--- _id: '14332' abstract: - lang: eng text: Learning data representations that are useful for various downstream tasks is a cornerstone of artificial intelligence. While existing methods are typically evaluated on downstream tasks such as classification or generative image quality, we propose to assess representations through their usefulness in downstream control tasks, such as reaching or pushing objects. By training over 10,000 reinforcement learning policies, we extensively evaluate to what extent different representation properties affect out-of-distribution (OOD) generalization. Finally, we demonstrate zero-shot transfer of these policies from simulation to the real world, without any domain randomization or fine-tuning. This paper aims to establish the first systematic characterization of the usefulness of learned representations for real-world OOD downstream tasks. article_processing_charge: No author: - first_name: Frederik full_name: Träuble, Frederik last_name: Träuble - first_name: Andrea full_name: Dittadi, Andrea last_name: Dittadi - first_name: Manuel full_name: Wuthrich, Manuel last_name: Wuthrich - first_name: Felix full_name: Widmaier, Felix last_name: Widmaier - first_name: Peter Vincent full_name: Gehler, Peter Vincent last_name: Gehler - first_name: Ole full_name: Winther, Ole last_name: Winther - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer citation: ama: 'Träuble F, Dittadi A, Wuthrich M, et al. Representation learning for out-of-distribution generalization in reinforcement learning. In: ICML 2021 Workshop on Unsupervised Reinforcement Learning. ; 2021.' apa: Träuble, F., Dittadi, A., Wuthrich, M., Widmaier, F., Gehler, P. V., Winther, O., … Bauer, S. (2021). Representation learning for out-of-distribution generalization in reinforcement learning. In ICML 2021 Workshop on Unsupervised Reinforcement Learning. Virtual. chicago: Träuble, Frederik, Andrea Dittadi, Manuel Wuthrich, Felix Widmaier, Peter Vincent Gehler, Ole Winther, Francesco Locatello, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “Representation Learning for Out-of-Distribution Generalization in Reinforcement Learning.” In ICML 2021 Workshop on Unsupervised Reinforcement Learning, 2021. ieee: F. Träuble et al., “Representation learning for out-of-distribution generalization in reinforcement learning,” in ICML 2021 Workshop on Unsupervised Reinforcement Learning, Virtual, 2021. ista: 'Träuble F, Dittadi A, Wuthrich M, Widmaier F, Gehler PV, Winther O, Locatello F, Bachem O, Schölkopf B, Bauer S. 2021. Representation learning for out-of-distribution generalization in reinforcement learning. ICML 2021 Workshop on Unsupervised Reinforcement Learning. ICML: International Conference on Machine Learning.' mla: Träuble, Frederik, et al. “Representation Learning for Out-of-Distribution Generalization in Reinforcement Learning.” ICML 2021 Workshop on Unsupervised Reinforcement Learning, 2021. short: F. Träuble, A. Dittadi, M. Wuthrich, F. Widmaier, P.V. Gehler, O. Winther, F. Locatello, O. Bachem, B. Schölkopf, S. Bauer, in:, ICML 2021 Workshop on Unsupervised Reinforcement Learning, 2021. conference: end_date: 2021-07-23 location: Virtual name: 'ICML: International Conference on Machine Learning' start_date: 2021-07-23 date_created: 2023-09-13T12:43:14Z date_published: 2021-07-23T00:00:00Z date_updated: 2023-09-13T12:44:00Z day: '23' department: - _id: FrLo extern: '1' language: - iso: eng month: '07' oa_version: None publication: ICML 2021 Workshop on Unsupervised Reinforcement Learning publication_status: published quality_controlled: '1' status: public title: Representation learning for out-of-distribution generalization in reinforcement learning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '14800' abstract: - lang: eng text: 'Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. ' article_number: '2108017' article_processing_charge: No article_type: review author: - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Wei full_name: Chen, Wei last_name: Chen - first_name: Ye full_name: Chen, Ye last_name: Chen - first_name: Yonghua full_name: Chen, Yonghua last_name: Chen - first_name: Yu full_name: Chen, Yu last_name: Chen - first_name: Feng full_name: Ding, Feng last_name: Ding - first_name: Chunhai full_name: Fan, Chunhai last_name: Fan - first_name: Hong Jin full_name: Fan, Hong Jin last_name: Fan - first_name: Zhanxi full_name: Fan, Zhanxi last_name: Fan - first_name: Cheng full_name: Gong, Cheng last_name: Gong - first_name: Yongji full_name: Gong, Yongji last_name: Gong - first_name: Qiyuan full_name: He, Qiyuan last_name: He - first_name: Xun full_name: Hong, Xun last_name: Hong - first_name: Sheng full_name: Hu, Sheng last_name: Hu - first_name: Weida full_name: Hu, Weida last_name: Hu - first_name: Wei full_name: Huang, Wei last_name: Huang - first_name: Yuan full_name: Huang, Yuan last_name: Huang - first_name: Wei full_name: Ji, Wei last_name: Ji - first_name: Dehui full_name: Li, Dehui last_name: Li - first_name: Lain Jong full_name: Li, Lain Jong last_name: Li - first_name: Qiang full_name: Li, Qiang last_name: Li - first_name: Li full_name: Lin, Li last_name: Lin - first_name: Chongyi full_name: Ling, Chongyi last_name: Ling - first_name: Minghua full_name: Liu, Minghua last_name: Liu - first_name: 'Nan' full_name: Liu, Nan last_name: Liu - first_name: Zhuang full_name: Liu, Zhuang last_name: Liu - first_name: Kian Ping full_name: Loh, Kian Ping last_name: Loh - first_name: Jianmin full_name: Ma, Jianmin last_name: Ma - first_name: Feng full_name: Miao, Feng last_name: Miao - first_name: Hailin full_name: Peng, Hailin last_name: Peng - first_name: Mingfei full_name: Shao, Mingfei last_name: Shao - first_name: Li full_name: Song, Li last_name: Song - first_name: Shao full_name: Su, Shao last_name: Su - first_name: Shuo full_name: Sun, Shuo last_name: Sun - first_name: Chaoliang full_name: Tan, Chaoliang last_name: Tan - first_name: Zhiyong full_name: Tang, Zhiyong last_name: Tang - first_name: Dingsheng full_name: Wang, Dingsheng last_name: Wang - first_name: Huan full_name: Wang, Huan last_name: Wang - first_name: Jinlan full_name: Wang, Jinlan last_name: Wang - first_name: Xin full_name: Wang, Xin last_name: Wang - first_name: Xinran full_name: Wang, Xinran last_name: Wang - first_name: Andrew T.S. full_name: Wee, Andrew T.S. last_name: Wee - first_name: Zhongming full_name: Wei, Zhongming last_name: Wei - first_name: Yuen full_name: Wu, Yuen last_name: Wu - first_name: Zhong Shuai full_name: Wu, Zhong Shuai last_name: Wu - first_name: Jie full_name: Xiong, Jie last_name: Xiong - first_name: Qihua full_name: Xiong, Qihua last_name: Xiong - first_name: Weigao full_name: Xu, Weigao last_name: Xu - first_name: Peng full_name: Yin, Peng last_name: Yin - first_name: Haibo full_name: Zeng, Haibo last_name: Zeng - first_name: Zhiyuan full_name: Zeng, Zhiyuan last_name: Zeng - first_name: Tianyou full_name: Zhai, Tianyou last_name: Zhai - first_name: Han full_name: Zhang, Han last_name: Zhang - first_name: Hui full_name: Zhang, Hui last_name: Zhang - first_name: Qichun full_name: Zhang, Qichun last_name: Zhang - first_name: Tierui full_name: Zhang, Tierui last_name: Zhang - first_name: Xiang full_name: Zhang, Xiang last_name: Zhang - first_name: Li Dong full_name: Zhao, Li Dong last_name: Zhao - first_name: Meiting full_name: Zhao, Meiting last_name: Zhao - first_name: Weijie full_name: Zhao, Weijie last_name: Zhao - first_name: Yunxuan full_name: Zhao, Yunxuan last_name: Zhao - first_name: Kai Ge full_name: Zhou, Kai Ge last_name: Zhou - first_name: Xing full_name: Zhou, Xing last_name: Zhou - first_name: Yu full_name: Zhou, Yu last_name: Zhou - first_name: Hongwei full_name: Zhu, Hongwei last_name: Zhu - first_name: Hua