at:ista:17206' apa: '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. https://doi.org/10.15479/at:ista:17206' 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. https://doi.org/10.15479/at:ista:17206.' ieee: 'J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.' ista: 'Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.' mla: 'Raices, Julia. 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, doi:10.15479/at:ista:17206.' 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.' corr_author: '1' das_tickbox: '0' date_created: 2024-07-05T14:15:29Z date_published: 2024-07-05T00:00:00Z date_updated: 2026-09-24T11:19:04Z day: '05' ddc: - '570' degree_awarded: PhD department: - _id: BeVi - _id: GradSch doi: 10.15479/at:ista:17206 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: d5e9234bde8667b005a8cfe18bb467d3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-07-11T07:18:01Z date_updated: 2025-01-11T23:30:04Z embargo_to: open_access file_id: '17223' file_name: ThesisRaices2024_postDefense.docx file_size: 13788479 relation: source_file - access_level: open_access checksum: f5ed0139aa3e11ce58369f0915647c5c content_type: application/pdf creator: cchlebak date_created: 2024-07-11T07:22:32Z date_updated: 2025-01-11T23:30:04Z embargo: 2025-01-11 file_id: '17224' file_name: ThesisRaices2024_nosignature.pdf file_size: 5580296 relation: main_file file_date_updated: 2025-01-11T23:30:04Z fulldoi: https://doi.org/10.15479/at:ista:17206 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '07' oa: 1 oa_version: Published Version page: '82' project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: no status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 supplementarymaterial: no title: 'Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- APC_amount: 3145,39 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17890' abstract: - lang: eng text: Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group. acknowledged_ssus: - _id: ScienComp 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. " article_number: e1011376 article_processing_charge: Yes article_type: original author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 2024;20(8). doi:10.1371/journal.pgen.1011376 apa: Elkrewi, M. N., & Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1011376 chicago: Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” PLoS Genetics. Public Library of Science, 2024. https://doi.org/10.1371/journal.pgen.1011376. ieee: M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” PLoS Genetics, vol. 20, no. 8. Public Library of Science, 2024. 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.” PLoS Genetics, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:10.1371/journal.pgen.1011376. short: M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024). corr_author: '1' das_tickbox: '1' 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' date_created: 2024-09-08T22:01:11Z date_published: 2024-08-30T00:00:00Z date_updated: 2026-11-09T23:31:00Z day: '30' ddc: - '570' department: - _id: BeVi doi: 10.1371/journal.pgen.1011376 external_id: isi: - '001304090200001' pmid: - '39213449' file: - access_level: open_access checksum: f5d96b9af57126fc1063e951440477d6 content_type: application/pdf creator: dernst date_created: 2024-09-11T07:54:12Z date_updated: 2024-09-11T07:54:12Z file_id: '18056' file_name: 2024_PloSGenetics_Elkrewi.pdf file_size: 8962687 relation: main_file success: 1 file_date_updated: 2024-09-11T07:54:12Z fulldoi: https://doi.org/10.1371/journal.pgen.1011376 has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/Melkrewi/Artemia-snRNAseq-Project record: - id: '17362' relation: research_data status: public - id: '19386' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- OA_place: publisher _id: '18101' abstract: - lang: eng text: "The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dario J full_name: Porley, Dario J id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87 last_name: Porley citation: ama: Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:10.15479/at:ista:18101 apa: Porley Esteves, D. (2024). Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18101 chicago: Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18101. ieee: D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024. ista: Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. mla: Porley Esteves, Darío. Structural Characterization of Spumavirus Capsid Assemblies. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18101. short: D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-20T10:21:03Z date_published: 2024-09-26T00:00:00Z date_updated: 2026-10-02T11:20:53Z day: '26' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:18101 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 3b8b0bacfe61112f3852744f3170e468 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dporley date_created: 2024-09-26T13:40:33Z date_updated: 2025-03-25T23:30:03Z embargo_to: open_access file_id: '18149' file_name: PhD_thesis_DPorley_final_20240919.docx file_size: 14213128 relation: source_file - access_level: open_access checksum: 6c3a652a8eede874118e11d66a63652f content_type: application/pdf creator: dporley date_created: 2024-09-26T13:41:39Z date_updated: 2025-03-25T23:30:03Z embargo: 2025-03-25 file_id: '18150' file_name: PhD_thesis_DPorley_final_20240926_pdfa1.pdf file_size: 18583031 relation: main_file file_date_updated: 2025-03-25T23:30:03Z fulldoi: https://doi.org/10.15479/at:ista:18101 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '131' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A grant_number: '25762' name: Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms publication_identifier: isbn: - 978-3-99078-041-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria researchdata_availability: unclear status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 supplementarymaterial: unclear title: Structural characterization of spumavirus capsid assemblies type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- APC_amount: 3062,93 EUR OA_place: publisher OA_type: hybrid _id: '18525' 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. 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. article_number: e2402340121 article_processing_charge: Yes article_type: original author: - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2402340121 apa: 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. National Academy of Sciences. https://doi.org/10.1073/pnas.2402340121 chicago: Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2402340121. ieee: N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024. 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.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:10.1073/pnas.2402340121. short: N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). corr_author: '1' das_tickbox: '1' 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 date_published: 2024-10-29T00:00:00Z date_updated: 2026-11-09T23:31:02Z day: '29' ddc: - '570' department: - _id: GaTk - _id: NiBa doi: 10.1073/pnas.2402340121 external_id: isi: - '001349462600001' pmid: - '39441639' file: - access_level: open_access checksum: d930e2ccf9ec900c7d7509a78cfb3564 content_type: application/pdf creator: dernst date_created: 2024-11-11T09:31:00Z date_updated: 2024-11-11T09:31:00Z file_id: '18536' file_name: 2024_PNAS_Ruzickova.pdf file_size: 25529709 relation: main_file success: 1 file_date_updated: 2024-11-11T09:31:00Z fulldoi: https://doi.org/10.1073/pnas.2402340121 has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '44' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e name: Collective behaviour of cells in pancreatic Islets of Langerhans - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: record: - id: '20357' relation: dissertation_contains status: public researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: yes title: Quantitative omnigenic model discovers interpretable genome-wide associations tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- OA_place: publisher _id: '17881' abstract: - lang: eng text: "This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 citation: ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881 apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881 chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881. ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024. ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881. short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-08T10:23:25Z date_published: 2024-09-10T00:00:00Z date_updated: 2026-10-02T11:12:07Z day: '10' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/at:ista:17881 doi_confirm: '1' file: - access_level: open_access checksum: ed7763c3bbd59e1d7e1b664de3a26f3c content_type: application/pdf creator: smukhopa date_created: 2024-09-12T10:46:04Z date_updated: 2025-03-13T23:30:04Z embargo: 2025-03-13 file_id: '18059' file_name: PhD_Thesis_Soham_Mukhopadhyay.pdf file_size: 10297052 relation: main_file - access_level: closed checksum: e352667482701dd18a9a0e7418aef465 content_type: application/zip creator: smukhopa date_created: 2024-09-12T10:50:58Z date_updated: 2025-03-13T23:30:04Z embargo_to: open_access file_id: '18060' file_name: PhD_Thesis_Soham_Mukhopadhyay_source.zip file_size: 29178634 relation: source_file file_date_updated: 2025-03-13T23:30:04Z fulldoi: https://doi.org/10.15479/at:ista:17881 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '82' project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition publication_identifier: isbn: - 978-3-99078-043-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14032' relation: part_of_dissertation status: public - id: '18057' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 supplementarymaterial: unclear title: Thermal effects in one dimensional Josephson chains type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '15009' abstract: - lang: eng 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. article_number: evae006 article_processing_charge: Yes article_type: original author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006 apa: Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006 chicago: Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006. ieee: V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 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.