full_name: Zhang, Hua last_name: Zhang - first_name: Zhongfan full_name: Liu, Zhongfan last_name: Liu citation: ama: Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017 apa: Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. Peking University. https://doi.org/10.3866/PKU.WHXB202108017 chicago: Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017. ieee: C. Chang et al., “Recent progress on two-dimensional materials,” Acta Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021. ista: Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017. mla: Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021, doi:10.3866/PKU.WHXB202108017. short: C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021). date_created: 2024-01-14T23:00:58Z date_published: 2021-10-13T00:00:00Z date_updated: 2025-09-10T10:12:25Z day: '13' department: - _id: MaIb doi: 10.3866/PKU.WHXB202108017 external_id: isi: - '000731879300002' intvolume: ' 37' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3866/PKU.WHXB202108017 month: '10' oa: 1 oa_version: Submitted Version publication: Acta Physico-Chimica Sinica publication_identifier: issn: - 1001-4861 publication_status: published publisher: Peking University quality_controlled: '1' scopus_import: '1' status: public title: Recent progress on two-dimensional materials type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 37 year: '2021' ... --- _id: '14889' abstract: - lang: eng text: We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2. acknowledgement: "Financial support by the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No. 754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227 (N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.), the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel Griesemer for helpful discussions." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Simone Anna Elvira full_name: Rademacher, Simone Anna Elvira id: 856966FE-A408-11E9-977E-802DE6697425 last_name: Rademacher orcid: 0000-0001-5059-4466 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 2021;3(4):653-676. doi:10.2140/paa.2021.3.653 apa: Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2021.3.653 chicago: Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.653. ieee: N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 653–676, 2021. ista: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 3(4), 653–676. mla: Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:10.2140/paa.2021.3.653. short: N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 653–676. corr_author: '1' date_created: 2024-01-28T23:01:43Z date_published: 2021-10-01T00:00:00Z date_updated: 2025-04-14T07:27:00Z day: '01' department: - _id: RoSe doi: 10.2140/paa.2021.3.653 ec_funded: 1 external_id: arxiv: - '2005.02098' intvolume: ' 3' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2005.02098 month: '10' oa: 1 oa_version: Preprint page: 653-676 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Pure and Applied Analysis publication_identifier: eissn: - 2578-5885 issn: - 2578-5893 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2021' ... --- _id: '14890' abstract: - lang: eng text: We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions. acknowledgement: "We are grateful for the hospitality of Central China Normal University (CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher, Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research\r\nTraining Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska-Curie Grant Agreement No. 754411." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Sören P full_name: Petrat, Sören P id: 40AC02DC-F248-11E8-B48F-1D18A9856A87 last_name: Petrat orcid: 0000-0002-9166-5889 - first_name: Peter full_name: Pickl, Peter last_name: Pickl - first_name: Avy full_name: Soffer, Avy last_name: Soffer citation: ama: Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 2021;3(4):677-726. doi:10.2140/paa.2021.3.677 apa: Bossmann, L., Petrat, S. P., Pickl, P., & Soffer, A. (2021). Beyond Bogoliubov dynamics. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2021.3.677 chicago: Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.677. ieee: L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 677–726, 2021. ista: Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 3(4), 677–726. mla: Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:10.2140/paa.2021.3.677. short: L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis 3 (2021) 677–726. corr_author: '1' date_created: 2024-01-28T23:01:43Z date_published: 2021-10-01T00:00:00Z date_updated: 2025-04-14T07:44:02Z day: '01' department: - _id: RoSe doi: 10.2140/paa.2021.3.677 ec_funded: 1 external_id: arxiv: - '1912.11004' intvolume: ' 3' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1912.11004 month: '10' oa: 1 oa_version: Preprint page: 677-726 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Pure and Applied Analysis publication_identifier: eissn: - 2578-5885 issn: - 2578-5893 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Beyond Bogoliubov dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2021' ... --- _id: '14984' abstract: - lang: eng text: Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them. article_processing_charge: No author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355' apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355 chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355. ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021. ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.' mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355. short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021. corr_author: '1' date_created: 2024-02-14T12:05:50Z date_published: 2021-05-28T00:00:00Z date_updated: 2024-10-09T21:08:11Z day: '28' department: - _id: NiBa doi: 10.1002/9780470015902.a0029355 intvolume: ' 2' language: - iso: eng month: '05' oa_version: None publication: Encyclopedia of Life Sciences publication_identifier: eisbn: - '9780470015902' isbn: - '9780470016176' publication_status: published publisher: Wiley quality_controlled: '1' series_title: eLS status: public title: Hybrid Zones type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2021' ... --- _id: '14987' abstract: - lang: eng text: "The goal of zero-shot learning is to construct a classifier that can identify object classes for which no training examples are available. When training data for some of the object classes is available but not for others, the name generalized zero-shot learning is commonly used.\r\nIn a wider sense, the phrase zero-shot is also used to describe other machine learning-based approaches that require no training data from the problem of interest, such as zero-shot action recognition or zero-shot machine translation." article_processing_charge: No author: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Lampert C. Zero-Shot Learning. In: Ikeuchi K, ed. Computer Vision. 2nd ed. Cham: Springer; 2021:1395-1397. doi:10.1007/978-3-030-63416-2_874' apa: 'Lampert, C. (2021). Zero-Shot Learning. In K. Ikeuchi (Ed.), Computer Vision (2nd ed., pp. 1395–1397). Cham: Springer. https://doi.org/10.1007/978-3-030-63416-2_874' chicago: 'Lampert, Christoph. “Zero-Shot Learning.” In Computer Vision, edited by Katsushi Ikeuchi, 2nd ed., 1395–97. Cham: Springer, 2021. https://doi.org/10.1007/978-3-030-63416-2_874.' ieee: 'C. Lampert, “Zero-Shot Learning,” in Computer Vision, 2nd ed., K. Ikeuchi, Ed. Cham: Springer, 2021, pp. 1395–1397.' ista: 'Lampert C. 2021.Zero-Shot Learning. In: Computer Vision. , 1395–1397.' mla: Lampert, Christoph. “Zero-Shot Learning.” Computer Vision, edited by Katsushi Ikeuchi, 2nd ed., Springer, 2021, pp. 1395–97, doi:10.1007/978-3-030-63416-2_874. short: C. Lampert, in:, K. Ikeuchi (Ed.), Computer Vision, 2nd ed., Springer, Cham, 2021, pp. 1395–1397. corr_author: '1' date_created: 2024-02-14T14:05:32Z date_published: 2021-10-13T00:00:00Z date_updated: 2024-10-09T21:08:12Z day: '13' department: - _id: ChLa doi: 10.1007/978-3-030-63416-2_874 edition: '2' editor: - first_name: Katsushi full_name: Ikeuchi, Katsushi last_name: Ikeuchi language: - iso: eng month: '10' oa_version: None page: 1395-1397 place: Cham publication: Computer Vision publication_identifier: eisbn: - '9783030634162' isbn: - '9783030634155' publication_status: published publisher: Springer quality_controlled: '1' status: public title: Zero-Shot Learning type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '14988' abstract: - lang: eng text: Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS article_processing_charge: No author: - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 citation: ama: Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100 apa: Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100 chicago: Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5747100. ieee: A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021. ista: Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100. mla: Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo, 2021, doi:10.5281/ZENODO.5747100. short: A.J. Johnson, (2021). corr_author: '1' date_created: 2024-02-14T14:13:48Z date_published: 2021-12-01T00:00:00Z date_updated: 2025-05-14T09:25:33Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.5281/ZENODO.5747100 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5747100 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '9887' relation: used_in_publication status: public status: public title: Raw data from Johnson et al, PNAS, 2021 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: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '15013' abstract: - lang: eng text: We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge. acknowledgement: Partially supported by ERC Starting Grant RandMat No. 715539 and the SwissMap grant of Swiss National Science Foundation. Partially supported by ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center for Mathematics in Bonn. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2021;2(2):221-280. doi:10.2140/pmp.2021.2.221 apa: Alt, J., Erdös, L., & Krüger, T. H. (2021). Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2021.2.221 chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random Matrices with Independent Entries.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/pmp.2021.2.221. ieee: J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with independent entries,” Probability and Mathematical Physics, vol. 2, no. 2. Mathematical Sciences Publishers, pp. 221–280, 2021. ista: Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2(2), 221–280. mla: Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent Entries.” Probability and Mathematical Physics, vol. 2, no. 2, Mathematical Sciences Publishers, 2021, pp. 221–80, doi:10.2140/pmp.2021.2.221. short: J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021) 221–280. corr_author: '1' date_created: 2024-02-18T23:01:03Z date_published: 2021-05-21T00:00:00Z date_updated: 2025-04-15T08:05:02Z day: '21' department: - _id: LaEr doi: 10.2140/pmp.2021.2.221 ec_funded: 1 external_id: arxiv: - '1907.13631' intvolume: ' 2' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1907.13631 month: '05' oa: 1 oa_version: Preprint page: 221-280 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Probability and Mathematical Physics publication_identifier: eissn: - 2690-1005 issn: - 2690-0998 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Spectral radius of random matrices with independent entries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2021' ... --- _id: '15137' abstract: - lang: eng text: Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range. article_number: '5033' article_processing_charge: Yes article_type: original author: - first_name: Jurre A. full_name: Steens, Jurre A. last_name: Steens - first_name: Yifan full_name: Zhu, Yifan last_name: Zhu - first_name: David W. full_name: Taylor, David W. last_name: Taylor - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Stijn H. P. full_name: Prinsen, Stijn H. P. last_name: Prinsen - first_name: Cor D. full_name: Schoen, Cor D. last_name: Schoen - first_name: Bart J. F. full_name: Keijser, Bart J. F. last_name: Keijser - first_name: Michel full_name: Ossendrijver, Michel last_name: Ossendrijver - first_name: L. Marije full_name: Hofstra, L. Marije last_name: Hofstra - first_name: Stan J. J. full_name: Brouns, Stan J. J. last_name: Brouns - first_name: Akeo full_name: Shinkai, Akeo last_name: Shinkai - first_name: John full_name: van der Oost, John last_name: van der Oost - first_name: Raymond H. J. full_name: Staals, Raymond H. J. last_name: Staals citation: ama: Steens JA, Zhu Y, Taylor DW, et al. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nature Communications. 2021;12. doi:10.1038/s41467-021-25337-5 apa: Steens, J. A., Zhu, Y., Taylor, D. W., Bravo, J. P. K., Prinsen, S. H. P., Schoen, C. D., … Staals, R. H. J. (2021). SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25337-5 chicago: Steens, Jurre A., Yifan Zhu, David W. Taylor, Jack Peter Kelly Bravo, Stijn H. P. Prinsen, Cor D. Schoen, Bart J. F. Keijser, et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease Activation.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25337-5. ieee: J. A. Steens et al., “SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF, Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ. 2021. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nature Communications. 12, 5033. mla: Steens, Jurre A., et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease Activation.” Nature Communications, vol. 12, 5033, Springer Nature, 2021, doi:10.1038/s41467-021-25337-5. short: J.A. Steens, Y. Zhu, D.W. Taylor, J.P.K. Bravo, S.H.P. Prinsen, C.D. Schoen, B.J.F. Keijser, M. Ossendrijver, L.M. Hofstra, S.J.J. Brouns, A. Shinkai, J. van der Oost, R.H.J. Staals, Nature Communications 12 (2021). date_created: 2024-03-20T10:42:33Z date_published: 2021-08-19T00:00:00Z date_updated: 2024-06-04T06:11:54Z day: '19' doi: 10.1038/s41467-021-25337-5 extern: '1' external_id: pmid: - '34413302' intvolume: ' 12' keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-021-25337-5 month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2021' ... --- _id: '15138' abstract: - lang: eng text: RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein‐RNA condensates that are formed via liquid–liquid phase separation of the viroplasm‐forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon mixing, these proteins readily form condensates at physiologically relevant low micromolar concentrations achieved in the cytoplasm of virus‐infected cells. Early infection stage condensates could be reversibly dissolved by 1,6‐hexanediol, as well as propylene glycol that released rotavirus transcripts from these condensates. During the early stages of infection, propylene glycol treatments reduced viral replication and phosphorylation of the condensate‐forming protein NSP5. During late infection, these condensates exhibited altered material properties and became resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some aspects of the assembly of cytoplasmic rotavirus replication factories mirror the formation of other ribonucleoprotein granules. Such viral RNA‐rich condensates that support replication of multi‐segmented genomes represent an attractive target for developing novel therapeutic approaches. article_number: e107711 article_processing_charge: Yes article_type: original author: - first_name: Florian full_name: Geiger, Florian last_name: Geiger - first_name: Julia full_name: Acker, Julia last_name: Acker - first_name: Guido full_name: Papa, Guido last_name: Papa - first_name: Xinyu full_name: Wang, Xinyu last_name: Wang - first_name: William E full_name: Arter, William E last_name: Arter - first_name: Kadi L full_name: Saar, Kadi L last_name: Saar - first_name: Nadia A full_name: Erkamp, Nadia A last_name: Erkamp - first_name: Runzhang full_name: Qi, Runzhang last_name: Qi - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Sebastian full_name: Strauss, Sebastian last_name: Strauss - first_name: Georg full_name: Krainer, Georg last_name: Krainer - first_name: Oscar R full_name: Burrone, Oscar R last_name: Burrone - first_name: Ralf full_name: Jungmann, Ralf last_name: Jungmann - first_name: Tuomas PJ full_name: Knowles, Tuomas PJ last_name: Knowles - first_name: Hanna full_name: Engelke, Hanna last_name: Engelke - first_name: Alexander full_name: Borodavka, Alexander last_name: Borodavka citation: ama: Geiger F, Acker J, Papa G, et al. Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. The EMBO Journal. 2021;40(21). doi:10.15252/embj.2021107711 apa: Geiger, F., Acker, J., Papa, G., Wang, X., Arter, W. E., Saar, K. L., … Borodavka, A. (2021). Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. The EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021107711 chicago: Geiger, Florian, Julia Acker, Guido Papa, Xinyu Wang, William E Arter, Kadi L Saar, Nadia A Erkamp, et al. “Liquid–Liquid Phase Separation Underpins the Formation of Replication Factories in Rotaviruses.” The EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021107711. ieee: F. Geiger et al., “Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses,” The EMBO Journal, vol. 40, no. 21. Embo Press, 2021. ista: Geiger F, Acker J, Papa G, Wang X, Arter WE, Saar KL, Erkamp NA, Qi R, Bravo JPK, Strauss S, Krainer G, Burrone OR, Jungmann R, Knowles TP, Engelke H, Borodavka A. 2021. Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. The EMBO Journal. 40(21), e107711. mla: Geiger, Florian, et al. “Liquid–Liquid Phase Separation Underpins the Formation of Replication Factories in Rotaviruses.” The EMBO Journal, vol. 40, no. 21, e107711, Embo Press, 2021, doi:10.15252/embj.2021107711. short: F. Geiger, J. Acker, G. Papa, X. Wang, W.E. Arter, K.L. Saar, N.A. Erkamp, R. Qi, J.P.K. Bravo, S. Strauss, G. Krainer, O.R. Burrone, R. Jungmann, T.P. Knowles, H. Engelke, A. Borodavka, The EMBO Journal 40 (2021). date_created: 2024-03-20T10:42:39Z date_published: 2021-11-02T00:00:00Z date_updated: 2024-06-04T06:08:16Z day: '02' doi: 10.15252/embj.2021107711 extern: '1' external_id: pmid: - '34524703' intvolume: ' 40' issue: '21' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.15252/embj.2021107711 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: The EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2021' ... --- _id: '15139' abstract: - lang: eng text: Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA–RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo–electron microscopy reconstructions of an NSP2–RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling. article_number: e2100198118 article_processing_charge: No article_type: original author: - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Kira full_name: Bartnik, Kira last_name: Bartnik - first_name: Luca full_name: Venditti, Luca last_name: Venditti - first_name: Julia full_name: Acker, Julia last_name: Acker - first_name: Emma H. full_name: Gail, Emma H. last_name: Gail - first_name: Alice full_name: Colyer, Alice last_name: Colyer - first_name: Chen full_name: Davidovich, Chen last_name: Davidovich - first_name: Don C. full_name: Lamb, Don C. last_name: Lamb - first_name: Roman full_name: Tuma, Roman last_name: Tuma - first_name: Antonio N. full_name: Calabrese, Antonio N. last_name: Calabrese - first_name: Alexander full_name: Borodavka, Alexander last_name: Borodavka citation: ama: Bravo JPK, Bartnik K, Venditti L, et al. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. 2021;118(41). doi:10.1073/pnas.2100198118 apa: Bravo, J. P. K., Bartnik, K., Venditti, L., Acker, J., Gail, E. H., Colyer, A., … Borodavka, A. (2021). Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2100198118 chicago: Bravo, Jack Peter Kelly, Kira Bartnik, Luca Venditti, Julia Acker, Emma H. Gail, Alice Colyer, Chen Davidovich, et al. “Structural Basis of Rotavirus RNA Chaperone Displacement and RNA Annealing.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2100198118. ieee: J. P. K. Bravo et al., “Structural basis of rotavirus RNA chaperone displacement and RNA annealing,” Proceedings of the National Academy of Sciences, vol. 118, no. 41. Proceedings of the National Academy of Sciences, 2021. ista: Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. 2021. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. 118(41), e2100198118. mla: Bravo, Jack Peter Kelly, et al. “Structural Basis of Rotavirus RNA Chaperone Displacement and RNA Annealing.” Proceedings of the National Academy of Sciences, vol. 118, no. 41, e2100198118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2100198118. short: J.P.K. Bravo, K. Bartnik, L. Venditti, J. Acker, E.H. Gail, A. Colyer, C. Davidovich, D.C. Lamb, R. Tuma, A.N. Calabrese, A. Borodavka, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2024-03-20T10:42:45Z date_published: 2021-10-06T00:00:00Z date_updated: 2024-06-04T06:04:07Z day: '06' doi: 10.1073/pnas.2100198118 extern: '1' external_id: pmid: - '34615715' intvolume: ' 118' issue: '41' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.2100198118 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Structural basis of rotavirus RNA chaperone displacement and RNA annealing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2021' ... --- _id: '15140' abstract: - lang: eng text: Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of 3 bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs. article_processing_charge: No article_type: original author: - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Tyler L. full_name: Dangerfield, Tyler L. last_name: Dangerfield - first_name: David W. full_name: Taylor, David W. last_name: Taylor - first_name: Kenneth A. full_name: Johnson, Kenneth A. last_name: Johnson citation: ama: Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Molecular Cell. 2021;81(7):1548-1552.e4. doi:10.1016/j.molcel.2021.01.035 apa: Bravo, J. P. K., Dangerfield, T. L., Taylor, D. W., & Johnson, K. A. (2021). Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2021.01.035 chicago: Bravo, Jack Peter Kelly, Tyler L. Dangerfield, David W. Taylor, and Kenneth A. Johnson. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.” Molecular Cell. Elsevier, 2021. https://doi.org/10.1016/j.molcel.2021.01.035. ieee: J. P. K. Bravo, T. L. Dangerfield, D. W. Taylor, and K. A. Johnson, “Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication,” Molecular Cell, vol. 81, no. 7. Elsevier, p. 1548–1552.e4, 2021. ista: Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. 2021. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Molecular Cell. 81(7), 1548–1552.e4. mla: Bravo, Jack Peter Kelly, et al. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.” Molecular Cell, vol. 81, no. 7, Elsevier, 2021, p. 1548–1552.e4, doi:10.1016/j.molcel.2021.01.035. short: J.P.K. Bravo, T.L. Dangerfield, D.W. Taylor, K.A. Johnson, Molecular Cell 81 (2021) 1548–1552.e4. date_created: 2024-03-20T10:42:53Z date_published: 2021-04-01T00:00:00Z date_updated: 2024-06-04T06:00:56Z day: '01' doi: 10.1016/j.molcel.2021.01.035 extern: '1' external_id: pmid: - '33631104' intvolume: ' 81' issue: '7' keyword: - Cell Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/2020.12.14.422718 ' month: '04' oa: 1 oa_version: Preprint page: 1548-1552.e4 pmid: 1 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2021' ... --- _id: '15141' abstract: - lang: eng text: We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined with a small subunit (Cas11) filament, but the complex lacks subunits for RNA processing and target DNA cleavage. Surprisingly, instead of assembling around a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of a regular length arranged in a pseudo-A-form configuration. These findings provide a high-resolution glimpse into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture, and suggesting a function for type IV-B RNPs that may be distinct from other class 1 CRISPR-associated systems. article_number: '102201' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Yi full_name: Zhou, Yi last_name: Zhou - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Hannah N. full_name: Taylor, Hannah N. last_name: Taylor - first_name: Jurre A. full_name: Steens, Jurre A. last_name: Steens - first_name: Ryan N. full_name: Jackson, Ryan N. last_name: Jackson - first_name: Raymond H.J. full_name: Staals, Raymond H.J. last_name: Staals - first_name: David W. full_name: Taylor, David W. last_name: Taylor citation: ama: Zhou Y, Bravo JPK, Taylor HN, et al. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. iScience. 2021;24(3). doi:10.1016/j.isci.2021.102201 apa: Zhou, Y., Bravo, J. P. K., Taylor, H. N., Steens, J. A., Jackson, R. N., Staals, R. H. J., & Taylor, D. W. (2021). Structure of a type IV CRISPR-Cas ribonucleoprotein complex. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102201 chicago: Zhou, Yi, Jack Peter Kelly Bravo, Hannah N. Taylor, Jurre A. Steens, Ryan N. Jackson, Raymond H.J. Staals, and David W. Taylor. “Structure of a Type IV CRISPR-Cas Ribonucleoprotein Complex.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102201. ieee: Y. Zhou et al., “Structure of a type IV CRISPR-Cas ribonucleoprotein complex,” iScience, vol. 24, no. 3. Elsevier, 2021. ista: Zhou Y, Bravo JPK, Taylor HN, Steens JA, Jackson RN, Staals RHJ, Taylor DW. 2021. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. iScience. 24(3), 102201. mla: Zhou, Yi, et al. “Structure of a Type IV CRISPR-Cas Ribonucleoprotein Complex.” IScience, vol. 24, no. 3, 102201, Elsevier, 2021, doi:10.1016/j.isci.2021.102201. short: Y. Zhou, J.P.K. Bravo, H.N. Taylor, J.A. Steens, R.N. Jackson, R.H.J. Staals, D.W. Taylor, IScience 24 (2021). date_created: 2024-03-20T10:43:00Z date_published: 2021-03-19T00:00:00Z date_updated: 2024-06-04T05:56:45Z day: '19' doi: 10.1016/j.isci.2021.102201 extern: '1' external_id: pmid: - '33733066' intvolume: ' 24' issue: '3' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.isci.2021.102201 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: iScience publication_identifier: issn: - 2589-0042 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Structure of a type IV CRISPR-Cas ribonucleoprotein complex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2021' ... --- _id: '15150' abstract: - lang: eng text: The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3,4,5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6,7,8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening. article_processing_charge: No article_type: original author: - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Lukas full_name: Burger, Lukas last_name: Burger - first_name: Cathrin full_name: Gräwe, Cathrin last_name: Gräwe - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Daniel full_name: Hess, Daniel last_name: Hess - first_name: Leslie full_name: Hoerner, Leslie last_name: Hoerner - first_name: Vytautas full_name: Iesmantavicius, Vytautas last_name: Iesmantavicius - first_name: Sevi full_name: Durdu, Sevi last_name: Durdu - first_name: Marco full_name: Pregnolato, Marco last_name: Pregnolato - first_name: Arnaud R. full_name: Krebs, Arnaud R. last_name: Krebs - first_name: Sébastien A. full_name: Smallwood, Sébastien A. last_name: Smallwood - first_name: Nicolas full_name: Thomä, Nicolas last_name: Thomä - first_name: Michiel full_name: Vermeulen, Michiel last_name: Vermeulen - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler citation: ama: Grand RS, Burger L, Gräwe C, et al. BANP opens chromatin and activates CpG-island-regulated genes. Nature. 2021;596:133-137. doi:10.1038/s41586-021-03689-8 apa: Grand, R. S., Burger, L., Gräwe, C., Michael, A. K., Isbel, L., Hess, D., … Schübeler, D. (2021). BANP opens chromatin and activates CpG-island-regulated genes. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03689-8 chicago: Grand, Ralph S., Lukas Burger, Cathrin Gräwe, Alicia K. Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03689-8. ieee: R. S. Grand et al., “BANP opens chromatin and activates CpG-island-regulated genes,” Nature, vol. 596. Springer Nature, pp. 133–137, 2021. ista: Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D. 2021. BANP opens chromatin and activates CpG-island-regulated genes. Nature. 596, 133–137. mla: Grand, Ralph S., et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” Nature, vol. 596, Springer Nature, 2021, pp. 133–37, doi:10.1038/s41586-021-03689-8. short: R.S. Grand, L. Burger, C. Gräwe, A.K. Michael, L. Isbel, D. Hess, L. Hoerner, V. Iesmantavicius, S. Durdu, M. Pregnolato, A.R. Krebs, S.A. Smallwood, N. Thomä, M. Vermeulen, D. Schübeler, Nature 596 (2021) 133–137. date_created: 2024-03-21T07:53:48Z date_published: 2021-08-05T00:00:00Z date_updated: 2024-03-25T12:34:31Z day: '05' doi: 10.1038/s41586-021-03689-8 extern: '1' intvolume: ' 596' language: - iso: eng month: '08' oa_version: None page: 133-137 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: BANP opens chromatin and activates CpG-island-regulated genes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 596 year: '2021' ... --- _id: '15151' abstract: - lang: eng text: Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair. article_processing_charge: No article_type: review author: - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611. doi:10.1016/j.cell.2021.05.029 apa: Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.05.029 chicago: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.05.029. ieee: A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” Cell, vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021. ista: Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14), 3599–3611. mla: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:10.1016/j.cell.2021.05.029. short: A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611. date_created: 2024-03-21T07:54:19Z date_published: 2021-07-08T00:00:00Z date_updated: 2024-03-25T12:31:39Z day: '08' doi: 10.1016/j.cell.2021.05.029 extern: '1' intvolume: ' 184' issue: '14' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2021.05.029 month: '07' oa: 1 oa_version: Published Version page: 3599-3611 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Reading the chromatinized genome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 184 year: '2021' ... --- _id: '15215' abstract: - lang: eng text: AT2019wey (SRGA J043520.9+552226, SRGE J043523.3+552234) is a transient first reported by the ATLAS optical survey in 2019 December. It rose to prominence upon detection, three months later, by the Spektrum-Roentgen-Gamma (SRG) mission in its first all-sky survey. X-ray observations reported in Yao et al. suggest that AT2019wey is a Galactic low-mass X-ray binary (LMXB) with a black hole (BH) or neutron star (NS) accretor. Here we present ultraviolet, optical, near-infrared, and radio observations of this object. We show that the companion is a short-period (P ≲ 16 hr) low-mass (<1 M⊙) star. We consider AT2019wey to be a candidate BH system since its locations on the Lradio–LX and Lopt–LX diagrams are closer to BH binaries than NS binaries. We demonstrate that from 2020 June to August, despite the more than 10 times brightening at radio and X-ray wavelengths, the optical luminosity of AT2019wey only increased by 1.3–1.4 times. We interpret the UV/optical emission before the brightening as thermal emission from a truncated disk in a hot accretion flow and the UV/optical emission after the brightening as reprocessing of the X-ray emission in the outer accretion disk. AT2019wey demonstrates that combining current wide-field optical surveys and SRG provides a way to discover the emerging population of short-period BH LMXB systems with faint X-ray outbursts. article_number: '120' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yuhan full_name: Yao, Yuhan last_name: Yao - first_name: S. R. full_name: Kulkarni, S. R. last_name: Kulkarni - first_name: Kevin B. full_name: Burdge, Kevin B. last_name: Burdge - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Kishalay full_name: De, Kishalay last_name: De - first_name: Dillon full_name: Dong, Dillon last_name: Dong - first_name: C. full_name: Fremling, C. last_name: Fremling - first_name: Mansi M. full_name: Kasliwal, Mansi M. last_name: Kasliwal - first_name: Thomas full_name: Kupfer, Thomas last_name: Kupfer - first_name: Jan full_name: van Roestel, Jan last_name: van Roestel - first_name: Jesper full_name: Sollerman, Jesper last_name: Sollerman - first_name: Ashot full_name: Bagdasaryan, Ashot last_name: Bagdasaryan - first_name: Eric C. full_name: Bellm, Eric C. last_name: Bellm - first_name: S. Bradley full_name: Cenko, S. Bradley last_name: Cenko - first_name: Andrew J. full_name: Drake, Andrew J. last_name: Drake - first_name: Dmitry A. full_name: Duev, Dmitry A. last_name: Duev - first_name: Matthew J. full_name: Graham, Matthew J. last_name: Graham - first_name: Stephen full_name: Kaye, Stephen last_name: Kaye - first_name: Frank J. full_name: Masci, Frank J. last_name: Masci - first_name: Nicolas full_name: Miranda, Nicolas last_name: Miranda - first_name: Thomas A. full_name: Prince, Thomas A. last_name: Prince - first_name: Reed full_name: Riddle, Reed last_name: Riddle - first_name: Ben full_name: Rusholme, Ben last_name: Rusholme - first_name: Maayane T. full_name: Soumagnac, Maayane T. last_name: Soumagnac citation: ama: 'Yao Y, Kulkarni SR, Burdge KB, et al. Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass X-ray binary. The Astrophysical Journal. 2021;920(2). doi:10.3847/1538-4357/ac15f9' apa: 'Yao, Y., Kulkarni, S. R., Burdge, K. B., Caiazzo, I., De, K., Dong, D., … Soumagnac, M. T. (2021). Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass X-ray binary. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ac15f9' chicago: 'Yao, Yuhan, S. R. Kulkarni, Kevin B. Burdge, Ilaria Caiazzo, Kishalay De, Dillon Dong, C. Fremling, et al. “Multi-Wavelength Observations of AT2019wey: A New Candidate Black Hole Low-Mass X-Ray Binary.” The Astrophysical Journal. American Astronomical Society, 2021. https://doi.org/10.3847/1538-4357/ac15f9.' ieee: 'Y. Yao et al., “Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass X-ray binary,” The Astrophysical Journal, vol. 920, no. 2. American Astronomical Society, 2021.' ista: 'Yao Y, Kulkarni SR, Burdge KB, Caiazzo I, De K, Dong D, Fremling C, Kasliwal MM, Kupfer T, van Roestel J, Sollerman J, Bagdasaryan A, Bellm EC, Cenko SB, Drake AJ, Duev DA, Graham MJ, Kaye S, Masci FJ, Miranda N, Prince TA, Riddle R, Rusholme B, Soumagnac MT. 2021. Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass X-ray binary. The Astrophysical Journal. 920(2), 120.' mla: 'Yao, Yuhan, et al. “Multi-Wavelength Observations of AT2019wey: A New Candidate Black Hole Low-Mass X-Ray Binary.” The Astrophysical Journal, vol. 920, no. 2, 120, American Astronomical Society, 2021, doi:10.3847/1538-4357/ac15f9.' short: Y. Yao, S.R. Kulkarni, K.B. Burdge, I. Caiazzo, K. De, D. Dong, C. Fremling, M.M. Kasliwal, T. Kupfer, J. van Roestel, J. Sollerman, A. Bagdasaryan, E.C. Bellm, S.B. Cenko, A.J. Drake, D.A. Duev, M.J. Graham, S. Kaye, F.J. Masci, N. Miranda, T.A. Prince, R. Riddle, B. Rusholme, M.T. Soumagnac, The Astrophysical Journal 920 (2021). date_created: 2024-03-26T10:32:06Z date_published: 2021-10-21T00:00:00Z date_updated: 2024-04-02T07:28:22Z day: '21' doi: 10.3847/1538-4357/ac15f9 extern: '1' external_id: arxiv: - '2012.00169' intvolume: ' 920' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.00169 month: '10' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass X-ray binary' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 920 year: '2021' ... --- _id: '15216' abstract: - lang: eng text: AM CVn systems are a rare type of accreting binary that consists of a white dwarf and a helium-rich, degenerate donor star. Using the Zwicky Transient Facility (ZTF), we searched for new AM CVn systems by focusing on blue, outbursting stars. We first selected outbursting stars using the ZTF alerts. We cross matched the candidates with Gaia and Pan-STARRS catalogs. The initial selection of candidates based on the Gaia BP-RP contains 1751 unknown objects. We used the Pan-STARRS g-r and r-i color in combination with the Gaia color to identify 59 strong AM CVn candidates. We obtained identification spectra of 35 sources, of which 18 are high-priority candidates, and discovered nine new AM CVn systems and one magnetic CV that shows only He-ii lines. Using the outburst recurrence time, we estimate the orbital periods of the nine new AM CVn systems that are in the range of 29–50 minutes. We conclude that targeted follow up of blue, outbursting sources is an efficient method to find new AM CVn systems and we plan to follow up all candidates we identified to systematically study the population of outbursting AM CVn systems. article_number: '113' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jan full_name: van Roestel, Jan last_name: van Roestel - first_name: Leah full_name: Creter, Leah last_name: Creter - first_name: Thomas full_name: Kupfer, Thomas last_name: Kupfer - first_name: Paula full_name: Szkody, Paula last_name: Szkody - first_name: Jim full_name: Fuller, Jim last_name: Fuller - first_name: Matthew J. full_name: Green, Matthew J. last_name: Green - first_name: R. Michael full_name: Rich, R. Michael last_name: Rich - first_name: John full_name: Sepikas, John last_name: Sepikas - first_name: Kevin full_name: Burdge, Kevin last_name: Burdge - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Przemek full_name: Mróz, Przemek last_name: Mróz - first_name: Thomas A. full_name: Prince, Thomas A. last_name: Prince - first_name: Dmitry A. full_name: Duev, Dmitry A. last_name: Duev - first_name: Matthew J. full_name: Graham, Matthew J. last_name: Graham - first_name: David L. full_name: Shupe, David L. last_name: Shupe - first_name: Russ R. full_name: Laher, Russ R. last_name: Laher - first_name: Ashish A. full_name: Mahabal, Ashish A. last_name: Mahabal - first_name: Frank J. full_name: Masci, Frank J. last_name: Masci citation: ama: van Roestel J, Creter L, Kupfer T, et al. A systematic search for outbursting AM CVn systems with the Zwicky transient facility. The Astronomical Journal. 2021;162(3). doi:10.3847/1538-3881/ac0622 apa: van Roestel, J., Creter, L., Kupfer, T., Szkody, P., Fuller, J., Green, M. J., … Masci, F. J. (2021). A systematic search for outbursting AM CVn systems with the Zwicky transient facility. The Astronomical Journal. American Astronomical Society. https://doi.org/10.3847/1538-3881/ac0622 chicago: Roestel, Jan van, Leah Creter, Thomas Kupfer, Paula Szkody, Jim Fuller, Matthew J. Green, R. Michael Rich, et al. “A Systematic Search for Outbursting AM CVn Systems with the Zwicky Transient Facility.” The Astronomical Journal. American Astronomical Society, 2021. https://doi.org/10.3847/1538-3881/ac0622. ieee: J. van Roestel et al., “A systematic search for outbursting AM CVn systems with the Zwicky transient facility,” The Astronomical Journal, vol. 162, no. 3. American Astronomical Society, 2021. ista: van Roestel J, Creter L, Kupfer T, Szkody P, Fuller J, Green MJ, Rich RM, Sepikas J, Burdge K, Caiazzo I, Mróz P, Prince TA, Duev DA, Graham MJ, Shupe DL, Laher RR, Mahabal AA, Masci FJ. 2021. A systematic search for outbursting AM CVn systems with the Zwicky transient facility. The Astronomical Journal. 162(3), 113. mla: van Roestel, Jan, et al. “A Systematic Search for Outbursting AM CVn Systems with the Zwicky Transient Facility.” The Astronomical Journal, vol. 162, no. 3, 113, American Astronomical Society, 2021, doi:10.3847/1538-3881/ac0622. short: J. van Roestel, L. Creter, T. Kupfer, P. Szkody, J. Fuller, M.J. Green, R.M. Rich, J. Sepikas, K. Burdge, I. Caiazzo, P. Mróz, T.A. Prince, D.A. Duev, M.J. Graham, D.L. Shupe, R.R. Laher, A.A. Mahabal, F.J. Masci, The Astronomical Journal 162 (2021). date_created: 2024-03-26T10:32:25Z date_published: 2021-08-19T00:00:00Z date_updated: 2024-04-02T07:28:50Z day: '19' doi: 10.3847/1538-3881/ac0622 extern: '1' external_id: arxiv: - '2105.02261' intvolume: ' 162' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2105.02261 month: '08' oa: 1 oa_version: Preprint publication: The Astronomical Journal publication_identifier: eissn: - 1538-3881 issn: - 0004-6256 publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: A systematic search for outbursting AM CVn systems with the Zwicky transient facility type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 162 year: '2021' ... --- _id: '15218' abstract: - lang: eng text: "White dwarfs represent the last stage of evolution of stars with mass less than about eight times that of the Sun and, like other stars, are often found in binaries1,2. If the orbital period of the binary is short enough, energy losses from gravitational-wave radiation can shrink the orbit until the two white dwarfs come into contact and merge3. Depending on the component masses, the merger can lead to a supernova of type Ia or result in a massive white dwarf4. In the latter case, the white dwarf remnant is expected to be highly magnetized5,6 because of the strong magnetic dynamo that should arise during the merger, and be rapidly spinning from the conservation of the orbital angular momentum7. Here we report observations of a white dwarf, ZTF J190132.9+145808.7, that exhibits these properties, but to an extreme: a rotation period of 6.94 minutes, a magnetic field ranging between 600 megagauss and 900 megagauss over its surface, and a stellar radius of \r\n kilometres, only slightly larger than the radius of the Moon. Such a small radius implies that the star’s mass is close to the maximum white dwarf mass, or Chandrasekhar mass. ZTF J190132.9+145808.7 is likely to be cooling through the Urca processes (neutrino emission from electron capture on sodium) because of the high densities reached in its core." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Kevin B. full_name: Burdge, Kevin B. last_name: Burdge - first_name: James full_name: Fuller, James last_name: Fuller - first_name: Jeremy full_name: Heyl, Jeremy last_name: Heyl - first_name: S. R. full_name: Kulkarni, S. R. last_name: Kulkarni - first_name: Thomas A. full_name: Prince, Thomas A. last_name: Prince - first_name: Harvey B. full_name: Richer, Harvey B. last_name: Richer - first_name: Josiah full_name: Schwab, Josiah last_name: Schwab - first_name: Igor full_name: Andreoni, Igor last_name: Andreoni - first_name: Eric C. full_name: Bellm, Eric C. last_name: Bellm - first_name: Andrew full_name: Drake, Andrew last_name: Drake - first_name: Dmitry A. full_name: Duev, Dmitry A. last_name: Duev - first_name: Matthew J. full_name: Graham, Matthew J. last_name: Graham - first_name: George full_name: Helou, George last_name: Helou - first_name: Ashish A. full_name: Mahabal, Ashish A. last_name: Mahabal - first_name: Frank J. full_name: Masci, Frank J. last_name: Masci - first_name: Roger full_name: Smith, Roger last_name: Smith - first_name: Maayane T. full_name: Soumagnac, Maayane T. last_name: Soumagnac citation: ama: Caiazzo I, Burdge KB, Fuller J, et al. A highly magnetized and rapidly rotating white dwarf as small as the Moon. Nature. 2021;595(7865):39-42. doi:10.1038/s41586-021-03615-y apa: Caiazzo, I., Burdge, K. B., Fuller, J., Heyl, J., Kulkarni, S. R., Prince, T. A., … Soumagnac, M. T. (2021). A highly magnetized and rapidly rotating white dwarf as small as the Moon. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03615-y chicago: Caiazzo, Ilaria, Kevin B. Burdge, James Fuller, Jeremy Heyl, S. R. Kulkarni, Thomas A. Prince, Harvey B. Richer, et al. “A Highly Magnetized and Rapidly Rotating White Dwarf as Small as the Moon.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03615-y. ieee: I. Caiazzo et al., “A highly magnetized and rapidly rotating white dwarf as small as the Moon,” Nature, vol. 595, no. 7865. Springer Nature, pp. 39–42, 2021. ista: Caiazzo I, Burdge KB, Fuller J, Heyl J, Kulkarni SR, Prince TA, Richer HB, Schwab J, Andreoni I, Bellm EC, Drake A, Duev DA, Graham MJ, Helou G, Mahabal AA, Masci FJ, Smith R, Soumagnac MT. 2021. A highly magnetized and rapidly rotating white dwarf as small as the Moon. Nature. 595(7865), 39–42. mla: Caiazzo, Ilaria, et al. “A Highly Magnetized and Rapidly Rotating White Dwarf as Small as the Moon.” Nature, vol. 595, no. 7865, Springer Nature, 2021, pp. 39–42, doi:10.1038/s41586-021-03615-y. short: I. Caiazzo, K.B. Burdge, J. Fuller, J. Heyl, S.R. Kulkarni, T.A. Prince, H.B. Richer, J. Schwab, I. Andreoni, E.C. Bellm, A. Drake, D.A. Duev, M.J. Graham, G. Helou, A.A. Mahabal, F.J. Masci, R. Smith, M.T. Soumagnac, Nature 595 (2021) 39–42. date_created: 2024-03-26T10:33:03Z date_published: 2021-06-30T00:00:00Z date_updated: 2024-10-14T12:33:57Z day: '30' doi: 10.1038/s41586-021-03615-y extern: '1' external_id: arxiv: - '2107.08458' intvolume: ' 595' issue: '7865' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2107.08458 month: '06' oa: 1 oa_version: Preprint page: 39-42 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-021-03799-3 scopus_import: '1' status: public title: A highly magnetized and rapidly rotating white dwarf as small as the Moon type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 595 year: '2021' ... --- _id: '15219' abstract: - lang: eng text: We have carried out a search for massive white dwarfs (WDs) in the direction of young open star clusters using the Gaia DR2 database. The aim of this survey was (1) to provide robust data for new and previously known high-mass WDs regarding cluster membership, (2) to highlight WDs previously included in the initial final mass relation (IFMR) that are unlikely members of their respective clusters according to Gaia astrometry, and (3) to select an unequivocal WD sample that could then be compared with the host clusters' turnoff masses. All promising WD candidates in each cluster color–magnitude diagram were followed up with spectroscopy from Gemini in order to determine whether they were indeed WDs and derive their masses, temperatures, and ages. In order to be considered cluster members, white dwarfs were required to (1) have proper motions and parallaxes within 2σ, 3σ, or 4σ of those of their potential parent cluster based on how contaminated the field was in their region of the sky, (2) have a cooling age that was less than the cluster age, and (3) have a mass that was broadly consistent with the IFMR. A number of WDs included in current versions of the IFMR turned out to be nonmembers, and a number of apparent members, based on Gaia's astrometric data alone, were rejected, as their mass and/or cooling times were incompatible with cluster membership. In this way, we developed a highly selected IFMR sample for high-mass WDs that, surprisingly, contained no precursor masses significantly in excess of ∼ 6 M⊙. article_number: '165' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Harvey B. full_name: Richer, Harvey B. last_name: Richer - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Helen full_name: Du, Helen last_name: Du - first_name: Steffani full_name: Grondin, Steffani last_name: Grondin - first_name: James full_name: Hegarty, James last_name: Hegarty - first_name: Jeremy full_name: Heyl, Jeremy last_name: Heyl - first_name: Ronan full_name: Kerr, Ronan last_name: Kerr - first_name: David R. full_name: Miller, David R. last_name: Miller - first_name: Sarah full_name: Thiele, Sarah last_name: Thiele citation: ama: Richer HB, Caiazzo I, Du H, et al. Massive white dwarfs in young star clusters. The Astrophysical Journal. 2021;912(2). doi:10.3847/1538-4357/abdeb7 apa: Richer, H. B., Caiazzo, I., Du, H., Grondin, S., Hegarty, J., Heyl, J., … Thiele, S. (2021). Massive white dwarfs in young star clusters. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/abdeb7 chicago: Richer, Harvey B., Ilaria Caiazzo, Helen Du, Steffani Grondin, James Hegarty, Jeremy Heyl, Ronan Kerr, David R. Miller, and Sarah Thiele. “Massive White Dwarfs in Young Star Clusters.” The Astrophysical Journal. American Astronomical Society, 2021. https://doi.org/10.3847/1538-4357/abdeb7. ieee: H. B. Richer et al., “Massive white dwarfs in young star clusters,” The Astrophysical Journal, vol. 912, no. 2. American Astronomical Society, 2021. ista: Richer HB, Caiazzo I, Du H, Grondin S, Hegarty J, Heyl J, Kerr R, Miller DR, Thiele S. 2021. Massive white dwarfs in young star clusters. The Astrophysical Journal. 912(2), 165. mla: Richer, Harvey B., et al. “Massive White Dwarfs in Young Star Clusters.” The Astrophysical Journal, vol. 912, no. 2, 165, American Astronomical Society, 2021, doi:10.3847/1538-4357/abdeb7. short: H.B. Richer, I. Caiazzo, H. Du, S. Grondin, J. Hegarty, J. Heyl, R. Kerr, D.R. Miller, S. Thiele, The Astrophysical Journal 912 (2021). date_created: 2024-03-26T10:33:23Z date_published: 2021-05-17T00:00:00Z date_updated: 2024-04-03T14:11:17Z day: '17' doi: 10.3847/1538-4357/abdeb7 extern: '1' external_id: arxiv: - '2101.08300' intvolume: ' 912' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2101.08300 month: '05' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: Massive white dwarfs in young star clusters type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 912 year: '2021' ... --- _id: '15222' abstract: - lang: eng text: We describe an implementation of a broad-band soft X-ray polarimeter, substantially based on previous designs. The Globe-Orbiting Soft X-ray Polarimeter (GOSoX) is a SmallSat. As in a related mission concept the PiSoX Polarimeter, the grating arrangement is designed optimally for the purpose of polarimetry matching the dispersion of a spectrometer to a laterally graded multilayer (LGML). For GOSoX, the optics are lightweight Si mirrors in a one-bounce parabolic configuration. The instrument covers the wavelength range from 31 A to 75 A (165 - 400 eV). Upon satellite rotation, the intensities of the dispersed spectra, after reflection and polarizing by the LGMLs, give the three Stokes parameters needed to determine a source's linear polarization fraction and orientation. The design can be extended to higher energies as LGMLs are developed further. We describe the potential scientific return and the proposed mission concept following the results of a JPL Team X concept study. article_processing_charge: No author: - first_name: Herman L. full_name: Marshall, Herman L. last_name: Marshall - first_name: Sarah full_name: Heine, Sarah last_name: Heine - first_name: Rosemary full_name: Davidson, Rosemary last_name: Davidson - first_name: Alan full_name: Garner, Alan last_name: Garner - first_name: Eric full_name: Gullikson, Eric last_name: Gullikson - first_name: Moritz full_name: Günther, Moritz last_name: Günther - first_name: Christopher full_name: Leitz, Christopher last_name: Leitz - first_name: Rebecca full_name: Masterson, Rebecca last_name: Masterson - first_name: Eric full_name: Miller, Eric last_name: Miller - first_name: June S. full_name: Stenzel, June S. last_name: Stenzel - first_name: William W. full_name: Zhang, William W. last_name: Zhang - first_name: Rozenn full_name: Boissay-Malaquin, Rozenn last_name: Boissay-Malaquin - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Deepto full_name: Chakrabarty, Deepto last_name: Chakrabarty - first_name: Luigi full_name: Gallo, Luigi last_name: Gallo - first_name: Ralf full_name: Heilmann, Ralf last_name: Heilmann - first_name: Jeremy full_name: Heyl, Jeremy last_name: Heyl - first_name: Erin full_name: Kara, Erin last_name: Kara - first_name: Norbert full_name: Schulz, Norbert last_name: Schulz citation: ama: 'Marshall HL, Heine S, Davidson R, et al. The Globe Orbiting Soft X-ray (GOSoX) polarimeter concept study. In: Optics for EUV, X-Ray, and Gamma-Ray Astronomy X. Vol 11822. SPIE; 2021. doi:10.1117/12.2596186' apa: 'Marshall, H. L., Heine, S., Davidson, R., Garner, A., Gullikson, E., Günther, M., … Schulz, N. (2021). The Globe Orbiting Soft X-ray (GOSoX) polarimeter concept study. In Optics for EUV, X-Ray, and Gamma-Ray Astronomy X (Vol. 11822). San Diego, CA, United States: SPIE. https://doi.org/10.1117/12.2596186' chicago: Marshall, Herman L., Sarah Heine, Rosemary Davidson, Alan Garner, Eric Gullikson, Moritz Günther, Christopher Leitz, et al. “The Globe Orbiting Soft X-Ray (GOSoX) Polarimeter Concept Study.” In Optics for EUV, X-Ray, and Gamma-Ray Astronomy X, Vol. 11822. SPIE, 2021. https://doi.org/10.1117/12.2596186. ieee: H. L. Marshall et al., “The Globe Orbiting Soft X-ray (GOSoX) polarimeter concept study,” in Optics for EUV, X-Ray, and Gamma-Ray Astronomy X, San Diego, CA, United States, 2021, vol. 11822. ista: Marshall HL, Heine S, Davidson R, Garner A, Gullikson E, Günther M, Leitz C, Masterson R, Miller E, Stenzel JS, Zhang WW, Boissay-Malaquin R, Caiazzo I, Chakrabarty D, Gallo L, Heilmann R, Heyl J, Kara E, Schulz N. 2021. The Globe Orbiting Soft X-ray (GOSoX) polarimeter concept study. Optics for EUV, X-Ray, and Gamma-Ray Astronomy X. Optical Engineering + Applications vol. 11822. mla: Marshall, Herman L., et al. “The Globe Orbiting Soft X-Ray (GOSoX) Polarimeter Concept Study.” Optics for EUV, X-Ray, and Gamma-Ray Astronomy X, vol. 11822, SPIE, 2021, doi:10.1117/12.2596186. short: H.L. Marshall, S. Heine, R. Davidson, A. Garner, E. Gullikson, M. Günther, C. Leitz, R. Masterson, E. Miller, J.S. Stenzel, W.W. Zhang, R. Boissay-Malaquin, I. Caiazzo, D. Chakrabarty, L. Gallo, R. Heilmann, J. Heyl, E. Kara, N. Schulz, in:, Optics for EUV, X-Ray, and Gamma-Ray Astronomy X, SPIE, 2021. conference: end_date: 2021-08-05 location: San Diego, CA, United States name: Optical Engineering + Applications start_date: 2021-08-01 date_created: 2024-03-26T10:34:21Z date_published: 2021-08-21T00:00:00Z date_updated: 2024-04-03T14:13:09Z day: '21' doi: 10.1117/12.2596186 extern: '1' intvolume: ' 11822' language: - iso: eng month: '08' oa_version: None publication: Optics for EUV, X-Ray, and Gamma-Ray Astronomy X publication_status: published publisher: SPIE quality_controlled: '1' scopus_import: '1' status: public title: The Globe Orbiting Soft X-ray (GOSoX) polarimeter concept study type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11822 year: '2021' ...