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006. short: V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024). corr_author: '1' das_tickbox: '1' 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. date_created: 2024-02-18T23:01:02Z date_published: 2024-01-20T00:00:00Z date_updated: 2026-11-09T23:31:02Z day: '20' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evae006 external_id: isi: - '001153952800001' pmid: - '38245839' file: - access_level: open_access checksum: 106a40f10443b2e7ba66749844ebbdf1 content_type: application/pdf creator: dernst date_created: 2024-02-26T09:54:59Z date_updated: 2024-02-26T09:54:59Z file_id: '15029' file_name: 2024_GBE_Bett.pdf file_size: 5213306 relation: main_file success: 1 file_date_updated: 2024-02-26T09:54:59Z fulldoi: https://doi.org/10.1093/gbe/evae006 has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology and Evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '14705' relation: research_data status: public - id: '19386' relation: dissertation_contains status: public - id: '20449' relation: dissertation_contains status: public - id: '20444' relation: dissertation_contains status: deleted researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 16 year: '2024' ... --- OA_place: repository _id: '18057' abstract: - lang: eng 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." acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: "We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n" article_number: '2408.07829' article_processing_charge: No arxiv: 1 author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 - first_name: Diego A full_name: Lancheros Naranjo, Diego A id: 6c55e976-15b2-11ec-abd3-d790e8937fde last_name: Lancheros Naranjo - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829 apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv. https://doi.org/10.48550/arXiv.2408.07829 chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829. ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” arXiv. . 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.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829. short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-09-11T09:25:22Z date_published: 2024-08-14T00:00:00Z date_updated: 2026-11-09T23:31:01Z day: '14' department: - _id: AnHi - _id: GradSch doi: 10.48550/arXiv.2408.07829 ec_funded: 1 external_id: arxiv: - '2408.07829' fulldoi: https://doi.org/10.48550/arXiv.2408.07829 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.07829 month: '08' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication: arXiv publication_status: draft related_material: record: - id: '20324' relation: later_version status: public - id: '17881' relation: dissertation_contains status: public researchdata_availability: no status: public supplementarymaterial: no title: Dual relaxation oscillations in a Josephson junction array type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '17119' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 citation: ama: Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:10.15479/at:ista:17119 apa: Kelemen, R. K. (2024). Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17119 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. https://doi.org/10.15479/at:ista:17119. 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. 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. Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17119. 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. corr_author: '1' date_created: 2024-06-07T16:14:13Z date_published: 2024-06-20T00:00:00Z date_updated: 2026-10-02T11:14:33Z day: '20' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:17119 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: fab59146e3b3dc2e5d214576984a2a63 content_type: application/zip creator: rkelemen date_created: 2024-06-07T16:09:17Z date_updated: 2025-01-10T23:30:10Z embargo_to: open_access file_id: '17121' file_name: thesis.zip file_size: 180557931 relation: source_file - access_level: open_access checksum: 91cc4c25a792239e8a7688e8aec7c62a content_type: application/pdf creator: rkelemen date_created: 2024-07-10T08:00:20Z date_updated: 2025-01-10T23:30:10Z embargo: 2025-01-10 file_id: '17213' file_name: thesis_to_archive.pdf file_size: 19405484 relation: main_file file_date_updated: 2025-01-10T23:30:10Z fulldoi: https://doi.org/10.15479/at:ista:17119 has_accepted_license: '1' keyword: - meiotic driver - neofunctionalization - single nucleus sequencing language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '06' oa: 1 oa_version: Published Version page: '105' project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: isbn: - 978-3-99078-039-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '542' relation: part_of_dissertation status: public - id: '10767' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 supplementarymaterial: unclear title: Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_embargo: '6' OA_place: publisher _id: '18531' abstract: - lang: eng text: "Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. " acknowledged_ssus: - _id: ScienComp - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac citation: ama: Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:10.15479/at:ista:18531 apa: Mrnjavac, A. (2024). Early stages of sex chromosome evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18531 chicago: Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18531. ieee: A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024. ista: Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria. mla: Mrnjavac, Andrea. Early Stages of Sex Chromosome Evolution. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18531. short: A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-11T08:40:45Z date_published: 2024-11-11T00:00:00Z date_updated: 2026-10-02T11:14:08Z day: '11' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:18531 doi_confirm: '1' file: - access_level: closed checksum: 3e48b163c22114ef5d5371f758668289 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amrnjava date_created: 2024-11-13T12:15:28Z date_updated: 2025-05-11T22:30:04Z embargo_to: open_access file_id: '18551' file_name: AMrnjavac_thesis_library.docx file_size: 26870629 relation: source_file title: Early stages of sex chromosome evolution - access_level: open_access checksum: 3ead60c1b678e7dcf018043aef3b5db2 content_type: application/pdf creator: amrnjava date_created: 2024-11-13T12:15:54Z date_updated: 2025-05-11T22:30:04Z embargo: 2025-05-11 file_id: '18552' file_name: AMrnjavac_thesis_library.pdf file_size: 4228766 relation: main_file title: Early stages of sex chromosome evolution file_date_updated: 2025-05-11T22:30:04Z fulldoi: https://doi.org/10.15479/at:ista:18531 has_accepted_license: '1' keyword: - Sex chromosomes - evolution - selection - sheltering language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '181' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12521' relation: part_of_dissertation status: public - id: '18549' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 supplementarymaterial: unclear title: Early stages of sex chromosome evolution tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '18661' 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 article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral citation: ama: 'Santana de Freitas Amaral M. Archaeal membranes: In silico modelling and design. 2024. doi:10.15479/at:ista:18661' apa: 'Santana de Freitas Amaral, M. (2024). Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661' chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal Membranes: In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.' ieee: 'M. Santana de Freitas Amaral, “Archaeal membranes: In silico modelling and design,” Institute of Science and Technology Austria, 2024.' ista: 'Santana de Freitas Amaral M. 2024. Archaeal membranes: In silico modelling and design. Institute of Science and Technology Austria.' mla: 'Santana de Freitas Amaral, Miguel. Archaeal Membranes: In Silico Modelling and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.' short: 'M. Santana de Freitas Amaral, Archaeal Membranes: In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-12-16T10:53:39Z date_published: 2024-12-17T00:00:00Z date_updated: 2026-10-02T11:12:49Z day: '17' ddc: - '572' - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnSa doi: 10.15479/at:ista:18661 doi_confirm: '1' file: - access_level: closed checksum: eca06497a29078558395455c890a32d9 content_type: application/zip creator: mamaral date_created: 2024-12-18T12:27:01Z date_updated: 2025-06-18T22:30:03Z embargo_to: open_access file_id: '18671' file_name: 2024_msfa_thesis.zip file_size: 19161387 relation: source_file - access_level: open_access checksum: 2dc30ea46c5daf48d07e4cccb3c3de00 content_type: application/pdf creator: mamaral date_created: 2024-12-18T12:26:30Z date_updated: 2025-06-18T22:30:03Z embargo: 2025-06-18 file_id: '18672' file_name: 2024_msfa_thesis.pdf file_size: 16530084 relation: main_file file_date_updated: 2025-06-18T22:30:03Z fulldoi: https://doi.org/10.15479/at:ista:18661 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '57' publication_identifier: isbn: - 978-3-99078-046-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18670' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 supplementarymaterial: unclear title: 'Archaeal membranes: In silico modelling and design' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository _id: '18549' abstract: - lang: eng 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" article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 biorxivid: 1 citation: ama: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. doi:10.1101/2024.07.02.601697 apa: Mrnjavac, A., & Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. https://doi.org/10.1101/2024.07.02.601697 chicago: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, n.d. https://doi.org/10.1101/2024.07.02.601697. ieee: A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” bioRxiv. . ista: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, 10.1101/2024.07.02.601697. mla: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, doi:10.1101/2024.07.02.601697. short: A. Mrnjavac, B. Vicoso, BioRxiv (n.d.). corr_author: '1' das_tickbox: '0' date_created: 2024-11-13T09:12:08Z date_published: 2024-07-04T00:00:00Z date_updated: 2026-11-09T23:31:03Z day: '04' department: - _id: BeVi doi: 10.1101/2024.07.02.601697 external_id: biorxivid: - 10.1101/2024.07.02.601697 fulldoi: https://doi.org/10.1101/2024.07.02.601697 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.07.02.601697 month: '07' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: draft related_material: record: - id: '19370' relation: later_version status: public - id: '18531' relation: dissertation_contains status: public researchdata_availability: no status: public supplementarymaterial: yes title: Evidence of a Slower-Z effect in Schistosoma japonicum tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ...