--- _id: '9678' abstract: - lang: eng text: We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively. acknowledgement: We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605. article_processing_charge: No author: - first_name: Sebastian full_name: Brandt, Sebastian last_name: Brandt - first_name: Barbara full_name: Keller, Barbara last_name: Keller - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Jukka full_name: Suomela, Jukka last_name: Suomela - first_name: Jara full_name: Uitto, Jara last_name: Uitto citation: ama: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785' apa: Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event, United States. https://doi.org/10.1145/3409964.3461785 chicago: Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021. https://doi.org/10.1145/3409964.3461785. ieee: S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2021, pp. 129–139. ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.' mla: Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–39, doi:10.1145/3409964.3461785. short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139. conference: end_date: 2021-07-08 location: ' Virtual Event, United States' name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures ' start_date: 2021-07-06 date_created: 2021-07-18T22:01:22Z date_published: 2021-07-06T00:00:00Z date_updated: 2024-03-05T07:13:12Z day: '06' department: - _id: DaAl doi: 10.1145/3409964.3461785 ec_funded: 1 external_id: arxiv: - '2005.07761' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2005.07761 month: '07' oa: 1 oa_version: Preprint page: 129-139 project: - _id: 26A5D39A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '840605' name: Coordination in constrained and natural distributed systems publication: Annual ACM Symposium on Parallelism in Algorithms and Architectures publication_identifier: isbn: - '9781450380706' publication_status: published quality_controlled: '1' related_material: record: - id: '15074' relation: earlier_version status: public scopus_import: '1' status: public title: Efficient load-balancing through distributed token dropping type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 year: '2021' ... --- _id: '8286' abstract: - lang: eng text: "We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of \U0001D4AA(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of \U0001D4AA (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. " acknowledgement: The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 - first_name: Amirmojtaba full_name: Sabour, Amirmojtaba id: bcc145fd-e77f-11ea-ae8b-80d661dbff67 last_name: Sabour citation: ama: Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. Algorithmica. 2021. doi:10.1007/s00453-021-00905-9 apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer Nature. https://doi.org/10.1007/s00453-021-00905-9' chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021. https://doi.org/10.1007/s00453-021-00905-9. ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica. Springer Nature, 2021. ista: Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica. mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9. short: D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021). conference: end_date: 2020-07-11 location: Virtual, Online; Germany name: 'ICALP: International Colloquium on Automata, Languages, and Programming ' start_date: 2020-07-08 date_created: 2020-08-24T06:24:04Z date_published: 2021-12-24T00:00:00Z date_updated: 2024-03-05T07:35:53Z day: '24' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00453-021-00905-9 ec_funded: 1 external_id: arxiv: - '2003.09297' isi: - '000734004600001' file: - access_level: open_access checksum: 21169b25b0c8e17b21e12af22bff9870 content_type: application/pdf creator: cchlebak date_created: 2021-12-27T10:36:40Z date_updated: 2021-12-27T10:36:40Z file_id: '10577' file_name: 2021_Algorithmica_Alistarh.pdf file_size: 525950 relation: main_file success: 1 file_date_updated: 2021-12-27T10:36:40Z has_accepted_license: '1' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: earlier_version url: https://doi.org/10.4230/LIPIcs.ICALP.2020.7 record: - id: '15077' relation: earlier_version status: public scopus_import: '1' status: public title: Dynamic averaging load balancing on cycles 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9733' abstract: - lang: eng text: This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 citation: ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733 apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733 chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733. ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021. ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria. mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733. short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021. date_created: 2021-07-27T15:48:30Z date_published: 2021-08-20T00:00:00Z date_updated: 2024-03-06T12:30:44Z day: '20' ddc: - '515' - '519' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe - _id: JaMa doi: 10.15479/at:ista:9733 ec_funded: 1 file: - access_level: open_access checksum: e88bb8ca43948abe060eb2d2fa719881 content_type: application/pdf creator: dfelicia date_created: 2021-08-19T14:03:48Z date_updated: 2021-09-06T09:28:56Z file_id: '9944' file_name: Thesis_FeliciangeliA.pdf file_size: 1958710 relation: main_file - access_level: closed checksum: 72810843abee83705853505b3f8348aa content_type: application/octet-stream creator: dfelicia date_created: 2021-08-19T14:06:35Z date_updated: 2022-03-10T12:13:57Z file_id: '9945' file_name: thesis.7z file_size: 3771669 relation: source_file file_date_updated: 2022-03-10T12:13:57Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: '180' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9787' relation: part_of_dissertation status: public - id: '9792' relation: part_of_dissertation status: public - id: '9225' relation: part_of_dissertation status: public - id: '9781' relation: part_of_dissertation status: public - id: '9791' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: The polaron at strong coupling tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9571' abstract: - lang: eng text: As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods. article_processing_charge: No article_type: original author: - first_name: Ali full_name: Ramezani-Kebrya, Ali last_name: Ramezani-Kebrya - first_name: Fartash full_name: Faghri, Fartash last_name: Faghri - first_name: Ilya full_name: Markov, Ilya last_name: Markov - first_name: Vitalii full_name: Aksenov, Vitalii id: 2980135A-F248-11E8-B48F-1D18A9856A87 last_name: Aksenov - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Daniel M. full_name: Roy, Daniel M. last_name: Roy citation: ama: 'Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 2021;22(114):1−43.' apa: 'Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., & Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. Journal of Machine Learning Research.' chicago: 'Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2021.' ieee: 'A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” Journal of Machine Learning Research, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.' ista: 'Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.' mla: 'Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.' short: A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43. date_created: 2021-06-20T22:01:33Z date_published: 2021-04-01T00:00:00Z date_updated: 2024-03-06T12:22:07Z day: '01' ddc: - '000' department: - _id: DaAl external_id: arxiv: - '1908.06077' file: - access_level: open_access checksum: 6428aa8bcb67768b6949c99b55d5281d content_type: application/pdf creator: asandaue date_created: 2021-06-23T07:09:41Z date_updated: 2021-06-23T07:09:41Z file_id: '9595' file_name: 2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf file_size: 11237154 relation: main_file success: 1 file_date_updated: 2021-06-23T07:09:41Z has_accepted_license: '1' intvolume: ' 22' issue: '114' language: - iso: eng main_file_link: - open_access: '1' url: https://www.jmlr.org/papers/v22/20-255.html month: '04' oa: 1 oa_version: Published Version page: 1−43 publication: Journal of Machine Learning Research publication_identifier: eissn: - '15337928' issn: - '15324435' publication_status: published publisher: Journal of Machine Learning Research quality_controlled: '1' scopus_import: '1' status: public title: 'NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2021' ... --- _id: '8544' abstract: - lang: eng text: The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis. acknowledgement: We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator. article_processing_charge: No article_type: original author: - first_name: Yukari H. full_name: Takeo, Yukari H. last_name: Takeo - first_name: S. Andrew full_name: Shuster, S. Andrew last_name: Shuster - first_name: Linnie full_name: Jiang, Linnie last_name: Jiang - first_name: Miley full_name: Hu, Miley last_name: Hu - first_name: David J. full_name: Luginbuhl, David J. last_name: Luginbuhl - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Mark J. full_name: Wagner, Mark J. last_name: Wagner - first_name: Surya full_name: Ganguli, Surya last_name: Ganguli - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 2021;109(4):P629-644.E8. doi:10.1016/j.neuron.2020.11.028 apa: Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.11.028 chicago: Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2020.11.028. ieee: Y. H. Takeo et al., “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” Neuron, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021. ista: Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8. mla: Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:10.1016/j.neuron.2020.11.028. short: Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8. date_created: 2020-09-21T11:59:47Z date_published: 2021-02-17T00:00:00Z date_updated: 2024-03-06T12:12:48Z day: '17' department: - _id: SiHi doi: 10.1016/j.neuron.2020.11.028 ec_funded: 1 intvolume: ' 109' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.06.14.151258 month: '02' oa: 1 oa_version: Preprint page: P629-644.E8 project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Neuron publication_identifier: eissn: - 1097-4199 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2021' ... --- _id: '9791' abstract: - lang: eng text: We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar. acknowledgement: We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged.. article_number: '2107.03720 ' article_processing_charge: No author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - 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: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv. apa: Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. arXiv. chicago: Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d. ieee: D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” arXiv. . ista: Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720. mla: Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, 2107.03720. short: D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.). date_created: 2021-08-06T08:49:45Z date_published: 2021-07-08T00:00:00Z date_updated: 2024-03-06T12:30:45Z day: '08' ddc: - '510' department: - _id: RoSe ec_funded: 1 external_id: arxiv: - '2107.03720' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2107.03720 month: '07' oa: 1 oa_version: Preprint 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: arXiv publication_status: submitted related_material: record: - id: '10755' relation: later_version status: public - id: '9733' relation: dissertation_contains status: public status: public title: The effective mass problem for the Landau-Pekar equations type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '7553' abstract: - lang: eng text: Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems. acknowledgement: The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018. article_processing_charge: No author: - first_name: Wiktor F full_name: Mlynarski, Wiktor F id: 358A453A-F248-11E8-B48F-1D18A9856A87 last_name: Mlynarski - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020 apa: Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020 chicago: Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020. ieee: W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021. ista: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5. mla: Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020. short: W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5. date_created: 2020-02-28T11:00:12Z date_published: 2021-04-07T00:00:00Z date_updated: 2024-03-06T14:22:51Z day: '07' department: - _id: GaTk doi: 10.1016/j.neuron.2021.01.020 ec_funded: 1 external_id: isi: - '000637809600006' intvolume: ' 109' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/848374 month: '04' oa: 1 oa_version: Preprint page: 1227-1241.e5 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Neuron publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/can-evolution-be-predicted/ record: - id: '15020' relation: dissertation_contains status: public scopus_import: '1' status: public title: Statistical analysis and optimality of neural systems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 109 year: '2021' ... --- _id: '10598' abstract: - lang: eng text: ' We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. ' acknowledgement: The authors would like to thank Andrea Montanari for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1. alternative_title: - Proceedings of Machine Learning Research article_processing_charge: Yes (via OA deal) author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Ramji full_name: Venkataramanan, Ramji last_name: Venkataramanan citation: ama: 'Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. In: Banerjee A, Fukumizu K, eds. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. Vol 130. ML Research Press; 2021:397-405.' apa: 'Mondelli, M., & Venkataramanan, R. (2021). Approximate message passing with spectral initialization for generalized linear models. In A. Banerjee & K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics (Vol. 130, pp. 397–405). Virtual, San Diego, CA, United States: ML Research Press.' chicago: Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” In Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press, 2021. ieee: M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” in Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Virtual, San Diego, CA, United States, 2021, vol. 130, pp. 397–405. ista: 'Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral initialization for generalized linear models. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405.' mla: Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp. 397–405. short: M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2021, pp. 397–405. conference: end_date: 2021-04-15 location: Virtual, San Diego, CA, United States name: 'AISTATS: Artificial Intelligence and Statistics' start_date: 2021-04-13 date_created: 2022-01-03T11:34:22Z date_published: 2021-04-01T00:00:00Z date_updated: 2024-03-07T10:36:53Z day: '01' department: - _id: MaMo editor: - first_name: Arindam full_name: Banerjee, Arindam last_name: Banerjee - first_name: Kenji full_name: Fukumizu, Kenji last_name: Fukumizu external_id: arxiv: - '2010.03460' intvolume: ' 130' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.mlr.press/v130/mondelli21a.html month: '04' oa: 1 oa_version: Preprint page: 397-405 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of The 24th International Conference on Artificial Intelligence and Statistics publication_identifier: issn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '12480' relation: later_version status: public scopus_import: '1' status: public title: Approximate message passing with spectral initialization for generalized linear models type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2021' ... --- _id: '8196' abstract: - lang: eng text: This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013) (Grant Agreement No. 616160). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Qiao-Li full_name: Dong, Qiao-Li last_name: Dong - first_name: Lu-Lu full_name: Liu, Lu-Lu last_name: Liu - first_name: Jen-Chih full_name: Yao, Jen-Chih last_name: Yao citation: ama: Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 2021;22:2627-2653. doi:10.1007/s11081-020-09544-5 apa: Shehu, Y., Dong, Q.-L., Liu, L.-L., & Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. Springer Nature. https://doi.org/10.1007/s11081-020-09544-5 chicago: Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering. Springer Nature, 2021. https://doi.org/10.1007/s11081-020-09544-5. ieee: Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” Optimization and Engineering, vol. 22. Springer Nature, pp. 2627–2653, 2021. ista: Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653. mla: Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:10.1007/s11081-020-09544-5. short: Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653. date_created: 2020-08-03T14:29:57Z date_published: 2021-02-25T00:00:00Z date_updated: 2024-03-07T14:39:29Z day: '25' ddc: - '510' department: - _id: VlKo doi: 10.1007/s11081-020-09544-5 ec_funded: 1 external_id: isi: - '000559345400001' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-03T15:24:39Z date_updated: 2020-08-03T15:24:39Z file_id: '8197' file_name: 2020_OptimizationEngineering_Shehu.pdf file_size: 2137860 relation: main_file success: 1 file_date_updated: 2020-08-03T15:24:39Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 2627-2653 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Optimization and Engineering publication_identifier: eissn: - 1573-2924 issn: - 1389-4420 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: New strong convergence method for the sum of two maximal monotone operators 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2021' ... --- _id: '8911' abstract: - lang: eng text: "In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. " acknowledgement: "G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT." article_processing_charge: No article_type: original author: - first_name: Giordano full_name: Scappucci, Giordano last_name: Scappucci - first_name: Christoph full_name: Kloeffel, Christoph last_name: Kloeffel - first_name: Floris A. full_name: Zwanenburg, Floris A. last_name: Zwanenburg - first_name: Daniel full_name: Loss, Daniel last_name: Loss - first_name: Maksym full_name: Myronov, Maksym last_name: Myronov - first_name: Jian-Jun full_name: Zhang, Jian-Jun last_name: Zhang - first_name: Silvano De full_name: Franceschi, Silvano De last_name: Franceschi - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X - first_name: Menno full_name: Veldhorst, Menno last_name: Veldhorst citation: ama: Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z apa: Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z chicago: Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z. ieee: G. Scappucci et al., “The germanium quantum information route,” Nature Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021. ista: Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943. mla: Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z. short: G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943. date_created: 2020-12-02T10:52:51Z date_published: 2021-10-01T00:00:00Z date_updated: 2024-03-07T14:48:57Z day: '01' department: - _id: GeKa doi: 10.1038/s41578-020-00262-z ec_funded: 1 external_id: arxiv: - '2004.08133' isi: - '000600826100003' intvolume: ' 6' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2004.08133 month: '10' oa: 1 oa_version: Preprint page: '926–943 ' project: - _id: 25517E86-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335497' name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires - _id: 2552F888-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y00715 name: Loch Spin-Qubits und Majorana-Fermionen in Germanium - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells publication: Nature Reviews Materials publication_identifier: eissn: - 2058-8437 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The germanium quantum information route type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2021' ... --- _id: '8338' abstract: - lang: eng text: Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory. acknowledgement: This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexander I. full_name: Bobenko, Alexander I. last_name: Bobenko - first_name: Wolfgang K. full_name: Schief, Wolfgang K. last_name: Schief - first_name: Jan full_name: Techter, Jan last_name: Techter citation: ama: Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 2021;66:938-976. doi:10.1007/s00454-020-00240-w apa: Akopyan, A., Bobenko, A. I., Schief, W. K., & Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00240-w chicago: Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00240-w. ieee: A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 938–976, 2021. ista: Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976. mla: Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 938–76, doi:10.1007/s00454-020-00240-w. short: A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976. date_created: 2020-09-06T22:01:13Z date_published: 2021-10-01T00:00:00Z date_updated: 2024-03-07T14:51:11Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-020-00240-w ec_funded: 1 external_id: arxiv: - '1908.00856' isi: - '000564488500002' intvolume: ' 66' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.00856 month: '10' oa: 1 oa_version: Preprint page: 938-976 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2021' ... --- _id: '7939' abstract: - lang: eng text: "We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. " acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Keren full_name: Censor-Hillel, Keren last_name: Censor-Hillel - first_name: Michal full_name: Dory, Michal last_name: Dory - first_name: Janne full_name: Korhonen, Janne id: C5402D42-15BC-11E9-A202-CA2BE6697425 last_name: Korhonen - first_name: Dean full_name: Leitersdorf, Dean last_name: Leitersdorf citation: ama: Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. Distributed Computing. 2021;34:463-487. doi:10.1007/s00446-020-00380-5 apa: Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-020-00380-5 chicago: Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing. Springer Nature, 2021. https://doi.org/10.1007/s00446-020-00380-5. ieee: K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” Distributed Computing, vol. 34. Springer Nature, pp. 463–487, 2021. ista: Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487. mla: Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing, vol. 34, Springer Nature, 2021, pp. 463–87, doi:10.1007/s00446-020-00380-5. short: K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487. date_created: 2020-06-07T22:00:54Z date_published: 2021-12-01T00:00:00Z date_updated: 2024-03-07T14:43:39Z day: '01' department: - _id: DaAl doi: 10.1007/s00446-020-00380-5 external_id: arxiv: - '1903.05956' isi: - '000556444600001' intvolume: ' 34' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00446-020-00380-5 month: '12' oa: 1 oa_version: Published Version page: 463-487 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Distributed Computing publication_identifier: eissn: - 1432-0452 issn: - 0178-2770 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '6933' relation: earlier_version status: public scopus_import: '1' status: public title: Fast approximate shortest paths in the congested clique type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2021' ... --- _id: '8248' abstract: - lang: eng text: 'We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic.' acknowledgement: "Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: Ramsay full_name: Dyer, Ramsay last_name: Dyer - first_name: Arijit full_name: Ghosh, Arijit last_name: Ghosh - first_name: Andre full_name: Lieutier, Andre last_name: Lieutier - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 2021;66:666-686. doi:10.1007/s00454-020-00233-9 apa: Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., & Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00233-9 chicago: Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00233-9. ieee: J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 666–686, 2021. ista: Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686. mla: Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 666–86, doi:10.1007/s00454-020-00233-9. short: J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686. date_created: 2020-08-11T07:11:51Z date_published: 2021-09-01T00:00:00Z date_updated: 2024-03-07T14:54:59Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s00454-020-00233-9 ec_funded: 1 external_id: isi: - '000558119300001' has_accepted_license: '1' intvolume: ' 66' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00454-020-00233-9 month: '09' oa: 1 oa_version: Published Version page: 666-686 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Local conditions for triangulating submanifolds of Euclidean space 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2021' ... --- _id: '7883' abstract: - lang: eng text: All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern. acknowledgement: 'Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037' article_number: e383 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Katarzyna full_name: Kuzmicz-Kowalska, Katarzyna id: 4CED352A-F248-11E8-B48F-1D18A9856A87 last_name: Kuzmicz-Kowalska - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: 'Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. 2021. doi:10.1002/wdev.383' apa: 'Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. Wiley. https://doi.org/10.1002/wdev.383' chicago: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383.' ieee: 'K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021.' ista: 'Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.' mla: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.' short: 'K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).' date_created: 2020-05-24T22:01:00Z date_published: 2021-04-15T00:00:00Z date_updated: 2024-03-07T15:03:00Z day: '15' ddc: - '570' department: - _id: AnKi doi: 10.1002/wdev.383 ec_funded: 1 external_id: isi: - '000531419400001' pmid: - '32391980' file: - access_level: open_access checksum: f0a7745d48afa09ea7025e876a0145a8 content_type: application/pdf creator: dernst date_created: 2020-11-24T13:11:39Z date_updated: 2020-11-24T13:11:39Z file_id: '8800' file_name: 2020_WIREs_DevBio_KuzmiczKowalska.pdf file_size: 2527276 relation: main_file success: 1 file_date_updated: 2020-11-24T13:11:39Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: 267AF0E4-B435-11E9-9278-68D0E5697425 name: The role of morphogens in the regulation of neural tube growth - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F07802 name: Morphogen control of growth and pattern in the spinal cord publication: 'Wiley Interdisciplinary Reviews: Developmental Biology' publication_identifier: eissn: - '17597692' issn: - '17597684' publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '14323' relation: dissertation_contains status: public scopus_import: '1' status: public title: Regulation of size and scale in vertebrate spinal cord development 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '7905' abstract: - lang: eng text: We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Adam full_name: Brown, Adam id: 70B7FDF6-608D-11E9-9333-8535E6697425 last_name: Brown - first_name: Bei full_name: Wang, Bei last_name: Wang citation: ama: Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 2021;65:1166-1198. doi:10.1007/s00454-020-00206-y apa: Brown, A., & Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00206-y chicago: Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00206-y. ieee: A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1166–1198, 2021. ista: Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198. mla: Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:10.1007/s00454-020-00206-y. short: A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198. date_created: 2020-05-30T10:26:04Z date_published: 2021-06-01T00:00:00Z date_updated: 2024-03-07T15:01:58Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s00454-020-00206-y external_id: arxiv: - '1712.07734' isi: - '000536324700001' file: - access_level: open_access checksum: 487a84ea5841b75f04f66d7ebd71b67e content_type: application/pdf creator: dernst date_created: 2020-11-25T09:06:41Z date_updated: 2020-11-25T09:06:41Z file_id: '8803' file_name: 2020_DiscreteCompGeometry_Brown.pdf file_size: 1013730 relation: main_file success: 1 file_date_updated: 2020-11-25T09:06:41Z has_accepted_license: '1' intvolume: ' 65' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1166-1198 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Sheaf-theoretic stratification learning from geometric and topological perspectives 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2021' ... --- _id: '8601' abstract: - lang: eng text: We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. 2021. doi:10.1007/s00440-020-01003-7 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-020-01003-7 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields. Springer Nature, 2021. https://doi.org/10.1007/s00440-020-01003-7. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2021. ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. mla: Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2021, doi:10.1007/s00440-020-01003-7. short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021). date_created: 2020-10-04T22:01:37Z date_published: 2021-02-01T00:00:00Z date_updated: 2024-03-07T15:07:53Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00440-020-01003-7 ec_funded: 1 external_id: arxiv: - '1908.00969' isi: - '000572724600002' file: - access_level: open_access checksum: 611ae28d6055e1e298d53a57beb05ef4 content_type: application/pdf creator: dernst date_created: 2020-10-05T14:53:40Z date_updated: 2020-10-05T14:53:40Z file_id: '8612' file_name: 2020_ProbTheory_Cipolloni.pdf file_size: 497032 relation: main_file success: 1 file_date_updated: 2020-10-05T14:53:40Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Probability Theory and Related Fields publication_identifier: eissn: - '14322064' issn: - '01788051' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Edge universality for non-Hermitian random matrices 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '7925' abstract: - lang: eng text: In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Aviv full_name: Gibali, Aviv last_name: Gibali citation: ama: Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. Optimization Letters. 2021;15:2109-2126. doi:10.1007/s11590-020-01603-1 apa: Shehu, Y., & Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. Optimization Letters. Springer Nature. https://doi.org/10.1007/s11590-020-01603-1 chicago: Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters. Springer Nature, 2021. https://doi.org/10.1007/s11590-020-01603-1. ieee: Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” Optimization Letters, vol. 15. Springer Nature, pp. 2109–2126, 2021. ista: Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126. mla: Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:10.1007/s11590-020-01603-1. short: Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126. date_created: 2020-06-04T11:28:33Z date_published: 2021-09-01T00:00:00Z date_updated: 2024-03-07T15:00:43Z day: '01' ddc: - '510' department: - _id: VlKo doi: 10.1007/s11590-020-01603-1 ec_funded: 1 external_id: isi: - '000537342300001' file: - access_level: open_access checksum: 63c5f31cd04626152a19f97a2476281b content_type: application/pdf creator: kschuh date_created: 2024-03-07T14:58:51Z date_updated: 2024-03-07T14:58:51Z file_id: '15089' file_name: 2021_OptimizationLetters_Shehu.pdf file_size: 2148882 relation: main_file success: 1 file_date_updated: 2024-03-07T14:58:51Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 2109-2126 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Optimization Letters publication_identifier: eissn: - 1862-4480 issn: - 1862-4472 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: New inertial relaxed method for solving split feasibilities 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 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: '9438' abstract: - lang: eng text: Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system. acknowledged_ssus: - _id: M-Shop acknowledgement: This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support. article_processing_charge: No article_type: original author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Yuji full_name: Okamoto, Yuji id: 3337E116-F248-11E8-B48F-1D18A9856A87 last_name: Okamoto orcid: 0000-0003-0408-6094 - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Victor M full_name: Vargas Barroso, Victor M id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87 last_name: Vargas Barroso - first_name: Benjamin full_name: Suter, Benjamin id: 4952F31E-F248-11E8-B48F-1D18A9856A87 last_name: Suter orcid: 0000-0002-9885-6936 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0 apa: Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0 chicago: Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0. ieee: D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021. ista: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967. mla: Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0. short: D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967. date_created: 2021-05-30T22:01:24Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-10T22:30:51Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1038/s41596-021-00526-0 ec_funded: 1 external_id: isi: - '000650528700003' pmid: - '33990799' file: - access_level: open_access checksum: 7eb580abd8893cdb0b410cf41bc8c263 content_type: application/pdf creator: cziletti date_created: 2021-07-08T12:27:55Z date_updated: 2021-12-02T23:30:05Z embargo: 2021-12-01 file_id: '9639' file_name: VandaeletalAuthorVersion2021.pdf file_size: 38574802 relation: main_file file_date_updated: 2021-12-02T23:30:05Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 2947–2967 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 2696E7FE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00739 name: Structural plasticity at mossy fiber-CA3 synapses publication: Nature Protocols publication_identifier: eissn: - '17502799' issn: - '17542189' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9992' abstract: - lang: eng text: "Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. " acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 citation: ama: Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992 apa: Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992 chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992. ieee: L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021. ista: Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. mla: Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992. short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021. date_created: 2021-09-09T07:37:20Z date_published: 2021-09-13T00:00:00Z date_updated: 2023-09-07T13:38:33Z day: '13' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:9992 ec_funded: 1 file: - access_level: closed checksum: c763064adaa720e16066c1a4f9682bbb content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lhoermaye date_created: 2021-09-09T07:29:48Z date_updated: 2021-09-15T22:30:26Z embargo_to: open_access file_id: '9993' file_name: Thesis_vupload.docx file_size: 25179004 relation: source_file - access_level: open_access checksum: 53911b06e93d7cdbbf4c7f4c162fa70f content_type: application/pdf creator: lhoermaye date_created: 2021-09-09T14:25:08Z date_updated: 2021-09-15T22:30:26Z embargo: 2021-09-09 file_id: '9996' file_name: Thesis_vfinal_pdfa.pdf file_size: 6246900 relation: main_file file_date_updated: 2021-09-15T22:30:26Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version page: '168' project: - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6351' relation: part_of_dissertation status: public - id: '6943' relation: part_of_dissertation status: public - id: '8002' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Wound healing in the Arabidopsis root meristem 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10816' abstract: - lang: eng text: Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks. acknowledged_ssus: - _id: SSU acknowledgement: We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.). article_processing_charge: No article_type: original author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Benjamin full_name: Suter, Benjamin id: 4952F31E-F248-11E8-B48F-1D18A9856A87 last_name: Suter orcid: 0000-0002-9885-6936 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1 apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1 chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1. ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021. ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842. mla: Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1. short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842. date_created: 2022-03-04T08:32:36Z date_published: 2021-12-16T00:00:00Z date_updated: 2023-08-10T22:30:10Z day: '16' ddc: - '610' department: - _id: PeJo doi: 10.1038/s43588-021-00157-1 ec_funded: 1 file: - access_level: open_access checksum: 9fec5b667909ef52be96d502e4f8c2ae content_type: application/pdf creator: patrickd date_created: 2022-06-02T12:51:07Z date_updated: 2022-06-18T22:30:03Z embargo: 2022-06-17 file_id: '11430' file_name: Guzmanetal2021.pdf file_size: 1699466 relation: main_file - access_level: open_access checksum: 52a005b13a114e3c3a28fa6bbe8b1a8d content_type: application/pdf creator: patrickd date_created: 2022-06-02T12:53:47Z date_updated: 2022-06-18T22:30:03Z embargo: 2022-06-17 file_id: '11431' file_name: Guzmanetal2021Suppl.pdf file_size: 3005651 relation: supplementary_material title: Supplementary Material file_date_updated: 2022-06-18T22:30:03Z has_accepted_license: '1' intvolume: ' 1' issue: '12' keyword: - general medicine language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/647800 month: '12' oa: 1 oa_version: Submitted Version page: 830-842 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Nature Computational Science publication_identifier: issn: - 2662-8457 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: press_release url: https://ista.ac.at/en/news/spot-the-difference/ record: - id: '10110' relation: software status: public scopus_import: '1' status: public title: How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2021' ... --- _id: '10110' abstract: - lang: eng text: Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks. author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Benjamin full_name: Suter, Benjamin id: 4952F31E-F248-11E8-B48F-1D18A9856A87 last_name: Suter orcid: 0000-0002-9885-6936 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110 apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110 chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110. ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021. ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110. mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110. short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021). date_created: 2021-10-08T06:44:22Z date_published: 2021-12-16T00:00:00Z date_updated: 2024-03-27T23:30:11Z day: '16' ddc: - '005' department: - _id: PeJo - _id: ScienComp doi: 10.15479/AT:ISTA:10110 file: - access_level: open_access checksum: f92f8931cad0aa7e411c1715337bf408 content_type: application/x-zip-compressed creator: cchlebak date_created: 2021-10-08T08:46:04Z date_updated: 2021-10-08T08:46:04Z file_id: '10114' file_name: patternseparation-main (1).zip file_size: 332990101 relation: main_file success: 1 file_date_updated: 2021-10-08T08:46:04Z has_accepted_license: '1' license: https://opensource.org/licenses/GPL-3.0 month: '12' oa: 1 publisher: IST Austria related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/spot-the-difference/ record: - id: '10816' relation: used_for_analysis_in status: public status: public title: How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network tmp: legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html name: GNU General Public License 3.0 short: GPL 3.0 type: software user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '10077' abstract: - lang: eng text: Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain. acknowledgement: We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award. article_processing_charge: No author: - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin citation: ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602 apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602 chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602. ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory. ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602. mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602. short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.). date_created: 2021-10-04T06:23:34Z date_published: 2021-09-29T00:00:00Z date_updated: 2024-03-27T23:30:16Z day: '29' department: - _id: GradSch - _id: JoCs - _id: GaTk doi: 10.1101/2021.09.28.460602 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2021.09.28.460602 month: '09' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory related_material: record: - id: '11932' relation: dissertation_contains status: public status: public title: The structure of hippocampal CA1 interactions optimizes spatial coding across experience 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9250' abstract: - lang: eng text: Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate. acknowledged_ssus: - _id: M-Shop acknowledgement: S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements. article_processing_charge: No article_type: original author: - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Andreas full_name: Windischbacher, Andreas last_name: Windischbacher - first_name: Daniel full_name: Mijailovic, Daniel last_name: Mijailovic - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Egbert full_name: Zojer, Egbert last_name: Zojer - first_name: Sergio full_name: Brutti, Sergio last_name: Brutti - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 2021;13(5):465-471. doi:10.1038/s41557-021-00643-z apa: Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-021-00643-z chicago: Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z. ieee: Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021. ista: Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471. mla: Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z. short: Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471. date_created: 2021-03-16T11:12:20Z date_published: 2021-03-15T00:00:00Z date_updated: 2023-09-05T15:34:44Z day: '15' ddc: - '540' department: - _id: StFr doi: 10.1038/s41557-021-00643-z external_id: isi: - '000629296400001' pmid: - '33723377' file: - access_level: open_access checksum: 3ee3f8dd79ed1b7bb0929fce184c8012 content_type: application/pdf creator: dernst date_created: 2021-03-22T11:46:00Z date_updated: 2021-09-16T22:30:03Z embargo: 2021-09-15 file_id: '9276' file_name: 2021_NatureChem_Petit_acceptedVersion.pdf file_size: 1811448 relation: main_file file_date_updated: 2021-09-16T22:30:03Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '5' keyword: - General Chemistry - General Chemical Engineering language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 465-471 pmid: 1 publication: Nature Chemistry publication_identifier: eissn: - 1755-4349 issn: - 1755-4330 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2021' ... --- _id: '9623' abstract: - lang: eng text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n" acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 citation: ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623 apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623 chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623. ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021. ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623. short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021. date_created: 2021-07-01T14:50:17Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-09-07T13:33:27Z ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:9623 file: - access_level: closed checksum: e039225a47ef32666d59bf35ddd30ecf content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: scaballe date_created: 2021-07-01T14:48:54Z date_updated: 2022-07-02T22:30:06Z embargo_to: open_access file_id: '9624' file_name: PhDThesis_SCM.docx file_size: 131946790 relation: source_file - access_level: open_access checksum: dd4d78962ea94ad95e97ca7d9af08f4b content_type: application/pdf creator: scaballe date_created: 2021-07-01T14:46:25Z date_updated: 2022-07-02T22:30:06Z embargo: 2022-07-01 file_id: '9625' file_name: PhDThesis_SCM.pdf file_size: 17094958 relation: main_file file_date_updated: 2022-07-02T22:30:06Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '111' publication_identifier: isbn: - 978-3-99078-012-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9750' relation: part_of_dissertation status: public - id: '9006' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9006' abstract: - lang: eng text: Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species. acknowledgement: We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript. article_processing_charge: No article_type: original author: - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002 apa: Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002 chicago: Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002. ieee: S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021. ista: Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226. mla: Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002. short: S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226. date_created: 2021-01-17T23:01:10Z date_published: 2021-01-25T00:00:00Z date_updated: 2024-03-27T23:30:18Z day: '25' department: - _id: CaHe doi: 10.1016/j.devcel.2020.12.002 external_id: isi: - '000613273900009' pmid: - '33321104' intvolume: ' 56' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2020.12.002 month: '01' oa: 1 oa_version: Published Version page: P213-226 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - '18781551' issn: - '15345807' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '9623' relation: dissertation_contains status: public scopus_import: '1' status: public title: Cytoplasm's got moves type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 56 year: '2021' ... --- _id: '9429' abstract: - lang: eng text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs. acknowledged_ssus: - _id: PreCl acknowledgement: We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27). article_number: '3058' article_processing_charge: No article_type: original author: - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Lena A full_name: Schwarz, Lena A id: 29A8453C-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Zoe full_name: Dobler, Zoe id: D23090A2-9057-11EA-883A-A8396FC7A38F last_name: Dobler - first_name: Emanuele full_name: Cacci, Emanuele last_name: Cacci - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x. ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058. mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x. short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021). date_created: 2021-05-28T11:49:46Z date_published: 2021-05-24T00:00:00Z date_updated: 2024-03-27T23:30:23Z day: '24' ddc: - '572' department: - _id: GaNo - _id: JoDa - _id: FlSc - _id: MiSi - _id: LifeSc - _id: Bio doi: 10.1038/s41467-021-23123-x ec_funded: 1 external_id: isi: - '000658769900010' file: - access_level: open_access checksum: 337e0f7959c35ec959984cacdcb472ba content_type: application/pdf creator: kschuh date_created: 2021-05-28T12:39:43Z date_updated: 2021-05-28T12:39:43Z file_id: '9430' file_name: 2021_NatureCommunications_Morandell.pdf file_size: 9358599 relation: main_file success: 1 file_date_updated: 2021-05-28T12:39:43Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 05A0D778-7A3F-11EA-A408-12923DDC885E grant_number: F07807 name: Neural stem cells in autism and epilepsy - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: press_release url: https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/ record: - id: '7800' relation: earlier_version status: public - id: '12401' relation: dissertation_contains status: public status: public title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10058' abstract: - lang: eng text: 'Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.' acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 citation: ama: Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058 apa: Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058 chicago: Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058. ieee: D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021. ista: Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. mla: Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058. short: D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021. date_created: 2021-09-30T07:53:49Z date_published: 2021-10-05T00:00:00Z date_updated: 2023-09-08T11:41:08Z day: '05' ddc: - '621' - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:10058 file: - access_level: closed checksum: ad6bcb24083ed7c02baaf1885c9ea3d5 content_type: application/x-zip-compressed creator: djirovec date_created: 2021-09-30T14:29:14Z date_updated: 2022-12-20T23:30:07Z embargo_to: open_access file_id: '10061' file_name: PHD_Thesis_Jirovec_Source.zip file_size: 32397600 relation: source_file - access_level: open_access checksum: 5fbe08d4f66d1153e04c47971538fae8 content_type: application/pdf creator: djirovec date_created: 2021-10-05T07:56:49Z date_updated: 2022-12-20T23:30:07Z embargo: 2022-10-06 file_id: '10087' file_name: PHD_Thesis_pdfa2b_1.pdf file_size: 26910829 relation: main_file file_date_updated: 2022-12-20T23:30:07Z has_accepted_license: '1' keyword: - qubits - quantum computing - holes language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '151' project: - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8831' relation: part_of_dissertation status: public - id: '10065' relation: part_of_dissertation status: public - id: '10066' relation: part_of_dissertation status: public - id: '8909' relation: part_of_dissertation status: public - id: '5816' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '8909' abstract: - lang: eng text: Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant. article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Andrea C full_name: Hofmann, Andrea C id: 340F461A-F248-11E8-B48F-1D18A9856A87 last_name: Hofmann - first_name: Andrea full_name: Ballabio, Andrea last_name: Ballabio - first_name: Philipp M. full_name: Mutter, Philipp M. last_name: Mutter - first_name: Giulio full_name: Tavani, Giulio last_name: Tavani - first_name: Marc full_name: Botifoll, Marc last_name: Botifoll - first_name: Alessandro full_name: Crippa, Alessandro id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425 last_name: Crippa orcid: 0000-0002-2968-611X - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Oliver full_name: Sagi, Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - first_name: Frederico full_name: Martins, Frederico id: 38F80F9A-1CB8-11EA-BC76-B49B3DDC885E last_name: Martins orcid: 0000-0003-2668-2401 - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Maksim full_name: Borovkov, Maksim id: 2ac7a0a2-3562-11eb-9256-fbd18ea55087 last_name: Borovkov - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2 apa: Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2 chicago: Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2. ieee: D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021. ista: Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112. mla: Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2. short: D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112. date_created: 2020-12-02T10:50:47Z date_published: 2021-08-01T00:00:00Z date_updated: 2024-03-27T23:30:26Z day: '01' department: - _id: GeKa - _id: NanoFab - _id: GradSch doi: 10.1038/s41563-021-01022-2 ec_funded: 1 external_id: arxiv: - '2011.13755' isi: - '000657596400001' intvolume: ' 20' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2011.13755 month: '08' oa: 1 oa_version: Preprint page: 1106–1112 project: - _id: 26A151DA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '844511' name: Majorana bound states in Ge/SiGe heterostructures - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices publication: Nature Materials publication_identifier: eissn: - 1476-4660 issn: - 1476-1122 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/quantum-computing-with-holes/ record: - id: '9323' relation: research_data status: public - id: '10058' relation: dissertation_contains status: public scopus_import: '1' status: public title: A singlet triplet hole spin qubit in planar Ge type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2021' ... --- _id: '9397' abstract: - lang: eng text: Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev citation: ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397 apa: Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397 chicago: Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397. ieee: K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021. ista: Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. mla: Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397. short: K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021. date_created: 2021-05-17T12:31:30Z date_published: 2021-05-18T00:00:00Z date_updated: 2023-09-07T13:32:32Z day: '18' ddc: - '571' degree_awarded: PhD department: - _id: CaHe - _id: GradSch doi: 10.15479/at:ista:9397 file: - access_level: closed checksum: 7f98532f5324a0b2f3fa8de2967baa19 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: khuljev date_created: 2021-05-17T12:29:12Z date_updated: 2022-05-21T22:30:04Z embargo_to: open_access file_id: '9398' file_name: KHuljev_Thesis_corrections.docx file_size: 47799741 relation: source_file - access_level: open_access checksum: bf512f8a1e572a543778fc4b227c01ba content_type: application/pdf creator: khuljev date_created: 2021-05-18T14:50:28Z date_updated: 2022-05-21T22:30:04Z embargo: 2022-05-20 file_id: '9401' file_name: new_KHuljev_Thesis_corrections.pdf file_size: 16542131 relation: main_file file_date_updated: 2022-05-21T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '101' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10066' abstract: - lang: eng text: The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning. acknowledged_ssus: - _id: NanoFab acknowledgement: "We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations." article_number: '2107.12975' article_processing_charge: No author: - first_name: B. full_name: Severin, B. last_name: Severin - first_name: D. T. full_name: Lennon, D. T. last_name: Lennon - first_name: L. C. full_name: Camenzind, L. C. last_name: Camenzind - first_name: F. full_name: Vigneau, F. last_name: Vigneau - first_name: F. full_name: Fedele, F. last_name: Fedele - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: A. full_name: Ballabio, A. last_name: Ballabio - first_name: D. full_name: Chrastina, D. last_name: Chrastina - first_name: G. full_name: Isella, G. last_name: Isella - first_name: M. de full_name: Kruijf, M. de last_name: Kruijf - first_name: M. J. full_name: Carballido, M. J. last_name: Carballido - first_name: S. full_name: Svab, S. last_name: Svab - first_name: A. V. full_name: Kuhlmann, A. V. last_name: Kuhlmann - first_name: F. R. full_name: Braakman, F. R. last_name: Braakman - first_name: S. full_name: Geyer, S. last_name: Geyer - first_name: F. N. M. full_name: Froning, F. N. M. last_name: Froning - first_name: H. full_name: Moon, H. last_name: Moon - first_name: M. A. full_name: Osborne, M. A. last_name: Osborne - first_name: D. full_name: Sejdinovic, D. last_name: Sejdinovic - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X - first_name: D. M. full_name: Zumbühl, D. M. last_name: Zumbühl - first_name: G. A. D. full_name: Briggs, G. A. D. last_name: Briggs - first_name: N. full_name: Ares, N. last_name: Ares citation: ama: Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975 apa: Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. https://doi.org/10.48550/arXiv.2107.12975 chicago: Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975. ieee: B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” arXiv. . ista: Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975. mla: Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975. short: B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.). date_created: 2021-10-01T12:40:22Z date_published: 2021-07-27T00:00:00Z date_updated: 2024-03-27T23:30:26Z day: '27' department: - _id: GeKa doi: 10.48550/arXiv.2107.12975 external_id: arxiv: - '2107.12975' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2107.12975 month: '07' oa: 1 oa_version: Preprint project: - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells publication: arXiv publication_status: submitted related_material: record: - id: '10058' relation: dissertation_contains status: public status: public title: Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9437' abstract: - lang: eng text: The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation. acknowledgement: We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik. article_number: e68274 article_processing_charge: No article_type: original author: - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Diego full_name: Fernández-Fernández, Diego last_name: Fernández-Fernández - first_name: Thorsten full_name: Fritzius, Thorsten last_name: Fritzius - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst - first_name: Hüseyin C full_name: Önal, Hüseyin C id: 4659D740-F248-11E8-B48F-1D18A9856A87 last_name: Önal orcid: 0000-0002-2771-2011 - first_name: Jacqueline-Claire full_name: Montanaro-Punzengruber, Jacqueline-Claire id: 3786AB44-F248-11E8-B48F-1D18A9856A87 last_name: Montanaro-Punzengruber - first_name: Martin full_name: Gassmann, Martin last_name: Gassmann - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Akos full_name: Kulik, Akos last_name: Kulik - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 citation: ama: Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274 apa: Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274 chicago: Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274. ieee: P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274. mla: Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274. short: P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021). date_created: 2021-05-30T22:01:23Z date_published: 2021-04-29T00:00:00Z date_updated: 2024-03-27T23:30:30Z day: '29' ddc: - '570' department: - _id: RySh - _id: PeJo doi: 10.7554/ELIFE.68274 ec_funded: 1 external_id: isi: - '000651761700001' file: - access_level: open_access checksum: 6ebcb79999f889766f7cd79ee134ad28 content_type: application/pdf creator: cziletti date_created: 2021-05-31T09:43:09Z date_updated: 2021-05-31T09:43:09Z file_id: '9440' file_name: 2021_eLife_Bhandari.pdf file_size: 8174719 relation: main_file success: 1 file_date_updated: 2021-05-31T09:43:09Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: link: - relation: earlier_version url: https://doi.org/10.1101/2020.04.16.045112 record: - id: '9562' relation: dissertation_contains status: public scopus_import: '1' status: public title: GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '9562' abstract: - lang: eng text: Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry. acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst citation: ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562' apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562' chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.' ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.' ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.' mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.' short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.' date_created: 2021-06-17T14:10:47Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-09-11T12:55:53Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:9562 file: - access_level: open_access checksum: 659df5518db495f679cb1df9e9bd1d94 content_type: application/pdf creator: dkleindienst date_created: 2021-06-17T14:03:14Z date_updated: 2022-07-02T22:30:04Z embargo: 2022-07-01 file_id: '9563' file_name: Thesis.pdf file_size: 77299142 relation: main_file - access_level: closed checksum: 3bcf63a2b19e5b6663be051bea332748 content_type: application/zip creator: dkleindienst date_created: 2021-06-17T14:04:30Z date_updated: 2022-07-02T22:30:04Z embargo_to: open_access file_id: '9564' file_name: Thesis_source.zip file_size: 369804895 relation: source_file file_date_updated: 2022-07-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '124' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9756' relation: part_of_dissertation status: public - id: '9437' relation: part_of_dissertation status: public - id: '8532' relation: part_of_dissertation status: public - id: '612' relation: part_of_dissertation status: public status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '8934' abstract: - lang: eng text: "In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades." acknowledgement: 'The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934 apa: Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934 chicago: Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934. ieee: A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021. ista: Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. mla: Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934. short: A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021. date_created: 2020-12-10T12:17:07Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-09-22T10:03:21Z day: '01' ddc: - '005' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/AT:ISTA:8934 file: - access_level: open_access checksum: d1b9db3725aed34dadd81274aeb9426c content_type: application/pdf creator: akafshda date_created: 2020-12-22T20:08:44Z date_updated: 2021-12-23T23:30:04Z embargo: 2021-12-22 file_id: '8969' file_name: Thesis-pdfa.pdf file_size: 5251507 relation: main_file - access_level: closed checksum: 1661df7b393e6866d2460eba3c905130 content_type: application/zip creator: akafshda date_created: 2020-12-22T20:08:50Z date_updated: 2021-03-04T23:30:04Z embargo_to: open_access file_id: '8970' file_name: source.zip file_size: 10636756 relation: source_file file_date_updated: 2021-12-23T23:30:04Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/publicdomain/zero/1.0/ month: '01' oa: 1 oa_version: Published Version page: '278' project: - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1386' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '311' relation: part_of_dissertation status: public - id: '6056' relation: part_of_dissertation status: public - id: '6380' relation: part_of_dissertation status: public - id: '639' relation: part_of_dissertation status: public - id: '66' relation: part_of_dissertation status: public - id: '6780' relation: part_of_dissertation status: public - id: '6918' relation: part_of_dissertation status: public - id: '7810' relation: part_of_dissertation status: public - id: '6175' relation: part_of_dissertation status: public - id: '6378' relation: part_of_dissertation status: public - id: '6490' relation: part_of_dissertation status: public - id: '7014' relation: part_of_dissertation status: public - id: '8089' relation: part_of_dissertation status: public - id: '8728' relation: part_of_dissertation status: public - id: '7158' relation: part_of_dissertation status: public - id: '5977' relation: part_of_dissertation status: public - id: '6009' relation: part_of_dissertation status: public - id: '6340' relation: part_of_dissertation status: public - id: '949' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Parameterized and algebro-geometric advances in static program analysis tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10307' abstract: - lang: eng text: Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response. acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: PreCl - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X citation: ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307 apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307 chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307. ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021. ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307. short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021. date_created: 2021-11-18T15:05:06Z date_published: 2021-11-18T00:00:00Z date_updated: 2023-09-07T13:34:38Z day: '18' ddc: - '570' degree_awarded: PhD department: - _id: MiSi - _id: CaGu - _id: GradSch doi: 10.15479/at:ista:10307 file: - access_level: open_access checksum: b39c9e0ef18d0484d537a67551effd02 content_type: application/pdf creator: ktomasek date_created: 2021-11-18T15:07:31Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-11-18 file_id: '10308' file_name: ThesisTomasekKathrin.pdf file_size: 13266088 relation: main_file - access_level: closed checksum: c0c440ee9e5ef1102a518a4f9f023e7c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ktomasek date_created: 2021-11-18T15:07:46Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10309' file_name: ThesisTomasekKathrin.docx file_size: 7539509 relation: source_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '73' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10316' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Pathogenic Escherichia coli hijack the host immune response type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10316' abstract: - lang: eng text: A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease. acknowledged_ssus: - _id: Bio - _id: PreCl - _id: EM-Fac acknowledgement: We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S. article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Ivana full_name: Glatzová, Ivana id: 727b3c7d-4939-11ec-89b3-b9b0750ab74d last_name: Glatzová - first_name: Michael S. full_name: Lukesch, Michael S. last_name: Lukesch - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X citation: ama: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770 apa: Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770 chicago: Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770. ieee: K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory. ista: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770. mla: Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770. short: K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.). date_created: 2021-11-19T12:24:16Z date_published: 2021-10-18T00:00:00Z date_updated: 2024-03-27T23:30:35Z day: '18' department: - _id: CaGu - _id: MiSi doi: 10.1101/2021.10.18.464770 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1 month: '10' oa: 1 oa_version: Preprint project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 26018E70-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29911 name: Mechanical adaptation of lamellipodial actin publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory related_material: record: - id: '11843' relation: later_version status: public - id: '10307' relation: dissertation_contains status: public status: public title: Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14 type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9010' abstract: - lang: eng text: Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments. acknowledged_ssus: - _id: Bio acknowledgement: 'We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F' article_number: e106862 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Marco full_name: Marconi, Marco last_name: Marconi - first_name: Andrea full_name: Vega, Andrea last_name: Vega - first_name: Jose full_name: O’Brien, Jose last_name: O’Brien - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 - first_name: Livio full_name: Antonielli, Livio last_name: Antonielli - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Christina full_name: Artner, Christina id: 45DF286A-F248-11E8-B48F-1D18A9856A87 last_name: Artner - first_name: Eleonore full_name: Bouguyon, Eleonore last_name: Bouguyon - first_name: Alain full_name: Gojon, Alain last_name: Gojon - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Rodrigo A. full_name: Gutiérrez, Rodrigo A. last_name: Gutiérrez - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862 apa: Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862 chicago: Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862. ieee: K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021. ista: Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862. mla: Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862. short: K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021). date_created: 2021-01-17T23:01:12Z date_published: 2021-02-01T00:00:00Z date_updated: 2024-03-27T23:30:39Z day: '01' ddc: - '580' department: - _id: JiFr - _id: EvBe doi: 10.15252/embj.2020106862 external_id: isi: - '000604645600001' pmid: - ' 33399250' file: - access_level: open_access checksum: dc55c900f3b061d6c2790b8813d759a3 content_type: application/pdf creator: dernst date_created: 2021-02-11T12:28:29Z date_updated: 2021-02-11T12:28:29Z file_id: '9110' file_name: 2021_Embo_Otvos.pdf file_size: 2358617 relation: main_file success: 1 file_date_updated: 2021-02-11T12:28:29Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development - _id: 2685A872-B435-11E9-9278-68D0E5697425 name: Hormonal regulation of plant adaptive responses to environmental signals - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: EMBO Journal publication_identifier: eissn: - '14602075' issn: - '02614189' publication_status: published publisher: Embo Press quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/ record: - id: '10303' relation: dissertation_contains status: public scopus_import: '1' status: public title: Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9913' abstract: - lang: eng text: Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate. acknowledgement: This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC). article_number: e51813 article_processing_charge: Yes article_type: original author: - first_name: Andrea full_name: Vega, Andrea last_name: Vega - first_name: Isabel full_name: Fredes, Isabel last_name: Fredes - first_name: José full_name: O’Brien, José last_name: O’Brien - first_name: Zhouxin full_name: Shen, Zhouxin last_name: Shen - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Steven P. full_name: Briggs, Steven P. last_name: Briggs - first_name: Rodrigo A. full_name: Gutiérrez, Rodrigo A. last_name: Gutiérrez citation: ama: Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813 apa: Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813 chicago: Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813. ieee: A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021. ista: Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813. mla: Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813. short: A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021). date_created: 2021-08-15T22:01:30Z date_published: 2021-09-06T00:00:00Z date_updated: 2024-03-27T23:30:39Z day: '06' ddc: - '580' department: - _id: EvBe - _id: GradSch doi: 10.15252/embr.202051813 external_id: isi: - '000681754200001' pmid: - '34357701 ' file: - access_level: open_access checksum: 750de03dc3b715c37090126c1548ba13 content_type: application/pdf creator: cchlebak date_created: 2021-10-05T13:36:42Z date_updated: 2021-10-05T13:36:42Z file_id: '10090' file_name: 2021_EmboR_Vega.pdf file_size: 3144854 relation: main_file success: 1 file_date_updated: 2021-10-05T13:36:42Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '10303' relation: dissertation_contains status: public scopus_import: '1' status: public title: Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2021' ... --- _id: '10303' abstract: - lang: eng text: 'Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 citation: ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303 apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303 chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303. ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021. ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303. short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021. date_created: 2021-11-18T11:20:59Z date_published: 2021-11-22T00:00:00Z date_updated: 2023-09-19T14:42:45Z day: '22' ddc: - '580' - '581' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10303 file: - access_level: open_access checksum: dea38b98aa4da1cea03dcd0f10862818 content_type: application/pdf creator: rabualia date_created: 2021-11-22T14:48:21Z date_updated: 2022-12-20T23:30:06Z embargo: 2022-11-23 file_id: '10331' file_name: AbualiaPhDthesisfinalv3.pdf file_size: 28005730 relation: main_file - access_level: closed checksum: 4cd62da5ec5ba4c32e61f0f6d9e61920 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rabualia date_created: 2021-11-22T14:48:34Z date_updated: 2022-12-20T23:30:06Z embargo_to: open_access file_id: '10332' file_name: AbualiaPhDthesisfinalv3.docx file_size: 62841883 relation: source_file file_date_updated: 2022-12-20T23:30:06Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '139' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9010' relation: part_of_dissertation status: public - id: '9913' relation: part_of_dissertation status: public - id: '47' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Role of hormones in nitrate regulated growth 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9962' abstract: - lang: eng text: The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen citation: ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962 apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962 chicago: Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962. ieee: A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021. ista: Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962. short: A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021. date_created: 2021-08-29T12:36:50Z date_published: 2021-09-02T00:00:00Z date_updated: 2023-09-22T09:58:30Z day: '02' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/at:ista:9962 file: - access_level: closed checksum: 66b56f5b988b233dc66a4f4b4fb2cdfe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ahansen date_created: 2021-08-30T09:17:39Z date_updated: 2022-09-03T22:30:04Z embargo_to: open_access file_id: '9971' file_name: Thesis_Hansen.docx file_size: 10629190 relation: source_file - access_level: open_access checksum: 204fa40321a1c6289b68c473634c4bf3 content_type: application/pdf creator: ahansen date_created: 2021-08-30T09:29:44Z date_updated: 2022-09-03T22:30:04Z embargo: 2022-09-02 file_id: '9972' file_name: Thesis_Hansen_PDFA-1a.pdf file_size: 13457469 relation: main_file file_date_updated: 2022-09-03T22:30:04Z has_accepted_license: '1' keyword: - Neuronal migration - Non-cell-autonomous - Cell-autonomous - Neurodevelopmental disease language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '182' project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular Mechanisms of Radial Neuronal Migration publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8569' relation: part_of_dissertation status: public - id: '960' relation: part_of_dissertation status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9428' abstract: - lang: eng text: Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology. acknowledgement: We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015. article_processing_charge: No article_type: review author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić citation: ama: Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2 apa: Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2 chicago: Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2. ieee: M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021. ista: Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685. mla: Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2. short: M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685. date_created: 2021-05-28T09:03:50Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-10-18T08:20:59Z day: '01' ddc: - '539' department: - _id: MaSe doi: 10.1038/s41567-021-01230-2 ec_funded: 1 external_id: arxiv: - '2011.09486' isi: - '000655563800002' file: - access_level: open_access checksum: 316ed42ea1b42b0f1a3025bb476266fc content_type: application/pdf creator: patrickd date_created: 2021-09-20T09:27:43Z date_updated: 2021-12-02T23:30:03Z embargo: 2021-12-01 file_id: '10026' file_name: RevisedQMBSreview.pdf file_size: 10028836 relation: main_file file_date_updated: 2021-12-02T23:30:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Preprint page: 675–685 project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Nature Physics publication_identifier: eissn: - 1745-2481 publication_status: published publisher: Nature Research quality_controlled: '1' status: public title: Quantum many-body scars and weak breaking of ergodicity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2021' ... --- _id: '8931' abstract: - lang: eng text: "Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č. article_number: '110750' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Markéta full_name: Pernisová, Markéta last_name: Pernisová - first_name: Géraldine full_name: Brunoud, Géraldine last_name: Brunoud - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Jaroslav full_name: Michalko, Jaroslav id: 483727CA-F248-11E8-B48F-1D18A9856A87 last_name: Michalko - first_name: Zlata full_name: Pavlovicova, Zlata last_name: Pavlovicova - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Milada full_name: Čovanová, Milada last_name: Čovanová - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Teva full_name: Vernoux, Teva last_name: Vernoux - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750 apa: Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750 chicago: Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750. ieee: Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021. ista: Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750. mla: Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750. short: Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021). date_created: 2020-12-09T14:48:28Z date_published: 2021-02-01T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '01' ddc: - '580' department: - _id: JiFr - _id: Bio doi: 10.1016/j.plantsci.2020.110750 ec_funded: 1 external_id: isi: - '000614154500001' pmid: - '33487339' file: - access_level: open_access checksum: a7f2562bdca62d67dfa88e271b62a629 content_type: application/pdf creator: dernst date_created: 2021-02-04T07:49:25Z date_updated: 2021-02-04T07:49:25Z file_id: '9083' file_name: 2021_PlantScience_Gelova.pdf file_size: 12563728 relation: main_file success: 1 file_date_updated: 2021-02-04T07:49:25Z has_accepted_license: '1' intvolume: ' 303' isi: 1 keyword: - Agronomy and Crop Science - Plant Science - Genetics - General Medicine language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Plant Science publication_identifier: issn: - 0168-9452 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '11626' relation: dissertation_contains status: public - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: Developmental roles of auxin binding protein 1 in Arabidopsis thaliana 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 303 year: '2021' ... --- _id: '9287' abstract: - lang: eng text: "The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. " acknowledged_ssus: - _id: M-Shop - _id: Bio acknowledgement: 'We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union''s Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: E full_name: Himschoot, E last_name: Himschoot - first_name: R full_name: Wang, R last_name: Wang - first_name: S full_name: Vanneste, S last_name: Vanneste - first_name: J full_name: Sánchez-Simarro, J last_name: Sánchez-Simarro - first_name: F full_name: Aniento, F last_name: Aniento - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 2021;186(2):1122–1142. doi:10.1093/plphys/kiab134 apa: Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiab134 chicago: Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134. ieee: M. Narasimhan et al., “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021. ista: Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142. mla: Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134. short: M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142. date_created: 2021-03-26T12:08:38Z date_published: 2021-06-01T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/plphys/kiab134 ec_funded: 1 external_id: isi: - '000671555900031' pmid: - '33734402' file: - access_level: open_access checksum: 532bb9469d3b665907f06df8c383eade content_type: application/pdf creator: cziletti date_created: 2021-11-11T15:07:51Z date_updated: 2021-11-11T15:07:51Z file_id: '10273' file_name: 2021_PlantPhysio_Narasimhan.pdf file_size: 2289127 relation: main_file success: 1 file_date_updated: 2021-11-11T15:07:51Z has_accepted_license: '1' intvolume: ' 186' isi: 1 issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1122–1142 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: 10.1093/plphys/kiab380 record: - id: '11626' relation: dissertation_contains status: public - id: '10083' relation: dissertation_contains status: public status: public title: Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 186 year: '2021' ... --- _id: '10083' abstract: - lang: eng text: "Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lanxin full_name: Li, Lanxin last_name: Li citation: ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083 apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083 chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083. ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021. ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083. short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021. date_created: 2021-10-04T13:33:10Z date_published: 2021-10-06T00:00:00Z date_updated: 2023-10-31T19:30:02Z day: '06' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:10083 ec_funded: 1 file: - access_level: open_access checksum: 3b2f55b3b8ae05337a0dcc1cd8595b10 content_type: application/pdf creator: cchlebak date_created: 2021-10-14T08:00:07Z date_updated: 2022-12-20T23:30:03Z embargo: 2022-10-14 file_id: '10138' file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf file_size: 8616142 relation: main_file - access_level: closed checksum: f23ed258ca894f6aabf58b0c128bf242 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2021-10-14T08:00:13Z date_updated: 2022-12-20T23:30:03Z embargo_to: open_access file_id: '10139' file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014.docx file_size: 15058499 relation: source_file file_date_updated: 2022-12-20T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '442' relation: part_of_dissertation status: public - id: '8931' relation: part_of_dissertation status: public - id: '9287' relation: part_of_dissertation status: public - id: '8283' relation: part_of_dissertation status: public - id: '8986' relation: part_of_dissertation status: public - id: '6627' relation: part_of_dissertation status: public - id: '10095' relation: part_of_dissertation status: public - id: '10015' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Rapid cell growth regulation in Arabidopsis 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10015' abstract: - lang: eng text: "Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip." acknowledgement: We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF). alternative_title: - Protein Phosphorylation and Cell Signaling in Plants article_number: '1665 ' article_processing_charge: Yes article_type: original author: - first_name: N full_name: Nikonorova, N last_name: Nikonorova - first_name: E full_name: Murphy, E last_name: Murphy - first_name: CF full_name: Fonseca de Lima, CF last_name: Fonseca de Lima - first_name: S full_name: Zhu, S last_name: Zhu - first_name: B full_name: van de Cotte, B last_name: van de Cotte - first_name: LD full_name: Vu, LD last_name: Vu - first_name: D full_name: Balcerowicz, D last_name: Balcerowicz - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: X full_name: Kong, X last_name: Kong - first_name: G full_name: De Rop, G last_name: De Rop - first_name: T full_name: Beeckman, T last_name: Beeckman - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: K full_name: Vissenberg, K last_name: Vissenberg - first_name: PC full_name: Morris, PC last_name: Morris - first_name: Z full_name: Ding, Z last_name: Ding - first_name: I full_name: De Smet, I last_name: De Smet citation: ama: Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665 apa: Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. MDPI. https://doi.org/10.3390/cells10071665 chicago: Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071665. ieee: N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” Cells, vol. 10. MDPI, 2021. ista: Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665. mla: Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells, vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665. short: N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021). date_created: 2021-09-14T11:36:20Z date_published: 2021-07-02T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '02' ddc: - '575' department: - _id: JiFr doi: 10.3390/cells10071665 ec_funded: 1 external_id: isi: - '000676604700001' pmid: - '34359847' file: - access_level: open_access checksum: 2a9f534b9c2200e72e2cde95afaf4eed content_type: application/pdf creator: cchlebak date_created: 2021-09-16T09:07:06Z date_updated: 2021-09-16T09:07:06Z file_id: '10021' file_name: 2021_Cells_Nikonorova.pdf file_size: 2667848 relation: main_file success: 1 file_date_updated: 2021-09-16T09:07:06Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - primary root - (phospho)proteomics - auxin - (receptor) kinase language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Cells publication_identifier: issn: - 2073-4409 publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public status: public title: The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2021' ... --- _id: '10095' abstract: - lang: eng text: Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment. acknowledged_ssus: - _id: LifeSc - _id: M-Shop - _id: Bio acknowledgement: We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C. article_number: '266395' article_processing_charge: No author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Mark full_name: Roosjen, Mark last_name: Roosjen - first_name: Koji full_name: Takahashi, Koji last_name: Takahashi - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Jian full_name: Chen, Jian last_name: Chen - first_name: Lana full_name: Shabala, Lana last_name: Shabala - first_name: Wouter full_name: Smet, Wouter last_name: Smet - first_name: Hong full_name: Ren, Hong last_name: Ren - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Sergey full_name: Shabala, Sergey last_name: Shabala - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Toshinori full_name: Kinoshita, Toshinori last_name: Kinoshita - first_name: William M. full_name: Gray, William M. last_name: Gray - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3 apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3 chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3. ieee: L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. . ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395. mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3. short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.). date_created: 2021-10-06T08:56:22Z date_published: 2021-09-09T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '09' department: - _id: JiFr - _id: NanoFab doi: 10.21203/rs.3.rs-266395/v3 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.21203/rs.3.rs-266395/v3 month: '09' oa: 1 oa_version: Preprint project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Research Square publication_identifier: issn: - 2693-5015 publication_status: accepted related_material: record: - id: '10223' relation: later_version status: public - id: '10083' relation: dissertation_contains status: public status: public title: Cell surface and intracellular auxin signalling for H+-fluxes in root growth 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: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '10293' abstract: - lang: eng text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 citation: ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293 apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293 chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293. ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021. ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293. short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021. date_created: 2021-11-15T17:12:57Z date_published: 2021-11-17T00:00:00Z date_updated: 2023-11-07T08:28:29Z day: '17' ddc: - '519' - '576' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/at:ista:10293 ec_funded: 1 file: - access_level: closed checksum: 86a05b430756ca12ae8107b6e6f3c1e5 content_type: application/zip creator: lschmid date_created: 2021-11-18T12:41:46Z date_updated: 2022-12-20T23:30:08Z embargo_to: open_access file_id: '10305' file_name: submission_new.zip file_size: 29703124 relation: source_file - access_level: open_access checksum: d940af042e94660c6b6a7b4f0b184d47 content_type: application/pdf creator: lschmid date_created: 2021-11-18T12:59:15Z date_updated: 2022-12-20T23:30:08Z embargo: 2022-10-18 file_id: '10306' file_name: thesis_new_upload.pdf file_size: 8320985 relation: main_file file_date_updated: 2022-12-20T23:30:08Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '171' project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9997' relation: part_of_dissertation status: public - id: '2' relation: part_of_dissertation status: public - id: '9402' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Evolution of cooperation via (in)direct reciprocity under imperfect information type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9997' abstract: - lang: eng text: Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms. acknowledgement: 'This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).' article_number: '17443' article_processing_charge: Yes article_type: original author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Pouya full_name: Shati, Pouya last_name: Shati - first_name: Christian full_name: Hilbe, Christian last_name: Hilbe - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1 apa: Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1 chicago: Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1. ieee: L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021. ista: Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443. mla: Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1. short: L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021). date_created: 2021-09-11T16:22:02Z date_published: 2021-08-31T00:00:00Z date_updated: 2024-03-27T23:30:44Z day: '31' ddc: - '003' department: - _id: GradSch - _id: KrCh doi: 10.1038/s41598-021-96932-1 ec_funded: 1 external_id: isi: - '000692406400018' pmid: - '34465830' file: - access_level: open_access checksum: 19df8816cf958b272b85841565c73182 content_type: application/pdf creator: cchlebak date_created: 2021-09-13T10:31:21Z date_updated: 2021-09-13T10:31:21Z file_id: '10006' file_name: 2021_ScientificReports_Schmid.pdf file_size: 2424943 relation: main_file success: 1 file_date_updated: 2021-09-13T10:31:21Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' keyword: - Multidisciplinary language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Scientific Reports publication_identifier: eissn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10293' relation: dissertation_contains status: public status: public title: The evolution of indirect reciprocity under action and assessment generosity 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '9402' abstract: - lang: eng text: Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability. acknowledgement: 'This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' article_processing_charge: No article_type: original author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8 apa: Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8 chicago: Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8. ieee: L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021. ista: Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302. mla: Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8. short: L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302. date_created: 2021-05-18T16:56:57Z date_published: 2021-05-13T00:00:00Z date_updated: 2024-03-27T23:30:44Z day: '13' ddc: - '000' department: - _id: KrCh - _id: GradSch doi: 10.1038/s41562-021-01114-8 ec_funded: 1 external_id: isi: - '000650304000002' pmid: - '33986519' file: - access_level: open_access checksum: 34f55e173f90dc1dab731063458ac780 content_type: application/pdf creator: dernst date_created: 2023-11-07T08:27:23Z date_updated: 2023-11-07T08:27:23Z file_id: '14496' file_name: 2021_NatureHumanBehaviour_Schmid_accepted.pdf file_size: 5232761 relation: main_file success: 1 file_date_updated: 2023-11-07T08:27:23Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '10' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 1292–1302 pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Nature Human Behaviour publication_identifier: eissn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/the-emergence-of-cooperation/ record: - id: '10293' relation: dissertation_contains status: public scopus_import: '1' status: public title: A unified framework of direct and indirect reciprocity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2021' ... --- _id: '9817' abstract: - lang: eng text: Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements. acknowledgement: "We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n" article_number: '126' article_processing_charge: No article_type: original author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459800 apa: 'Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves. ACM Transactions on Graphics. Virtual: Association for Computing Machinery. https://doi.org/10.1145/3450626.3459800' chicago: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459800. ieee: C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021. ista: Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126. mla: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459800. short: C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021). conference: end_date: 2021-08-13 location: Virtual name: 'SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2021-08-09 date_created: 2021-08-08T22:01:26Z date_published: 2021-07-19T00:00:00Z date_updated: 2024-03-27T23:30:45Z day: '19' ddc: - '516' department: - _id: BeBi doi: 10.1145/3450626.3459800 ec_funded: 1 external_id: isi: - '000674930900091' file: - access_level: open_access checksum: 7e5d08ce46b0451b3102eacd3d00f85f content_type: application/pdf creator: chafner date_created: 2021-10-18T10:42:15Z date_updated: 2021-10-18T10:42:15Z file_id: '10150' file_name: elastic-curves-paper.pdf file_size: 17064290 relation: main_file success: 1 - access_level: open_access checksum: 0088643478be7c01a703b5b10767348f content_type: application/pdf creator: chafner date_created: 2021-10-18T10:42:22Z date_updated: 2021-10-18T10:42:22Z file_id: '10151' file_name: elastic-curves-supp.pdf file_size: 547156 relation: supplementary_material file_date_updated: 2021-10-18T10:42:22Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '4' keyword: - Computing methodologies - shape modeling - modeling and simulation - theory of computation - computational geometry - mathematics of computing - mathematical optimization language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/designing-with-elastic-structures/ record: - id: '12897' relation: dissertation_contains status: public scopus_import: '1' status: public title: The design space of plane elastic curves 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10135' abstract: - lang: eng text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hana full_name: Semerádová, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semerádová citation: ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135 apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135 chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135. ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021. ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135. short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021. date_created: 2021-10-13T13:42:48Z date_published: 2021-10-13T00:00:00Z date_updated: 2024-01-25T10:53:29Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10135 file: - access_level: closed checksum: ce7108853e6cec6224f17cd6429b51fe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cziletti date_created: 2021-10-27T07:45:37Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10186' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx file_size: 28508629 relation: source_file - access_level: open_access checksum: 0d7afb846e8e31ec794de47bf44e12ef content_type: application/pdf creator: cziletti date_created: 2021-10-27T07:45:57Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-10-28 file_id: '10187' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf file_size: 10623525 relation: main_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis. publication_identifier: isbn: - 978-3-99078-014-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9728' abstract: - lang: eng text: "Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nishchal full_name: Agrawal, Nishchal id: 469E6004-F248-11E8-B48F-1D18A9856A87 last_name: Agrawal citation: ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728 apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728 chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728. ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021. ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728. short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021. date_created: 2021-07-27T13:40:30Z date_published: 2021-07-29T00:00:00Z date_updated: 2024-02-28T13:14:39Z day: '29' ddc: - '532' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:9728 file: - access_level: closed checksum: 77436be3563a90435024307b1b5ee7e8 content_type: application/x-zip-compressed creator: nagrawal date_created: 2021-07-28T13:32:02Z date_updated: 2022-07-29T22:30:05Z embargo_to: open_access file_id: '9744' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip file_size: 22859658 relation: source_file - access_level: open_access checksum: 72a891d7daba85445c29b868c22575ed content_type: application/pdf creator: nagrawal date_created: 2021-07-28T13:32:05Z date_updated: 2022-07-29T22:30:05Z embargo: 2022-07-28 file_id: '9745' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf file_size: 18658048 relation: main_file file_date_updated: 2022-07-29T22:30:05Z has_accepted_license: '1' keyword: - Drag Reduction - Transition to Turbulence - Multiphase Flows - particle Laden Flows - Complex Flows - Experiments - Fluid Dynamics language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '118' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6189' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Transition to turbulence and drag reduction in particle-laden pipe flows 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10336' abstract: - lang: eng text: Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context. acknowledgement: We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1. article_processing_charge: No article_type: original author: - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098. doi:10.1073/pnas.2007694117 apa: Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117 chicago: Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117. ieee: J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” Proceedings of the National Academy of Sciences, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020. ista: Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098. mla: Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117. short: J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098. date_created: 2021-11-25T15:07:09Z date_published: 2020-12-16T00:00:00Z date_updated: 2021-11-25T15:35:58Z day: '16' doi: 10.1073/pnas.2007694117 extern: '1' external_id: pmid: - '33328273' intvolume: ' 117' issue: '52' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2 month: '12' oa: 1 oa_version: Published Version page: 33090-33098 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Physical mechanisms of amyloid nucleation on fluid membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 117 year: '2020' ... --- _id: '10342' abstract: - lang: eng text: The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across. acknowledgement: 'Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.' article_number: 'eabc4397 ' article_processing_charge: No article_type: original author: - first_name: Xiaohe full_name: Tian, Xiaohe last_name: Tian - first_name: Diana M. full_name: Leite, Diana M. last_name: Leite - first_name: Edoardo full_name: Scarpa, Edoardo last_name: Scarpa - first_name: Sophie full_name: Nyberg, Sophie last_name: Nyberg - first_name: Gavin full_name: Fullstone, Gavin last_name: Fullstone - first_name: Joe full_name: Forth, Joe last_name: Forth - first_name: Diana full_name: Matias, Diana last_name: Matias - first_name: Azzurra full_name: Apriceno, Azzurra last_name: Apriceno - first_name: Alessandro full_name: Poma, Alessandro last_name: Poma - first_name: Aroa full_name: Duro-Castano, Aroa last_name: Duro-Castano - first_name: Manish full_name: Vuyyuru, Manish last_name: Vuyyuru - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Zhongping full_name: Zhang, Zhongping last_name: Zhang - first_name: Pan full_name: Xiang, Pan last_name: Xiang - first_name: Bin full_name: Fang, Bin last_name: Fang - first_name: Yupeng full_name: Tian, Yupeng last_name: Tian - first_name: Lei full_name: Luo, Lei last_name: Luo - first_name: Loris full_name: Rizzello, Loris last_name: Rizzello - first_name: Giuseppe full_name: Battaglia, Giuseppe last_name: Battaglia citation: ama: 'Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 2020;6(48). doi:10.1126/sciadv.abc4397' apa: 'Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abc4397' chicago: 'Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.abc4397.' ieee: 'X. Tian et al., “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” Science Advances, vol. 6, no. 48. American Association for the Advancement of Science, 2020.' ista: 'Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397.' mla: 'Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.abc4397.' short: X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020). date_created: 2021-11-26T06:40:28Z date_published: 2020-11-27T00:00:00Z date_updated: 2021-11-26T07:00:24Z day: '27' ddc: - '611' doi: 10.1126/sciadv.abc4397 extern: '1' external_id: pmid: - '33246953' file: - access_level: open_access checksum: 3ba2eca975930cdb0b1ce1ae876885a7 content_type: application/pdf creator: cchlebak date_created: 2021-11-26T06:50:09Z date_updated: 2021-11-26T06:50:09Z file_id: '10343' file_name: 2020_SciAdv_Tian.pdf file_size: 10381298 relation: main_file success: 1 file_date_updated: 2021-11-26T06:50:09Z has_accepted_license: '1' intvolume: ' 6' issue: '48' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: 'On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias' 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2020' ... --- _id: '10344' abstract: - lang: eng text: In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry. acknowledgement: We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1). article_number: '228101' article_processing_charge: No article_type: original author: - first_name: Joel C. full_name: Forster, Joel C. last_name: Forster - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Manish R. full_name: Vuyyuru, Manish R. last_name: Vuyyuru - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 2020;125(22). doi:10.1103/physrevlett.125.228101 apa: Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., & Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.228101 chicago: Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.228101. ieee: J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” Physical Review Letters, vol. 125, no. 22. American Physical Society, 2020. ista: Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101. mla: Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:10.1103/physrevlett.125.228101. short: J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020). date_created: 2021-11-26T07:10:43Z date_published: 2020-11-23T00:00:00Z date_updated: 2021-11-30T08:33:14Z day: '23' ddc: - '530' doi: 10.1103/physrevlett.125.228101 extern: '1' external_id: pmid: - '33315453' file: - access_level: open_access checksum: fbf2e1415e332d6add90222d60401a1d content_type: application/pdf creator: cchlebak date_created: 2021-11-26T07:16:49Z date_updated: 2021-11-26T07:16:49Z file_id: '10345' file_name: 2020_PhysRevLett_Forster.pdf file_size: 844353 relation: main_file success: 1 file_date_updated: 2021-11-26T07:16:49Z has_accepted_license: '1' intvolume: ' 125' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Exploring the design rules for efficient membrane-reshaping nanostructures 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 125 year: '2020' ... --- _id: '10341' abstract: - lang: eng text: Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes. acknowledgement: We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.). article_processing_charge: No article_type: original author: - first_name: V. E. full_name: Debets, V. E. last_name: Debets - first_name: L. M. C. full_name: Janssen, L. M. C. last_name: Janssen - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 2020;16(47):10628-10639. doi:10.1039/d0sm00712a apa: Debets, V. E., Janssen, L. M. C., & Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm00712a chicago: Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter. Royal Society of Chemistry, 2020. https://doi.org/10.1039/d0sm00712a. ieee: V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” Soft Matter, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020. ista: Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639. mla: Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:10.1039/d0sm00712a. short: V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639. date_created: 2021-11-26T06:29:41Z date_published: 2020-10-06T00:00:00Z date_updated: 2021-11-26T07:00:33Z day: '06' doi: 10.1039/d0sm00712a extern: '1' external_id: pmid: - '33084724' intvolume: ' 16' issue: '47' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1 month: '10' oa: 1 oa_version: Published Version page: 10628-10639 pmid: 1 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 16 year: '2020' ... --- _id: '10346' abstract: - lang: eng text: One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications. acknowledgement: We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1). article_processing_charge: No article_type: original author: - first_name: Anne E. full_name: Hafner, Anne E. last_name: Hafner - first_name: Noemi G. full_name: Gyori, Noemi G. last_name: Gyori - first_name: Ciaran A. full_name: Bench, Ciaran A. last_name: Bench - first_name: Luke K. full_name: Davis, Luke K. last_name: Davis - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 2020;119(9):1791-1799. doi:10.1016/j.bpj.2020.09.013 apa: Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., & Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. Cell Press. https://doi.org/10.1016/j.bpj.2020.09.013 chicago: Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal. Cell Press, 2020. https://doi.org/10.1016/j.bpj.2020.09.013. ieee: A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” Biophysical Journal, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020. ista: Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799. mla: Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” Biophysical Journal, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:10.1016/j.bpj.2020.09.013. short: A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799. date_created: 2021-11-26T07:27:24Z date_published: 2020-09-23T00:00:00Z date_updated: 2021-11-26T07:45:24Z day: '23' doi: 10.1016/j.bpj.2020.09.013 extern: '1' external_id: pmid: - '33049216' intvolume: ' 119' issue: '9' keyword: - biophysics language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1 month: '09' oa: 1 oa_version: Published Version page: 1791-1799 pmid: 1 publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Modeling fibrillogenesis of collagen-mimetic molecules type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 119 year: '2020' ... --- _id: '10350' abstract: - lang: eng text: The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation. acknowledgement: We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL). article_processing_charge: No article_type: original author: - first_name: Alexander J. full_name: Dear, Alexander J. last_name: Dear - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Thomas C. T. full_name: Michaels, Thomas C. T. last_name: Michaels - first_name: Magnus full_name: Kjaergaard, Magnus last_name: Kjaergaard - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: ama: Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 2020;11(24):6236-6247. doi:10.1039/c9sc06501f apa: Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., & Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c9sc06501f chicago: Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science. Royal Society of Chemistry, 2020. https://doi.org/10.1039/c9sc06501f. ieee: A. J. Dear et al., “Identification of on- and off-pathway oligomers in amyloid fibril formation,” Chemical Science, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020. ista: Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247. mla: Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” Chemical Science, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:10.1039/c9sc06501f. short: A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247. date_created: 2021-11-26T09:08:19Z date_published: 2020-06-08T00:00:00Z date_updated: 2021-11-26T11:21:20Z day: '08' doi: 10.1039/c9sc06501f extern: '1' external_id: pmid: - '32953019' intvolume: ' 11' issue: '24' keyword: - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f month: '06' oa: 1 oa_version: Published Version page: 6236-6247 pmid: 1 publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Identification of on- and off-pathway oligomers in amyloid fibril formation tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11 year: '2020' ... --- _id: '10349' abstract: - lang: eng text: Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control. acknowledgement: "We thank the MRC LMCB at UCL for their support; the flow cytometry STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help early on in this project; the entire Baum lab for their input throughout the project; the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D. Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice." article_processing_charge: No article_type: original author: - first_name: Gabriel full_name: Tarrason Risa, Gabriel last_name: Tarrason Risa - first_name: Fredrik full_name: Hurtig, Fredrik last_name: Hurtig - first_name: Sian full_name: Bray, Sian last_name: Bray - first_name: Anne E. full_name: Hafner, Anne E. last_name: Hafner - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Peter full_name: Faull, Peter last_name: Faull - first_name: Colin full_name: Davis, Colin last_name: Davis - first_name: Dimitra full_name: Papatziamou, Dimitra last_name: Papatziamou - first_name: Delyan R. full_name: Mutavchiev, Delyan R. last_name: Mutavchiev - first_name: Catherine full_name: Fan, Catherine last_name: Fan - first_name: Leticia full_name: Meneguello, Leticia last_name: Meneguello - first_name: Andre full_name: Arashiro Pulschen, Andre last_name: Arashiro Pulschen - first_name: Gautam full_name: Dey, Gautam last_name: Dey - first_name: Siân full_name: Culley, Siân last_name: Culley - first_name: Mairi full_name: Kilkenny, Mairi last_name: Kilkenny - first_name: Diorge P. full_name: Souza, Diorge P. last_name: Souza - first_name: Luca full_name: Pellegrini, Luca last_name: Pellegrini - first_name: Robertus A. M. full_name: de Bruin, Robertus A. M. last_name: de Bruin - first_name: Ricardo full_name: Henriques, Ricardo last_name: Henriques - first_name: Ambrosius P. full_name: Snijders, Ambrosius P. last_name: Snijders - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Ann-Christin full_name: Lindås, Ann-Christin last_name: Lindås - first_name: Nicholas P. full_name: Robinson, Nicholas P. last_name: Robinson - first_name: Buzz full_name: Baum, Buzz last_name: Baum citation: ama: Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 2020;369(6504). doi:10.1126/science.aaz2532 apa: Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck, L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaz2532 chicago: Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aaz2532. ieee: G. Tarrason Risa et al., “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” Science, vol. 369, no. 6504. American Association for the Advancement of Science, 2020. ista: Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504). mla: Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” Science, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:10.1126/science.aaz2532. short: G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck, P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A. Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini, R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson, B. Baum, Science 369 (2020). date_created: 2021-11-26T08:21:34Z date_published: 2020-08-07T00:00:00Z date_updated: 2021-11-26T08:58:33Z day: '07' doi: 10.1126/science.aaz2532 extern: '1' external_id: pmid: - '32764038' intvolume: ' 369' issue: '6504' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/774273v1 month: '08' oa: 1 oa_version: Preprint pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: The proteasome controls ESCRT-III–mediated cell division in an archaeon type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 369 year: '2020' ... --- _id: '10347' abstract: - lang: eng text: Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors. acknowledgement: We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969). article_processing_charge: No article_type: original author: - first_name: Thomas C. T. full_name: Michaels, Thomas C. T. last_name: Michaels - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Gabriella T. full_name: Heller, Gabriella T. last_name: Heller - first_name: Samo full_name: Curk, Samo last_name: Curk - first_name: Paolo full_name: Arosio, Paolo last_name: Arosio - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: ama: Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117 apa: Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117 chicago: Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117. ieee: T. C. T. Michaels et al., “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” Proceedings of the National Academy of Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020. ista: Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257. mla: Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:10.1073/pnas.2006684117. short: T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257. date_created: 2021-11-26T07:48:27Z date_published: 2020-09-14T00:00:00Z date_updated: 2021-11-26T08:59:06Z day: '14' doi: 10.1073/pnas.2006684117 extern: '1' external_id: pmid: - '32929030' intvolume: ' 117' issue: '39' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.02.22.960716 month: '09' oa: 1 oa_version: Published Version page: 24251-24257 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 117 year: '2020' ... --- _id: '10351' abstract: - lang: eng text: Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases. acknowledgement: We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969). article_processing_charge: No article_type: original author: - first_name: Thomas C. T. full_name: Michaels, Thomas C. T. last_name: Michaels - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Samo full_name: Curk, Samo last_name: Curk - first_name: Katja full_name: Bernfur, Katja last_name: Bernfur - first_name: Paolo full_name: Arosio, Paolo last_name: Arosio - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Alexander J. full_name: Dear, Alexander J. last_name: Dear - first_name: Samuel I. A. full_name: Cohen, Samuel I. A. last_name: Cohen - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: ama: Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 2020;12(5):445-451. doi:10.1038/s41557-020-0452-1 apa: Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-020-0452-1 chicago: Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry. Springer Nature, 2020. https://doi.org/10.1038/s41557-020-0452-1. ieee: T. C. T. Michaels et al., “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” Nature Chemistry, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020. ista: Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451. mla: Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” Nature Chemistry, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:10.1038/s41557-020-0452-1. short: T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451. date_created: 2021-11-26T09:15:13Z date_published: 2020-04-13T00:00:00Z date_updated: 2021-11-26T11:21:08Z day: '13' doi: 10.1038/s41557-020-0452-1 extern: '1' external_id: pmid: - '32303714' intvolume: ' 12' issue: '5' keyword: - general chemical engineering - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.01.08.897488 month: '04' oa: 1 oa_version: None page: 445-451 pmid: 1 publication: Nature Chemistry publication_identifier: eissn: - 1755-4349 issn: - 1755-4330 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41557-020-0468-6 scopus_import: '1' status: public title: Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2020' ... --- _id: '10348' abstract: - lang: eng text: The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity. acknowledgement: The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin]). article_processing_charge: No article_type: original author: - first_name: Anna-Katharina full_name: Pfitzner, Anna-Katharina last_name: Pfitzner - first_name: Vincent full_name: Mercier, Vincent last_name: Mercier - first_name: Xiuyun full_name: Jiang, Xiuyun last_name: Jiang - first_name: Joachim full_name: Moser von Filseck, Joachim last_name: Moser von Filseck - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Aurélien full_name: Roux, Aurélien last_name: Roux citation: ama: Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 2020;182(5):1140-1155.e18. doi:10.1016/j.cell.2020.07.021 apa: Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., & Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.07.021 chicago: Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.07.021. ieee: A.-K. Pfitzner et al., “An ESCRT-III polymerization sequence drives membrane deformation and fission,” Cell, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020. ista: Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18. mla: Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” Cell, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:10.1016/j.cell.2020.07.021. short: A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18. date_created: 2021-11-26T08:02:27Z date_published: 2020-08-18T00:00:00Z date_updated: 2021-11-26T08:58:37Z day: '18' doi: 10.1016/j.cell.2020.07.021 extern: '1' external_id: pmid: - '32814015' intvolume: ' 182' issue: '5' keyword: - general biochemistry - genetics and molecular biology language: - iso: eng main_file_link: - open_access: '1' url: https://www.sciencedirect.com/science/article/pii/S0092867420309296 month: '08' oa: 1 oa_version: Published Version page: 1140-1155.e18 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: An ESCRT-III polymerization sequence drives membrane deformation and fission type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 182 year: '2020' ... --- _id: '10352' abstract: - lang: eng text: In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events. acknowledgement: We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.). article_number: '022420' article_processing_charge: No article_type: original author: - first_name: Luke K. full_name: Davis, Luke K. last_name: Davis - first_name: Ian J. full_name: Ford, Ian J. last_name: Ford - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Bart W. full_name: Hoogenboom, Bart W. last_name: Hoogenboom citation: ama: Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 2020;101(2). doi:10.1103/physreve.101.022420 apa: Davis, L. K., Ford, I. J., Šarić, A., & Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.101.022420 chicago: Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E. American Physical Society, 2020. https://doi.org/10.1103/physreve.101.022420. ieee: L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” Physical Review E, vol. 101, no. 2. American Physical Society, 2020. ista: Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420. mla: Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” Physical Review E, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:10.1103/physreve.101.022420. short: L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020). date_created: 2021-11-26T09:41:04Z date_published: 2020-02-28T00:00:00Z date_updated: 2021-11-26T11:21:16Z day: '28' doi: 10.1103/physreve.101.022420 extern: '1' external_id: pmid: - '32168597' intvolume: ' 101' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/571687 month: '02' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 101 year: '2020' ... --- _id: '10353' abstract: - lang: eng text: Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content. acknowledgement: We thank Samantha Miller, Bert Poolman, and the members of Šarić and Pilizota laboratories for useful discussion. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic Biology Research Centre (T.P.), and the Royal Society (A.Š.). article_number: '048102' article_processing_charge: No article_type: original author: - first_name: Alexandru full_name: Paraschiv, Alexandru last_name: Paraschiv - first_name: Smitha full_name: Hegde, Smitha last_name: Hegde - first_name: Raman full_name: Ganti, Raman last_name: Ganti - first_name: Teuta full_name: Pilizota, Teuta last_name: Pilizota - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 2020;124(4). doi:10.1103/physrevlett.124.048102 apa: Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., & Šarić, A. (2020). Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.124.048102 chicago: Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.124.048102. ieee: A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering regulates activity of mechanosensitive membrane channels,” Physical Review Letters, vol. 124, no. 4. American Physical Society, 2020. ista: Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 124(4), 048102. mla: Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” Physical Review Letters, vol. 124, no. 4, 048102, American Physical Society, 2020, doi:10.1103/physrevlett.124.048102. short: A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review Letters 124 (2020). date_created: 2021-11-26T09:57:01Z date_published: 2020-01-31T00:00:00Z date_updated: 2021-11-26T11:21:12Z day: '31' doi: 10.1103/physrevlett.124.048102 extern: '1' external_id: pmid: - '32058787' intvolume: ' 124' issue: '4' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/553248 month: '01' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering regulates activity of mechanosensitive membrane channels type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 124 year: '2020' ... --- _id: '10557' abstract: - lang: eng text: Data storage and retrieval systems, methods, and computer-readable media utilize a cryptographically verifiable data structure that facilitates verification of a transaction in a decentralized peer-to-peer environment using multi-hop backwards and forwards links. Backward links are cryptographic hashes of past records. Forward links are cryptographic signatures of future records that are added retroactively to records once the target block has been appended to the data structure. applicant: - Ecole Polytechnique Federale de Lausanne application_date: 2017-06-09 article_processing_charge: No author: - first_name: Bryan full_name: Ford, Bryan last_name: Ford - first_name: Linus full_name: Gasse, Linus last_name: Gasse - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic citation: ama: Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. 2020. apa: Ford, B., Gasse, L., Kokoris Kogias, E., & Jovanovic, P. (2020). Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. chicago: Ford, Bryan, Linus Gasse, Eleftherios Kokoris Kogias, and Philipp Jovanovic. “Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods,” 2020. ieee: B. Ford, L. Gasse, E. Kokoris Kogias, and P. Jovanovic, “Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.” 2020. ista: Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. 2020. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. mla: Ford, Bryan, et al. Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods. 2020. short: B. Ford, L. Gasse, E. Kokoris Kogias, P. Jovanovic, (2020). date_created: 2021-12-16T13:28:59Z date_published: 2020-03-03T00:00:00Z date_updated: 2021-12-21T10:04:50Z day: '03' department: - _id: ElKo extern: '1' ipc: ' H04L9/3247 ; G06Q20/29 ; G06Q20/382 ; H04L9/3236' ipn: '10581613' main_file_link: - open_access: '1' url: https://patents.google.com/patent/US10581613B2/en month: '03' oa: 1 oa_version: Published Version publication_date: 2020-03-03 related_material: link: - relation: earlier_version url: https://patents.google.com/patent/US20180359096A1/en status: public title: Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '10618' abstract: - lang: eng text: Magnetism typically arises from the joint effect of Fermi statistics and repulsive Coulomb interactions, which favours ground states with non-zero electron spin. As a result, controlling spin magnetism with electric fields—a longstanding technological goal in spintronics and multiferroics1,2—can be achieved only indirectly. Here we experimentally demonstrate direct electric-field control of magnetic states in an orbital Chern insulator3,4,5,6, a magnetic system in which non-trivial band topology favours long-range order of orbital angular momentum but the spins are thought to remain disordered7,8,9,10,11,12,13,14. We use van der Waals heterostructures consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked bilayer to realize narrow and topologically non-trivial valley-projected moiré minibands15,16,17. At fillings of one and three electrons per moiré unit cell within these bands, we observe quantized anomalous Hall effects18 with transverse resistance approximately equal to h/2e2 (where h is Planck’s constant and e is the charge on the electron), which is indicative of spontaneous polarization of the system into a single-valley-projected band with a Chern number equal to two. At a filling of three electrons per moiré unit cell, we find that the sign of the quantum anomalous Hall effect can be reversed via field-effect control of the chemical potential; moreover, this transition is hysteretic, which we use to demonstrate non-volatile electric-field-induced reversal of the magnetic state. A theoretical analysis19 indicates that the effect arises from the topological edge states, which drive a change in sign of the magnetization and thus a reversal in the favoured magnetic state. Voltage control of magnetic states can be used to electrically pattern non-volatile magnetic-domain structures hosting chiral edge states, with applications ranging from reconfigurable microwave circuit elements to ultralow-power magnetic memories. acknowledgement: We acknowledge discussions with J. Checkelsky, S. Chen, C. Dean, M. Yankowitz, D. Reilly, I. Sodemann and M. Zaletel. Work at UCSB was primarily supported by the ARO under MURI W911NF-16-1-0361. Measurements of twisted bilayer graphene (Extended Data Fig. 8) and measurements at elevated temperatures (Extended Data Fig. 3) were supported by a SEED grant and made use of shared facilities of the UCSB MRSEC (NSF DMR 1720256), a member of the Materials Research Facilities Network (www.mrfn.org). A.F.Y. acknowledges the support of the David and Lucille Packard Foundation under award 2016-65145. A.H.M. and J.Z. were supported by the National Science Foundation through the Center for Dynamics and Control of Materials, an NSF MRSEC under Cooperative Agreement number DMR-1720595, and by the Welch Foundation under grant TBF1473. C.L.T. acknowledges support from the Hertz Foundation and from the National Science Foundation Graduate Research Fellowship Program under grant 1650114. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001, JSPS KAKENHI grant numbers JP20H00354 and the CREST(JPMJCR15F3), JST. article_processing_charge: No article_type: original author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: J. full_name: Zhu, J. last_name: Zhu - first_name: M. A. full_name: Kumar, M. A. last_name: Kumar - first_name: Y. full_name: Zhang, Y. last_name: Zhang - first_name: F. full_name: Yang, F. last_name: Yang - first_name: C. L. full_name: Tschirhart, C. L. last_name: Tschirhart - first_name: M. full_name: Serlin, M. last_name: Serlin - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: A. H. full_name: MacDonald, A. H. last_name: MacDonald - first_name: A. F. full_name: Young, A. F. last_name: Young citation: ama: Polshyn H, Zhu J, Kumar MA, et al. Electrical switching of magnetic order in an orbital Chern insulator. Nature. 2020;588(7836):66-70. doi:10.1038/s41586-020-2963-8 apa: Polshyn, H., Zhu, J., Kumar, M. A., Zhang, Y., Yang, F., Tschirhart, C. L., … Young, A. F. (2020). Electrical switching of magnetic order in an orbital Chern insulator. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2963-8 chicago: Polshyn, Hryhoriy, J. Zhu, M. A. Kumar, Y. Zhang, F. Yang, C. L. Tschirhart, M. Serlin, et al. “Electrical Switching of Magnetic Order in an Orbital Chern Insulator.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2963-8. ieee: H. Polshyn et al., “Electrical switching of magnetic order in an orbital Chern insulator,” Nature, vol. 588, no. 7836. Springer Nature, pp. 66–70, 2020. ista: Polshyn H, Zhu J, Kumar MA, Zhang Y, Yang F, Tschirhart CL, Serlin M, Watanabe K, Taniguchi T, MacDonald AH, Young AF. 2020. Electrical switching of magnetic order in an orbital Chern insulator. Nature. 588(7836), 66–70. mla: Polshyn, Hryhoriy, et al. “Electrical Switching of Magnetic Order in an Orbital Chern Insulator.” Nature, vol. 588, no. 7836, Springer Nature, 2020, pp. 66–70, doi:10.1038/s41586-020-2963-8. short: H. Polshyn, J. Zhu, M.A. Kumar, Y. Zhang, F. Yang, C.L. Tschirhart, M. Serlin, K. Watanabe, T. Taniguchi, A.H. MacDonald, A.F. Young, Nature 588 (2020) 66–70. date_created: 2022-01-13T14:12:17Z date_published: 2020-11-23T00:00:00Z date_updated: 2022-01-13T14:21:04Z day: '23' doi: 10.1038/s41586-020-2963-8 extern: '1' external_id: arxiv: - '2004.11353' pmid: - '33230333' intvolume: ' 588' issue: '7836' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2004.11353 month: '11' oa: 1 oa_version: Preprint page: 66-70 pmid: 1 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: Electrical switching of magnetic order in an orbital Chern insulator type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 588 year: '2020' ... --- _id: '10650' abstract: - lang: eng text: The understanding of material systems with strong electron-electron interactions is the central problem in modern condensed matter physics. Despite this, the essential physics of many of these materials is still not understood and we have no overall perspective on their properties. Moreover, we have very little ability to make predictions in this class of systems. In this manuscript we share our personal views of what the major open problems are in correlated electron systems and we discuss some possible routes to make progress in this rich and fascinating field. This manuscript is the result of the vigorous discussions and deliberations that took place at Johns Hopkins University during a three-day workshop January 27, 28, and 29, 2020 that brought together six senior scientists and 46 more junior scientists. Our hope, is that the topics we have presented will provide inspiration for others working in this field and motivation for the idea that significant progress can be made on very hard problems if we focus our collective energies. acknowledgement: "We thank NSF CMP program for suggestions regarding the topic and general structure of the workshop. This project was supported by the NSF DMR-2002329 and The Gordon and Betty Moore Foundation (GBMF) EPiQS initiative. We would like to sincerely thank A. Kapitulnik, A. J. Leggett, M.B. Maple, T.M. McQueen, M. Norman, P. S. Riseborough, and G. A. Sawatzky for their lectures at the workshop and advice on the writing of this manuscript. We would also like to thank G. Blumberg, C. Broholm, S. Crooker, N. Drichko, and A. Patel for helpful consultation on topics discussed\r\nherein. A number of individuals also had independent support: (AA, EH; GBMF-4305), (IMH; GBMF-9071), (HJC; NHMFL is supported by the NSF DMR-1644779 and the state of Florida), (YH, AZ; Miller Institute for Basic Research in Science), (YC; US DOE-BES DEAC02-06CH11357), (AS; Spallation Neutron Source, a DOE Office of Science User Facility operated by ORNL), (SAAG; ARO-W911NF-18-1-0290, NSF DMR-1455233), (YW; DOE-BES DE-SC0019331, GBMF-4532)." article_processing_charge: No author: - first_name: A full_name: Alexandradinata, A last_name: Alexandradinata - first_name: N.P. full_name: Armitage, N.P. last_name: Armitage - first_name: Andrey full_name: Baydin, Andrey last_name: Baydin - first_name: Wenli full_name: Bi, Wenli last_name: Bi - first_name: Yue full_name: Cao, Yue last_name: Cao - first_name: Hitesh J. full_name: Changlani, Hitesh J. last_name: Changlani - first_name: Eli full_name: Chertkov, Eli last_name: Chertkov - first_name: Eduardo H. full_name: da Silva Neto, Eduardo H. last_name: da Silva Neto - first_name: Luca full_name: Delacretaz, Luca last_name: Delacretaz - first_name: Ismail full_name: El Baggari, Ismail last_name: El Baggari - first_name: G.M. full_name: Ferguson, G.M. last_name: Ferguson - first_name: William J. full_name: Gannon, William J. last_name: Gannon - first_name: Sayed Ali Akbar full_name: Ghorashi, Sayed Ali Akbar last_name: Ghorashi - first_name: Berit H. full_name: Goodge, Berit H. last_name: Goodge - first_name: Olga full_name: Goulko, Olga last_name: Goulko - first_name: G. full_name: Grissonnache, G. last_name: Grissonnache - first_name: Alannah full_name: Hallas, Alannah last_name: Hallas - first_name: Ian M. full_name: Hayes, Ian M. last_name: Hayes - first_name: Yu full_name: He, Yu last_name: He - first_name: Edwin W. full_name: Huang, Edwin W. last_name: Huang - first_name: Anshu full_name: Kogar, Anshu last_name: Kogar - first_name: Divine full_name: Kumah, Divine last_name: Kumah - first_name: Jong Yeon full_name: Lee, Jong Yeon last_name: Lee - first_name: A. full_name: Legros, A. last_name: Legros - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Yulia full_name: Maximenko, Yulia last_name: Maximenko - first_name: Nick full_name: Pellatz, Nick last_name: Pellatz - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Tarapada full_name: Sarkar, Tarapada last_name: Sarkar - first_name: Allen full_name: Scheie, Allen last_name: Scheie - first_name: Kyle L. full_name: Seyler, Kyle L. last_name: Seyler - first_name: Zhenzhong full_name: Shi, Zhenzhong last_name: Shi - first_name: Brian full_name: Skinner, Brian last_name: Skinner - first_name: Lucia full_name: Steinke, Lucia last_name: Steinke - first_name: K. full_name: Thirunavukkuarasu, K. last_name: Thirunavukkuarasu - first_name: Thaís Victa full_name: Trevisan, Thaís Victa last_name: Trevisan - first_name: Michael full_name: Vogl, Michael last_name: Vogl - first_name: Pavel A. full_name: Volkov, Pavel A. last_name: Volkov - first_name: Yao full_name: Wang, Yao last_name: Wang - first_name: Yishu full_name: Wang, Yishu last_name: Wang - first_name: Di full_name: Wei, Di last_name: Wei - first_name: Kaya full_name: Wei, Kaya last_name: Wei - first_name: Shuolong full_name: Yang, Shuolong last_name: Yang - first_name: Xian full_name: Zhang, Xian last_name: Zhang - first_name: Ya-Hui full_name: Zhang, Ya-Hui last_name: Zhang - first_name: Liuyan full_name: Zhao, Liuyan last_name: Zhao - first_name: Alfred full_name: Zong, Alfred last_name: Zong citation: ama: Alexandradinata A, Armitage NP, Baydin A, et al. The future of the correlated electron problem. arXiv. apa: Alexandradinata, A., Armitage, N. P., Baydin, A., Bi, W., Cao, Y., Changlani, H. J., … Zong, A. (n.d.). The future of the correlated electron problem. arXiv. chicago: Alexandradinata, A, N.P. Armitage, Andrey Baydin, Wenli Bi, Yue Cao, Hitesh J. Changlani, Eli Chertkov, et al. “The Future of the Correlated Electron Problem.” ArXiv, n.d. ieee: A. Alexandradinata et al., “The future of the correlated electron problem,” arXiv. . ista: Alexandradinata A, Armitage NP, Baydin A, Bi W, Cao Y, Changlani HJ, Chertkov E, da Silva Neto EH, Delacretaz L, El Baggari I, Ferguson GM, Gannon WJ, Ghorashi SAA, Goodge BH, Goulko O, Grissonnache G, Hallas A, Hayes IM, He Y, Huang EW, Kogar A, Kumah D, Lee JY, Legros A, Mahmood F, Maximenko Y, Pellatz N, Polshyn H, Sarkar T, Scheie A, Seyler KL, Shi Z, Skinner B, Steinke L, Thirunavukkuarasu K, Trevisan TV, Vogl M, Volkov PA, Wang Y, Wang Y, Wei D, Wei K, Yang S, Zhang X, Zhang Y-H, Zhao L, Zong A. The future of the correlated electron problem. arXiv, . mla: Alexandradinata, A., et al. “The Future of the Correlated Electron Problem.” ArXiv. short: A. Alexandradinata, N.P. Armitage, A. Baydin, W. Bi, Y. Cao, H.J. Changlani, E. Chertkov, E.H. da Silva Neto, L. Delacretaz, I. El Baggari, G.M. Ferguson, W.J. Gannon, S.A.A. Ghorashi, B.H. Goodge, O. Goulko, G. Grissonnache, A. Hallas, I.M. Hayes, Y. He, E.W. Huang, A. Kogar, D. Kumah, J.Y. Lee, A. Legros, F. Mahmood, Y. Maximenko, N. Pellatz, H. Polshyn, T. Sarkar, A. Scheie, K.L. Seyler, Z. Shi, B. Skinner, L. Steinke, K. Thirunavukkuarasu, T.V. Trevisan, M. Vogl, P.A. Volkov, Y. Wang, Y. Wang, D. Wei, K. Wei, S. Yang, X. Zhang, Y.-H. Zhang, L. Zhao, A. Zong, ArXiv (n.d.). date_created: 2022-01-20T10:55:36Z date_published: 2020-10-01T00:00:00Z date_updated: 2022-01-24T08:05:51Z day: '01' extern: '1' external_id: arxiv: - '2010.00584' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2010.00584 month: '10' oa: 1 oa_version: Preprint page: '55' publication: arXiv publication_status: submitted status: public title: The future of the correlated electron problem type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '10673' abstract: - lang: eng text: We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level. acknowledgement: "RH and RG are partially supported by Horizon-2020 ECSEL Project grant No. 783163 (iDev40), Productive 4.0, and ATBMBFW CPS-IoT Ecosystem. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award). AA is supported by the National Science Foundation (NSF) Graduate Research Fellowship\r\nProgram. RH and DR are partially supported by The Boeing Company and JP Morgan Chase. This research work is\r\npartially drawn from the PhD dissertation of RH.\r\n" alternative_title: - PMLR article_processing_charge: No author: - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Daniela full_name: Rus, Daniela last_name: Rus - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In: Proceedings of the 37th International Conference on Machine Learning. PMLR. ; 2020:4082-4093.' apa: 'Hasani, R., Lechner, M., Amini, A., Rus, D., & Grosu, R. (2020). A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In Proceedings of the 37th International Conference on Machine Learning (pp. 4082–4093). Virtual.' chicago: 'Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu Grosu. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” In Proceedings of the 37th International Conference on Machine Learning, 4082–93. PMLR, 2020.' ieee: 'R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, pp. 4082–4093.' ista: 'Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2020. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. Proceedings of the 37th International Conference on Machine Learning. ML: Machine LearningPMLR, PMLR, , 4082–4093.' mla: 'Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–93.' short: R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–4093. conference: end_date: 2020-07-18 location: Virtual name: 'ML: Machine Learning' start_date: 2020-07-12 date_created: 2022-01-25T15:50:34Z date_published: 2020-01-01T00:00:00Z date_updated: 2022-01-26T11:14:27Z ddc: - '000' department: - _id: GradSch - _id: ToHe file: - access_level: open_access checksum: c9a4a29161777fc1a89ef451c040e3b1 content_type: application/pdf creator: cchlebak date_created: 2022-01-26T11:08:51Z date_updated: 2022-01-26T11:08:51Z file_id: '10691' file_name: 2020_PMLR_Hasani.pdf file_size: 2329798 relation: main_file success: 1 file_date_updated: 2022-01-26T11:08:51Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ main_file_link: - open_access: '1' url: http://proceedings.mlr.press/v119/hasani20a.html oa: 1 oa_version: Published Version page: 4082-4093 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings of the 37th International Conference on Machine Learning publication_identifier: issn: - 2640-3498 publication_status: published quality_controlled: '1' scopus_import: '1' series_title: PMLR status: public title: 'A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '10693' abstract: - lang: eng text: High quality graphene heterostructures host an array of fractional quantum Hall isospin ferromagnets with diverse spin and valley orders. While a variety of phase transitions have been observed, disentangling the isospin phase diagram of these states is hampered by the absence of direct probes of spin and valley order. I will describe nonlocal transport measurements based on launching spin waves from a gate defined lateral heterojunction, performed in ultra-clean Corbino geometry graphene devices. At high magnetic fields, we find that the spin-wave transport signal is detected in all FQH states between ν = 0 and 1; however, between ν = 1 and 2 only odd numerator FQH states show finite nonlocal transport, despite the identical ground state spin polarizations in odd- and even numerator states. The results reveal that the neutral spin-waves are both spin and sublattice polarized making them a sensitive probe of ground state sublattice structure. Armed with this understanding, we use nonlocal transport signal to a magnetic field tuned isospin phase transition, showing that the emergent even denominator state at ν = 1/2 in monolayer graphene is indeed a multicomponent state featuring equal populations on each sublattice. alternative_title: - Bulletin of the American Physical Society article_number: B54. 00007 article_processing_charge: No author: - first_name: Haoxin full_name: Zhou, Haoxin last_name: Zhou - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Takashi full_name: Tanaguchi, Takashi last_name: Tanaguchi - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Andrea full_name: Young, Andrea last_name: Young citation: ama: 'Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.' apa: 'Zhou, H., Polshyn, H., Tanaguchi, T., Watanabe, K., & Young, A. (2020). Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.' chicago: Zhou, Haoxin, Hryhoriy Polshyn, Takashi Tanaguchi, Kenji Watanabe, and Andrea Young. “Sublattice Resolved Spin Wave Transport through Graphene Fractional Quantum Hall States as a Probe of Isospin Order.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020. ieee: H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, and A. Young, “Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1. ista: 'Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. 2020. Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B54. 00007.' mla: Zhou, Haoxin, et al. “Sublattice Resolved Spin Wave Transport through Graphene Fractional Quantum Hall States as a Probe of Isospin Order.” APS March Meeting 2020, vol. 65, no. 1, B54. 00007, American Physical Society, 2020. short: H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020. conference: end_date: 2020-03-06 location: Denver, CO, United States name: 'APS: American Physical Society' start_date: 2020-03-02 date_created: 2022-01-27T10:50:10Z date_published: 2020-03-01T00:00:00Z date_updated: 2022-01-27T10:58:38Z day: '01' extern: '1' intvolume: ' 65' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR20/Session/B54.7 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2020 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 65 year: '2020' ... --- _id: '10698' abstract: - lang: eng text: This is the second of three talks describing the observation and characterization of a ferromagnetic moiré heterostructure based on twisted bilayer graphene aligned to hexagonal boron nitride. I will compare the qualitative and quantitative features of this observed quantum anomalous Hall state to traditional systems engineered from thin film (Bi,Sb)2Te3 topological insulators. In particular, we find that the measured electronic energy gap of ~30K is several times higher than the Curie temperature, consistent with a lack of disorder associated with magnetic dopants. In this system, the quantization arises from spontaneous ferromagnetic polarization into a single spin and valley moiré subband, which is topological despite the lack of spin orbit coupling. I will also discuss the observation of current induced switching, which allows the magnetic state of the heterostructure to be controllably reversed with currents as small as a few nanoamperes. acknowledgement: I would like to thank the MURI Program, AFOSR, Sloan Foundation, and the ARO for their generous support of this work. alternative_title: - Bulletin of the American Physical Society article_number: B59.00011 article_processing_charge: No author: - first_name: Marec full_name: Serlin, Marec last_name: Serlin - first_name: Charles full_name: Tschirhart, Charles last_name: Tschirhart - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Yuxuan full_name: Zhang, Yuxuan last_name: Zhang - first_name: Jiacheng full_name: Zhu, Jiacheng last_name: Zhu - first_name: Martin E. full_name: Huber, Martin E. last_name: Huber - first_name: Leon full_name: Balents, Leon last_name: Balents - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Takashi full_name: Tanaguchi, Takashi last_name: Tanaguchi - first_name: Andrea full_name: Young, Andrea last_name: Young citation: ama: 'Serlin M, Tschirhart C, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.' apa: 'Serlin, M., Tschirhart, C., Polshyn, H., Zhang, Y., Zhu, J., Huber, M. E., … Young, A. (2020). Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.' chicago: 'Serlin, Marec, Charles Tschirhart, Hryhoriy Polshyn, Yuxuan Zhang, Jiacheng Zhu, Martin E. Huber, Leon Balents, Kenji Watanabe, Takashi Tanaguchi, and Andrea Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part II: Temperature Dependence and Current Switching.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.' ieee: 'M. Serlin et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.' ista: 'Serlin M, Tschirhart C, Polshyn H, Zhang Y, Zhu J, Huber ME, Balents L, Watanabe K, Tanaguchi T, Young A. 2020. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B59.00011.' mla: 'Serlin, Marec, et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part II: Temperature Dependence and Current Switching.” APS March Meeting 2020, vol. 65, no. 1, B59.00011, American Physical Society, 2020.' short: M. Serlin, C. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, M.E. Huber, L. Balents, K. Watanabe, T. Tanaguchi, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020. conference: end_date: 2020-03-06 location: Denver, CO, United States name: 'APS: American Physical Society' start_date: 2020-03-02 date_created: 2022-01-28T10:46:57Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-02-21T15:57:52Z day: '01' extern: '1' external_id: arxiv: - '1907.00261' intvolume: ' 65' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR20/Session/B59.11 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2020 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '10619' relation: other status: public status: public title: 'Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 65 year: '2020' ... --- _id: '10699' abstract: - lang: eng text: This is the third of three talks describing the observation and characterization of a ferromagnetic moiré heterostructure based on twisted bilayer graphene aligned to hexagonal boron nitride. In this segment I will present scanning probe magnetometry data acquired using a nanoSQUID-on-tip microscope, which provides ~150 nm spatial resolution and a field sensitivity of ~10 nT/rtHz. We study the distribution of magnetic domains within the device as a function of density, magnetic field training, and DC current. Our data allow us to constrain the magnitude of the orbital magnetic moment of the electrons in the QAH state. Comparison with simultaneously acquired transport data allows us to precisely correlate single domain dynamics with discrete jumps in the observed anomalous Hall signal. acknowledgement: I would like to thank the MURI program, Sloan foundation, AFOSR, and ARO for their generous support of this work. I would also like to thank the NSF GRFP and the Hertz foundation for their generous support of my graduate studies. alternative_title: - Bulletin of the American Physical Society article_number: B59.00013 article_processing_charge: No author: - first_name: Charles full_name: Tschirhart, Charles last_name: Tschirhart - first_name: Marec full_name: Serlin, Marec last_name: Serlin - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Yuxuan full_name: Zhang, Yuxuan last_name: Zhang - first_name: Jiacheng full_name: Zhu, Jiacheng last_name: Zhu - first_name: Leon full_name: Balents, Leon last_name: Balents - first_name: Martin E. full_name: Huber, Martin E. last_name: Huber - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Takashi full_name: Tanaguchi, Takashi last_name: Tanaguchi - first_name: Andrea full_name: Young, Andrea last_name: Young citation: ama: 'Tschirhart C, Serlin M, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.' apa: 'Tschirhart, C., Serlin, M., Polshyn, H., Zhang, Y., Zhu, J., Balents, L., … Young, A. (2020). Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.' chicago: 'Tschirhart, Charles, Marec Serlin, Hryhoriy Polshyn, Yuxuan Zhang, Jiacheng Zhu, Leon Balents, Martin E. Huber, Kenji Watanabe, Takashi Tanaguchi, and Andrea Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part III: Scanning Probe Magnetometry.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.' ieee: 'C. Tschirhart et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.' ista: 'Tschirhart C, Serlin M, Polshyn H, Zhang Y, Zhu J, Balents L, Huber ME, Watanabe K, Tanaguchi T, Young A. 2020. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B59.00013.' mla: 'Tschirhart, Charles, et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part III: Scanning Probe Magnetometry.” APS March Meeting 2020, vol. 65, no. 1, B59.00013, American Physical Society, 2020.' short: C. Tschirhart, M. Serlin, H. Polshyn, Y. Zhang, J. Zhu, L. Balents, M.E. Huber, K. Watanabe, T. Tanaguchi, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020. conference: end_date: 2020-03-06 location: Denver, CO, United States name: 'APS: American Physical Society' start_date: 2020-03-02 date_created: 2022-01-28T10:57:49Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-02-21T15:57:52Z day: '01' extern: '1' external_id: arxiv: - '1907.00261' intvolume: ' 65' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR20/Session/B59.13 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2020 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '10619' relation: other status: public status: public title: 'Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 65 year: '2020' ... --- _id: '10697' abstract: - lang: eng text: We report the observation of a quantized anomalous Hall effect in a moiré heterostructure consisting of twisted bilayer graphene aligned to an encapsulating hBN substrate. The effect occurs at a density of 3 electrons per superlattice unit cell, where we observe magnetic hysteresis and a Hall resistance quantized to within 0.1% of the resistance quantum at temperatures as high as 3K. In this first of 3 talks, I will describe the fabrication procedure for our device as well as basic transport characterization measurements. I will introduce the phenomenology of twisted bilayer graphene and present evidence for hBN alignment as manifested in the hierarchy of symmetry-breaking gaps and anomalous magnetoresistance. acknowledgement: I would like to thank the MURI program, Sloan foundation, AFOSR, and ARO for their generous support of this work. alternative_title: - Bulletin of the American Physical Society article_number: B59.00012 article_processing_charge: No author: - first_name: Yuxuan full_name: Zhang, Yuxuan last_name: Zhang - first_name: Marec full_name: Serlin, Marec last_name: Serlin - first_name: Charles full_name: Tschirhart, Charles last_name: Tschirhart - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Jiacheng full_name: Zhu, Jiacheng last_name: Zhu - first_name: Leon full_name: Balents, Leon last_name: Balents - first_name: Martin E. full_name: Huber, Martin E. last_name: Huber - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Andrea full_name: Young, Andrea last_name: Young citation: ama: 'Zhang Y, Serlin M, Tschirhart C, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.' apa: 'Zhang, Y., Serlin, M., Tschirhart, C., Polshyn, H., Zhu, J., Balents, L., … Young, A. (2020). Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.' chicago: 'Zhang, Yuxuan, Marec Serlin, Charles Tschirhart, Hryhoriy Polshyn, Jiacheng Zhu, Leon Balents, Martin E. Huber, Takashi Taniguchi, Kenji Watanabe, and Andrea Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part I: Device Fabrication and Transport.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020.' ieee: 'Y. Zhang et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1.' ista: 'Zhang Y, Serlin M, Tschirhart C, Polshyn H, Zhu J, Balents L, Huber ME, Taniguchi T, Watanabe K, Young A. 2020. Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B59.00012.' mla: 'Zhang, Yuxuan, et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure, Part I: Device Fabrication and Transport.” APS March Meeting 2020, vol. 65, no. 1, B59.00012, American Physical Society, 2020.' short: Y. Zhang, M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, L. Balents, M.E. Huber, T. Taniguchi, K. Watanabe, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020. conference: end_date: 2020-03-06 location: Denver, CO, United States name: 'APS: American Physical Society' start_date: 2020-03-02 date_created: 2022-01-28T10:28:35Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-02-21T15:57:52Z day: '01' extern: '1' external_id: arxiv: - '1907.00261' intvolume: ' 65' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR20/Session/B59.12 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2020 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '10619' relation: other status: public status: public title: 'Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 65 year: '2020' ... --- _id: '10696' abstract: - lang: eng text: We experimentally investigate twisted van der Waals heterostructures of monolayer graphene rotated with respect to a bernal stacked graphene bilayer. We report transport measurements for devices with twist angles between 0.9 and 1.4°. The electric field allows efficient tuning of the width, isolation and the topology of the moiré bands in this system. By comparing magnetoresistance measurements to numerical simulations, we develop an understanding of the band structure. Finally, we observe correlated states at half- and quarter-fillings, which arise when narrow moire sublattice band is isolated by energy gaps from dispersive bands. We investigate the effects of in-plane and out-of-plane magnetic field on these states and discuss the implication for their spin- and valley- polarization. alternative_title: - Bulletin of the American Physical Society article_number: B51.00005 article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Jihang full_name: Zhu, Jihang last_name: Zhu - first_name: Manish full_name: Kumar, Manish last_name: Kumar - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Allan full_name: MacDonald, Allan last_name: MacDonald - first_name: Andrea full_name: Young, Andrea last_name: Young citation: ama: 'Polshyn H, Zhu J, Kumar M, et al. Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures. In: APS March Meeting 2020. Vol 65. American Physical Society; 2020.' apa: 'Polshyn, H., Zhu, J., Kumar, M., Taniguchi, T., Watanabe, K., MacDonald, A., & Young, A. (2020). Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures. In APS March Meeting 2020 (Vol. 65). Denver, CO, United States: American Physical Society.' chicago: Polshyn, Hryhoriy, Jihang Zhu, Manish Kumar, Takashi Taniguchi, Kenji Watanabe, Allan MacDonald, and Andrea Young. “Correlated States and Tunable Topological Bands in Twisted Monolayer-Bilayer Graphene Heterostructures.” In APS March Meeting 2020, Vol. 65. American Physical Society, 2020. ieee: H. Polshyn et al., “Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures,” in APS March Meeting 2020, Denver, CO, United States, 2020, vol. 65, no. 1. ista: 'Polshyn H, Zhu J, Kumar M, Taniguchi T, Watanabe K, MacDonald A, Young A. 2020. Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures. APS March Meeting 2020. APS: American Physical Society, Bulletin of the American Physical Society, vol. 65, B51.00005.' mla: Polshyn, Hryhoriy, et al. “Correlated States and Tunable Topological Bands in Twisted Monolayer-Bilayer Graphene Heterostructures.” APS March Meeting 2020, vol. 65, no. 1, B51.00005, American Physical Society, 2020. short: H. Polshyn, J. Zhu, M. Kumar, T. Taniguchi, K. Watanabe, A. MacDonald, A. Young, in:, APS March Meeting 2020, American Physical Society, 2020. conference: end_date: 2020-03-06 location: Denver, CO, United States name: 'APS: American Physical Society' start_date: 2020-03-02 date_created: 2022-01-28T10:09:19Z date_published: 2020-03-01T00:00:00Z date_updated: 2022-02-08T10:22:08Z day: '01' extern: '1' intvolume: ' 65' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR20/Session/B51.5 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2020 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 65 year: '2020' ... --- _id: '10701' abstract: - lang: eng text: Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders. acknowledgement: We acknowledge discussions with B. Halperin, C. Huang, A. Macdonald and M. Zalatel. Experimental work at UCSB was supported by the Army Research Office under awards nos. MURI W911NF-16-1-0361 and W911NF-16-1-0482. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by MEXT (Japan) and CREST (JPMJCR15F3), JST. A.F.Y. acknowledges the support of the David and Lucile Packard Foundation and and Alfred. P. Sloan Foundation. article_processing_charge: No article_type: original author: - first_name: Haoxin full_name: Zhou, Haoxin last_name: Zhou - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young citation: ama: Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. Skyrmion solids in monolayer graphene. Nature Physics. 2020;16(2):154-158. doi:10.1038/s41567-019-0729-8 apa: Zhou, H., Polshyn, H., Taniguchi, T., Watanabe, K., & Young, A. F. (2020). Skyrmion solids in monolayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0729-8 chicago: Zhou, Haoxin, Hryhoriy Polshyn, Takashi Taniguchi, Kenji Watanabe, and Andrea F. Young. “Skyrmion Solids in Monolayer Graphene.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-019-0729-8. ieee: H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young, “Skyrmion solids in monolayer graphene,” Nature Physics, vol. 16, no. 2. Springer Nature, pp. 154–158, 2020. ista: Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. 2020. Skyrmion solids in monolayer graphene. Nature Physics. 16(2), 154–158. mla: Zhou, Haoxin, et al. “Skyrmion Solids in Monolayer Graphene.” Nature Physics, vol. 16, no. 2, Springer Nature, 2020, pp. 154–58, doi:10.1038/s41567-019-0729-8. short: H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, A.F. Young, Nature Physics 16 (2020) 154–158. date_created: 2022-01-28T12:04:09Z date_published: 2020-02-01T00:00:00Z date_updated: 2022-01-31T07:10:07Z day: '01' doi: 10.1038/s41567-019-0729-8 extern: '1' external_id: arxiv: - '1904.11485' intvolume: ' 16' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.11485 month: '02' oa: 1 oa_version: Preprint page: 154-158 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Skyrmion solids in monolayer graphene type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 16 year: '2020' ... --- _id: '11056' abstract: - lang: eng text: Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established. article_number: '2000044' article_processing_charge: No article_type: original author: - first_name: Simone full_name: Bersini, Simone last_name: Bersini - first_name: Rafael full_name: Arrojo e Drigo, Rafael last_name: Arrojo e Drigo - first_name: Ling full_name: Huang, Ling last_name: Huang - first_name: Maxim N. full_name: Shokhirev, Maxim N. last_name: Shokhirev - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 2020;4(5). doi:10.1002/adbi.202000044 apa: Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., & Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. Wiley. https://doi.org/10.1002/adbi.202000044 chicago: Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” Advanced Biosystems. Wiley, 2020. https://doi.org/10.1002/adbi.202000044. ieee: S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” Advanced Biosystems, vol. 4, no. 5. Wiley, 2020. ista: Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044. mla: Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” Advanced Biosystems, vol. 4, no. 5, 2000044, Wiley, 2020, doi:10.1002/adbi.202000044. short: S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020). date_created: 2022-04-07T07:43:57Z date_published: 2020-05-01T00:00:00Z date_updated: 2022-07-18T08:30:48Z day: '01' ddc: - '570' doi: 10.1002/adbi.202000044 extern: '1' external_id: pmid: - '32402127' file: - access_level: open_access checksum: 5584d9a1609812dc75c02ce1e35d2ec0 content_type: application/pdf creator: dernst date_created: 2022-04-08T07:06:05Z date_updated: 2022-04-08T07:06:05Z file_id: '11134' file_name: 2020_AdvancedBiosystems_Bersini.pdf file_size: 2490829 relation: main_file success: 1 file_date_updated: 2022-04-08T07:06:05Z has_accepted_license: '1' intvolume: ' 4' issue: '5' keyword: - General Biochemistry - Genetics and Molecular Biology - Biomedical Engineering - Biomaterials language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Advanced Biosystems publication_identifier: issn: - 2366-7478 - 2366-7478 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease 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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 4 year: '2020' ... --- _id: '11055' abstract: - lang: eng text: Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro. article_number: e54383 article_processing_charge: No article_type: original author: - first_name: Simone full_name: Bersini, Simone last_name: Bersini - first_name: Roberta full_name: Schulte, Roberta last_name: Schulte - first_name: Ling full_name: Huang, Ling last_name: Huang - first_name: Hannah full_name: Tsai, Hannah last_name: Tsai - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 2020;9. doi:10.7554/elife.54383 apa: Bersini, S., Schulte, R., Huang, L., Tsai, H., & Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.54383 chicago: Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.54383. ieee: S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383. mla: Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” ELife, vol. 9, e54383, eLife Sciences Publications, 2020, doi:10.7554/elife.54383. short: S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020). date_created: 2022-04-07T07:43:48Z date_published: 2020-09-08T00:00:00Z date_updated: 2022-07-18T08:30:37Z day: '08' ddc: - '570' doi: 10.7554/elife.54383 extern: '1' external_id: pmid: - '32896271' file: - access_level: open_access checksum: f8b3821349a194050be02570d8fe7d4b content_type: application/pdf creator: dernst date_created: 2022-04-08T06:53:10Z date_updated: 2022-04-08T06:53:10Z file_id: '11132' file_name: 2020_eLife_Bersini.pdf file_size: 4399825 relation: main_file success: 1 file_date_updated: 2022-04-08T06:53:10Z has_accepted_license: '1' intvolume: ' 9' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome 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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 9 year: '2020' ... --- _id: '11054' abstract: - lang: eng text: In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging. article_processing_charge: No article_type: review author: - first_name: Ukrae H. full_name: Cho, Ukrae H. last_name: Cho - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: 'Cho UH, Hetzer M. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. 2020;106(6):899-911. doi:10.1016/j.neuron.2020.05.031' apa: 'Cho, U. H., & Hetzer, M. (2020). Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.031' chicago: 'Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.031.' ieee: 'U. H. Cho and M. Hetzer, “Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging,” Neuron, vol. 106, no. 6. Elsevier, pp. 899–911, 2020.' ista: 'Cho UH, Hetzer M. 2020. Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging. Neuron. 106(6), 899–911.' mla: 'Cho, Ukrae H., and Martin Hetzer. “Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.” Neuron, vol. 106, no. 6, Elsevier, 2020, pp. 899–911, doi:10.1016/j.neuron.2020.05.031.' short: U.H. Cho, M. Hetzer, Neuron 106 (2020) 899–911. date_created: 2022-04-07T07:43:36Z date_published: 2020-06-17T00:00:00Z date_updated: 2022-07-18T08:29:35Z day: '17' doi: 10.1016/j.neuron.2020.05.031 extern: '1' external_id: pmid: - '32553207' intvolume: ' 106' issue: '6' keyword: - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2020.05.031 month: '06' oa: 1 oa_version: Published Version page: 899-911 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging' type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 106 year: '2020' ... --- _id: '11057' abstract: - lang: eng text: During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division. article_processing_charge: No article_type: original author: - first_name: Hyeseon full_name: Kang, Hyeseon last_name: Kang - first_name: Maxim N. full_name: Shokhirev, Maxim N. last_name: Shokhirev - first_name: Zhichao full_name: Xu, Zhichao last_name: Xu - first_name: Sahaana full_name: Chandran, Sahaana last_name: Chandran - first_name: Jesse R. full_name: Dixon, Jesse R. last_name: Dixon - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. 2020;34(13-14):913-930. doi:10.1101/gad.335794.119 apa: Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., & Hetzer, M. (2020). Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.335794.119 chicago: Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” Genes & Development. Cold Spring Harbor Laboratory Press, 2020. https://doi.org/10.1101/gad.335794.119. ieee: H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer, “Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation,” Genes & Development, vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020. ista: Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. 34(13–14), 913–930. mla: Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” Genes & Development, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press, 2020, pp. 913–30, doi:10.1101/gad.335794.119. short: H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes & Development 34 (2020) 913–930. date_created: 2022-04-07T07:44:09Z date_published: 2020-04-28T00:00:00Z date_updated: 2022-07-18T08:31:08Z day: '28' ddc: - '570' doi: 10.1101/gad.335794.119 extern: '1' external_id: pmid: - '32499403' file: - access_level: open_access checksum: 84e92d40e67936c739628315c238daf9 content_type: application/pdf creator: dernst date_created: 2022-04-08T07:12:33Z date_updated: 2022-04-08T07:12:33Z file_id: '11136' file_name: 2020_GenesDevelopment_Kang.pdf file_size: 4406772 relation: main_file success: 1 file_date_updated: 2022-04-08T07:12:33Z has_accepted_license: '1' intvolume: ' 34' issue: 13-14 keyword: - Developmental Biology - Genetics language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 913-930 pmid: 1 publication: Genes & Development publication_identifier: issn: - 0890-9369 - 1549-5477 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation 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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 34 year: '2020' ... --- _id: '11058' abstract: - lang: eng text: Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis. article_number: e201900623 article_processing_charge: No article_type: original author: - first_name: Simone full_name: Bersini, Simone last_name: Bersini - first_name: Nikki K full_name: Lytle, Nikki K last_name: Lytle - first_name: Roberta full_name: Schulte, Roberta last_name: Schulte - first_name: Ling full_name: Huang, Ling last_name: Huang - first_name: Geoffrey M full_name: Wahl, Geoffrey M last_name: Wahl - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 2020;3(1). doi:10.26508/lsa.201900623 apa: Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., & Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. Life Science Alliance. https://doi.org/10.26508/lsa.201900623 chicago: Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance. Life Science Alliance, 2020. https://doi.org/10.26508/lsa.201900623. ieee: S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer, “Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling,” Life Science Alliance, vol. 3, no. 1. Life Science Alliance, 2020. ista: Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 3(1), e201900623. mla: Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” Life Science Alliance, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:10.26508/lsa.201900623. short: S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020). date_created: 2022-04-07T07:44:18Z date_published: 2020-01-01T00:00:00Z date_updated: 2022-07-18T08:31:20Z day: '01' ddc: - '570' doi: 10.26508/lsa.201900623 extern: '1' external_id: pmid: - '31959624' file: - access_level: open_access checksum: 3bf33e7e93bef7823287807206b69b38 content_type: application/pdf creator: dernst date_created: 2022-04-08T07:33:01Z date_updated: 2022-04-08T07:33:01Z file_id: '11137' file_name: 2020_LifeScienceAlliance_Bersini.pdf file_size: 2653960 relation: main_file success: 1 file_date_updated: 2022-04-08T07:33:01Z has_accepted_license: '1' intvolume: ' 3' issue: '1' keyword: - Health - Toxicology and Mutagenesis - Plant Science - Biochemistry - Genetics and Molecular Biology (miscellaneous) - Ecology language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Life Science Alliance publication_identifier: issn: - 2575-1077 publication_status: published publisher: Life Science Alliance quality_controlled: '1' scopus_import: '1' status: public title: Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling 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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 3 year: '2020' ... --- _id: '11503' abstract: - lang: eng text: "Context. The Lyα emitter (LAE) fraction, XLAE, is a potentially powerful probe of the evolution of the intergalactic neutral hydrogen gas fraction. However, uncertainties in the measurement of XLAE are still under debate.\r\nAims. Thanks to deep data obtained with the integral field spectrograph Multi Unit Spectroscopic Explorer (MUSE), we can measure the evolution of the LAE fraction homogeneously over a wide redshift range of z ≈ 3–6 for UV-faint galaxies (down to UV magnitudes of M1500 ≈ −17.75). This is a significantly fainter range than in former studies (M1500 ≤ −18.75) and it allows us to probe the bulk of the population of high-redshift star-forming galaxies.\r\nMethods. We constructed a UV-complete photometric-redshift sample following UV luminosity functions and measured the Lyα emission with MUSE using the latest (second) data release from the MUSE Hubble Ultra Deep Field Survey.\r\nResults. We derived the redshift evolution of XLAE for M1500 ∈ [ − 21.75; −17.75] for the first time with a equivalent width range EW(Lyα) ≥ 65 Å and found low values of XLAE ≲ 30% at z ≲ 6. The best-fit linear relation is XLAE = 0.07+0.06−0.03z − 0.22+0.12−0.24. For M1500 ∈ [ − 20.25; −18.75] and EW(Lyα) ≥ 25 Å, our XLAE values are consistent with those in the literature within 1σ at z ≲ 5, but our median values are systematically lower than reported values over the whole redshift range. In addition, we do not find a significant dependence of XLAE on M1500 for EW(Lyα) ≥ 50 Å at z ≈ 3–4, in contrast with previous work. The differences in XLAE mainly arise from selection biases for Lyman Break Galaxies (LBGs) in the literature: UV-faint LBGs are more easily selected if they have strong Lyα emission, hence XLAE is biased towards higher values when those samples are used.\r\nConclusions. Our results suggest either a lower increase of XLAE towards z ≈ 6 than previously suggested, or even a turnover of XLAE at z ≈ 5.5, which may be the signature of a late or patchy reionization process. We compared our results with predictions from a cosmological galaxy evolution model. We find that a model with a bursty star formation (SF) can reproduce our observed LAE fractions much better than models where SF is a smooth function of time." acknowledgement: We thank the anonymous referee for constructive comments and suggestions. We would like to express our gratitude to Stephane De Barros and Pablo Arrabal Haro for kindly providing their data plotted in Figs. 1, 2, and 8. We are grateful to Kazuhiro Shimasaku, Masami Ouchi, Rieko Momose, Daniel Schaerer, Hidenobu Yajima, Taku Okamura, Makoto Ando, and Hinako Goto for giving insightful comments and suggestions. This work is based on observations taken by VLT, which is operated by European Southern Observatory. This research made use of Astropy (http://www.astropy.org), which is a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018), MARZ, MPDAF, and matplotlib (Hunter 2007). H.K. acknowledges support from Japan Society for the Promotion of Science (JSPS) through the JSPS Research Fellowship for Young Scientists and Overseas Challenge Program for Young Researchers. AV acknowledges support from the ERC starting grant 757258-TRIPLE and the SNF Professorship 176808-TRIPLE. This work was supported by the project FOGHAR (Agence Nationale de la Recherche, ANR-13-BS05-0010-02). JB acknowledges support from the ORAGE project from the Agence Nationale de la Recherche under grant ANR-14-CE33-0016-03. JR acknowledges support from the ERC starting grant 336736-CALENDS. T. H. acknowledges supports by the Grant-inAid for Scientic Research 19J01620. article_number: A12 article_processing_charge: No article_type: original author: - first_name: Haruka full_name: Kusakabe, Haruka last_name: Kusakabe - first_name: Jérémy full_name: Blaizot, Jérémy last_name: Blaizot - first_name: Thibault full_name: Garel, Thibault last_name: Garel - first_name: Anne full_name: Verhamme, Anne last_name: Verhamme - first_name: Roland full_name: Bacon, Roland last_name: Bacon - first_name: Johan full_name: Richard, Johan last_name: Richard - first_name: Takuya full_name: Hashimoto, Takuya last_name: Hashimoto - first_name: Hanae full_name: Inami, Hanae last_name: Inami - first_name: Simon full_name: Conseil, Simon last_name: Conseil - first_name: Bruno full_name: Guiderdoni, Bruno last_name: Guiderdoni - first_name: Alyssa B. full_name: Drake, Alyssa B. last_name: Drake - first_name: Edmund full_name: Christian Herenz, Edmund last_name: Christian Herenz - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Pascal full_name: Oesch, Pascal last_name: Oesch - 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: Raffaella full_name: Anna Marino, Raffaella last_name: Anna Marino - first_name: Kasper full_name: Borello Schmidt, Kasper last_name: Borello Schmidt - first_name: Roser full_name: Pelló, Roser last_name: Pelló - first_name: Michael full_name: Maseda, Michael last_name: Maseda - first_name: Floriane full_name: Leclercq, Floriane last_name: Leclercq - first_name: Josephine full_name: Kerutt, Josephine last_name: Kerutt - first_name: Guillaume full_name: Mahler, Guillaume last_name: Mahler citation: ama: 'Kusakabe H, Blaizot J, Garel T, et al. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics. 2020;638. doi:10.1051/0004-6361/201937340' apa: 'Kusakabe, H., Blaizot, J., Garel, T., Verhamme, A., Bacon, R., Richard, J., … Mahler, G. (2020). The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201937340' chicago: 'Kusakabe, Haruka, Jérémy Blaizot, Thibault Garel, Anne Verhamme, Roland Bacon, Johan Richard, Takuya Hashimoto, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201937340.' ieee: 'H. Kusakabe et al., “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6,” Astronomy & Astrophysics, vol. 638. EDP Sciences, 2020.' ista: 'Kusakabe H, Blaizot J, Garel T, Verhamme A, Bacon R, Richard J, Hashimoto T, Inami H, Conseil S, Guiderdoni B, Drake AB, Christian Herenz E, Schaye J, Oesch P, Matthee JJ, Anna Marino R, Borello Schmidt K, Pelló R, Maseda M, Leclercq F, Kerutt J, Mahler G. 2020. The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6. Astronomy & Astrophysics. 638, A12.' mla: 'Kusakabe, Haruka, et al. “The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα Emitter Fraction from z = 3 to z = 6.” Astronomy & Astrophysics, vol. 638, A12, EDP Sciences, 2020, doi:10.1051/0004-6361/201937340.' short: H. Kusakabe, J. Blaizot, T. Garel, A. Verhamme, R. Bacon, J. Richard, T. Hashimoto, H. Inami, S. Conseil, B. Guiderdoni, A.B. Drake, E. Christian Herenz, J. Schaye, P. Oesch, J.J. Matthee, R. Anna Marino, K. Borello Schmidt, R. Pelló, M. Maseda, F. Leclercq, J. Kerutt, G. Mahler, Astronomy & Astrophysics 638 (2020). date_created: 2022-07-06T09:50:48Z date_published: 2020-06-03T00:00:00Z date_updated: 2022-07-19T09:35:20Z day: '03' doi: 10.1051/0004-6361/201937340 extern: '1' external_id: arxiv: - '2003.12083' intvolume: ' 638' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'dark ages / reionization / first stars / early Universe / cosmology: observations / galaxies: evolution / galaxies: high-redshift / intergalactic medium' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2003.12083 month: '06' 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' scopus_import: '1' status: public title: 'The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 638 year: '2020' ... --- _id: '11504' abstract: - lang: eng text: We present spatially resolved maps of six individually-detected Lyman α haloes (LAHs) as well as a first statistical analysis of the Lyman α (Lyα) spectral signature in the circum-galactic medium of high-redshift star-forming galaxies (−17.5 >  MUV >  −21.5) using the Multi-Unit Spectroscopic Explorer. Our resolved spectroscopic analysis of the LAHs reveals significant intrahalo variations of the Lyα line profile. Using a three-dimensional two-component model for the Lyα emission, we measured the full width at half maximum (FWHM), the peak velocity shift, and the asymmetry of the Lyα line in the core and in the halo of 19 galaxies. We find that the Lyα line shape is statistically different in the halo compared to the core (in terms of width, peak wavelength, and asymmetry) for ≈40% of our galaxies. Similarly to object-by-object based studies and a recent resolved study using lensing, we find a correlation between the peak velocity shift and the width of the Lyα line both at the interstellar and circum-galactic scales. This trend has been predicted by radiative transfer simulations of galactic winds as a result of resonant scattering in outflows. While there is a lack of correlation between the spectral properties and the spatial scale lengths of our LAHs, we find a correlation between the width of the line in the LAH and the halo flux fraction. Interestingly, UV bright galaxies (MUV <  −20) show broader, more redshifted, and less asymmetric Lyα lines in their haloes. The most significant correlation found is for the FWHM of the line and the UV continuum slope of the galaxy, suggesting that the redder galaxies have broader Lyα lines. The generally broad and red line shapes found in the halo component suggest that the Lyα haloes are powered either by scattering processes through an outflowing medium, fluorescent emission from outflowing cold clumps of gas, or a mix of both. Considering the large diversity of the Lyα line profiles observed in our sample and the lack of strong correlation, the interpretation of our results is still broadly open and underlines the need for realistic spatially resolved models of the LAHs. acknowledgement: F.L., R.B., and S.C. acknowledge support from the ERC advanced grant 339659-MUSICOS. F.L., T.G., H.K., and A.V. acknowledge support from the ERC starting grant ERC-757258-TRIPLE. A.C. and J.R. acknowledge support from the ERC starting grant 336736-CALENDS. J.B. acknowledges support by FCT/MCTES through national funds (PID-DAC) by grant UID/FIS/04434/2019 and through Investigador FCT Contract No.IF/01654/2014/CP1215/CT0003. T.H. was supported by Leading Initiative for Excellent Young Researchers, MEXT, Japan. article_number: A82 article_processing_charge: No article_type: original author: - first_name: Floriane full_name: Leclercq, Floriane last_name: Leclercq - first_name: Roland full_name: Bacon, Roland last_name: Bacon - first_name: Anne full_name: Verhamme, Anne last_name: Verhamme - first_name: Thibault full_name: Garel, Thibault last_name: Garel - first_name: Jérémy full_name: Blaizot, Jérémy last_name: Blaizot - first_name: Jarle full_name: Brinchmann, Jarle last_name: Brinchmann - first_name: Sebastiano full_name: Cantalupo, Sebastiano last_name: Cantalupo - first_name: Adélaïde full_name: Claeyssens, Adélaïde last_name: Claeyssens - first_name: Simon full_name: Conseil, Simon last_name: Conseil - first_name: Thierry full_name: Contini, Thierry last_name: Contini - first_name: Takuya full_name: Hashimoto, Takuya last_name: Hashimoto - first_name: Edmund Christian full_name: Herenz, Edmund Christian last_name: Herenz - first_name: Haruka full_name: Kusakabe, Haruka last_name: Kusakabe - first_name: Raffaella Anna full_name: Marino, Raffaella Anna last_name: Marino - first_name: Michael full_name: Maseda, Michael last_name: Maseda - 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: Peter full_name: Mitchell, Peter last_name: Mitchell - first_name: Gabriele full_name: Pezzulli, Gabriele last_name: Pezzulli - first_name: Johan full_name: Richard, Johan last_name: Richard - first_name: Kasper Borello full_name: Schmidt, Kasper Borello last_name: Schmidt - first_name: Lutz full_name: Wisotzki, Lutz last_name: Wisotzki citation: ama: 'Leclercq F, Bacon R, Verhamme A, et al. The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3. Astronomy & Astrophysics. 2020;635. doi:10.1051/0004-6361/201937339' apa: 'Leclercq, F., Bacon, R., Verhamme, A., Garel, T., Blaizot, J., Brinchmann, J., … Wisotzki, L. (2020). The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201937339' chicago: 'Leclercq, Floriane, Roland Bacon, Anne Verhamme, Thibault Garel, Jérémy Blaizot, Jarle Brinchmann, Sebastiano Cantalupo, et al. “The MUSE Hubble Ultra Deep Field Survey: XIII. Spatially Resolved Spectral Properties of Lyman α Haloes around Star-Forming Galaxies at z > 3.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/201937339.' ieee: 'F. Leclercq et al., “The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3,” Astronomy & Astrophysics, vol. 635. EDP Sciences, 2020.' ista: 'Leclercq F, Bacon R, Verhamme A, Garel T, Blaizot J, Brinchmann J, Cantalupo S, Claeyssens A, Conseil S, Contini T, Hashimoto T, Herenz EC, Kusakabe H, Marino RA, Maseda M, Matthee JJ, Mitchell P, Pezzulli G, Richard J, Schmidt KB, Wisotzki L. 2020. The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3. Astronomy & Astrophysics. 635, A82.' mla: 'Leclercq, Floriane, et al. “The MUSE Hubble Ultra Deep Field Survey: XIII. Spatially Resolved Spectral Properties of Lyman α Haloes around Star-Forming Galaxies at z > 3.” Astronomy & Astrophysics, vol. 635, A82, EDP Sciences, 2020, doi:10.1051/0004-6361/201937339.' short: F. Leclercq, R. Bacon, A. Verhamme, T. Garel, J. Blaizot, J. Brinchmann, S. Cantalupo, A. Claeyssens, S. Conseil, T. Contini, T. Hashimoto, E.C. Herenz, H. Kusakabe, R.A. Marino, M. Maseda, J.J. Matthee, P. Mitchell, G. Pezzulli, J. Richard, K.B. Schmidt, L. Wisotzki, Astronomy & Astrophysics 635 (2020). date_created: 2022-07-06T09:56:20Z date_published: 2020-03-11T00:00:00Z date_updated: 2022-07-19T09:36:58Z day: '11' doi: 10.1051/0004-6361/201937339 extern: '1' external_id: arxiv: - '2002.05731' intvolume: ' 635' keyword: - Space and Planetary Science - 'Astronomy and Astrophysics galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.05731 month: '03' 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' scopus_import: '1' status: public title: 'The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 635 year: '2020' ... --- _id: '11501' abstract: - lang: eng text: We investigated the ultraviolet (UV) spectral properties of faint Lyman-α emitters (LAEs) in the redshift range 2.9 ≤ z ≤ 4.6, and we provide material to prepare future observations of the faint Universe. We used data from the MUSE Hubble Ultra Deep Survey to construct mean rest-frame spectra of continuum-faint (median MUV of −18 and down to MUV of −16), low stellar mass (median value of 108.4 M⊙ and down to 107 M⊙) LAEs at redshift z ≳ 3. We computed various averaged spectra of LAEs, subsampled on the basis of their observational (e.g., Lyα strength, UV magnitude and spectral slope) and physical (e.g., stellar mass and star-formation rate) properties. We searched for UV spectral features other than Lyα, such as higher ionization nebular emission lines and absorption features. We successfully observed the O III]λ1666 and [C III]λ1907+C III]λ1909 collisionally excited emission lines and the He IIλ1640 recombination feature, as well as the resonant C IVλλ1548,1551 doublet either in emission or P-Cygni. We compared the observed spectral properties of the different mean spectra and find the emission lines to vary with the observational and physical properties of the LAEs. In particular, the mean spectra of LAEs with larger Lyα equivalent widths, fainter UV magnitudes, bluer UV spectral slopes, and lower stellar masses show the strongest nebular emission. The line ratios of these lines are similar to those measured in the spectra of local metal-poor galaxies, while their equivalent widths are weaker compared to the handful of extreme values detected in individual spectra of z >  2 galaxies. This suggests that weak UV features are likely ubiquitous in high z, low-mass, and faint LAEs. We publicly released the stacked spectra, as they can serve as empirical templates for the design of future observations, such as those with the James Webb Space Telescope and the Extremely Large Telescope. acknowledgement: 'We thank Margherita Talia, Stéphane Charlot, Adele Plat and Alba Vidal-García for helpful discussions. This work is supported by the ERC advanced grant 339659-MUSICOS (R. Bacon). AF acknowledges the support from grant PRIN MIUR 2017 20173ML3WW. MVM and JP would like to thank the Leiden/ESA Astrophysics Program for Summer Students (LEAPS) for funding at the outset of this project. FL, HK, and AV acknowledge support from the ERC starting grant ERC-757258-TRIPLE. TH was supported by Leading Initiative for Excellent Young Researchers, MEXT, Japan. JB acknowledges support by FCT/MCTES through national funds by the grant UID/FIS/04434/2019, UIDB/04434/2020 and UIDP/04434/2020 and through the Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. HI acknowledges support from JSPS KAKENHI Grant Number JP19K23462. We would also like to thank the organizers and participants of the Leiden Lorentz Center workshop: Revolutionary Spectroscopy of Today as a Springboard to Webb. This work made use of several open source python packages: NUMPY (van der Walt et al. 2011), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration 2013) and MPDAF (MUSE Python Data Analysis Framework, Piqueras et al. 2019).' article_number: A118 article_processing_charge: No article_type: original author: - first_name: Anna full_name: Feltre, Anna last_name: Feltre - first_name: Michael V. full_name: Maseda, Michael V. last_name: Maseda - first_name: Roland full_name: Bacon, Roland last_name: Bacon - first_name: Jayadev full_name: Pradeep, Jayadev last_name: Pradeep - first_name: Floriane full_name: Leclercq, Floriane last_name: Leclercq - first_name: Haruka full_name: Kusakabe, Haruka last_name: Kusakabe - first_name: Lutz full_name: Wisotzki, Lutz last_name: Wisotzki - first_name: Takuya full_name: Hashimoto, Takuya last_name: Hashimoto - first_name: Kasper B. full_name: Schmidt, Kasper B. last_name: Schmidt - first_name: Jeremy full_name: Blaizot, Jeremy last_name: Blaizot - first_name: Jarle full_name: Brinchmann, Jarle last_name: Brinchmann - first_name: Leindert full_name: Boogaard, Leindert last_name: Boogaard - first_name: Sebastiano full_name: Cantalupo, Sebastiano last_name: Cantalupo - first_name: David full_name: Carton, David last_name: Carton - first_name: Hanae full_name: Inami, Hanae last_name: Inami - first_name: Wolfram full_name: Kollatschny, Wolfram last_name: Kollatschny - first_name: Raffaella A. full_name: Marino, Raffaella A. last_name: Marino - 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: Themiya full_name: Nanayakkara, Themiya last_name: Nanayakkara - first_name: Johan full_name: Richard, Johan last_name: Richard - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Laurence full_name: Tresse, Laurence last_name: Tresse - first_name: Tanya full_name: Urrutia, Tanya last_name: Urrutia - first_name: Anne full_name: Verhamme, Anne last_name: Verhamme - first_name: Peter M. full_name: Weilbacher, Peter M. last_name: Weilbacher citation: ama: 'Feltre A, Maseda MV, Bacon R, et al. The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics. 2020;641. doi:10.1051/0004-6361/202038133' apa: 'Feltre, A., Maseda, M. V., Bacon, R., Pradeep, J., Leclercq, F., Kusakabe, H., … Weilbacher, P. M. (2020). The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202038133' chicago: 'Feltre, Anna, Michael V. Maseda, Roland Bacon, Jayadev Pradeep, Floriane Leclercq, Haruka Kusakabe, Lutz Wisotzki, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z > 3.” Astronomy & Astrophysics. EDP Sciences, 2020. https://doi.org/10.1051/0004-6361/202038133.' ieee: 'A. Feltre et al., “The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3,” Astronomy & Astrophysics, vol. 641. EDP Sciences, 2020.' ista: 'Feltre A, Maseda MV, Bacon R, Pradeep J, Leclercq F, Kusakabe H, Wisotzki L, Hashimoto T, Schmidt KB, Blaizot J, Brinchmann J, Boogaard L, Cantalupo S, Carton D, Inami H, Kollatschny W, Marino RA, Matthee JJ, Nanayakkara T, Richard J, Schaye J, Tresse L, Urrutia T, Verhamme A, Weilbacher PM. 2020. The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3. Astronomy & Astrophysics. 641, A118.' mla: 'Feltre, Anna, et al. “The MUSE Hubble Ultra Deep Field Survey: XV. The Mean Rest-UV Spectra of Lyα Emitters at z > 3.” Astronomy & Astrophysics, vol. 641, A118, EDP Sciences, 2020, doi:10.1051/0004-6361/202038133.' short: A. Feltre, M.V. Maseda, R. Bacon, J. Pradeep, F. Leclercq, H. Kusakabe, L. Wisotzki, T. Hashimoto, K.B. Schmidt, J. Blaizot, J. Brinchmann, L. Boogaard, S. Cantalupo, D. Carton, H. Inami, W. Kollatschny, R.A. Marino, J.J. Matthee, T. Nanayakkara, J. Richard, J. Schaye, L. Tresse, T. Urrutia, A. Verhamme, P.M. Weilbacher, Astronomy & Astrophysics 641 (2020). date_created: 2022-07-06T09:38:16Z date_published: 2020-09-18T00:00:00Z date_updated: 2022-07-19T09:35:43Z day: '18' doi: 10.1051/0004-6361/202038133 extern: '1' external_id: arxiv: - '2007.01878' intvolume: ' 641' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution / galaxies: high-redshift / ISM: lines and bands / ultraviolet: ISM / ultraviolet: galaxies' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.01878 month: '09' 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' scopus_import: '1' status: public title: 'The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 641 year: '2020' ... --- _id: '11513' abstract: - lang: eng text: We report the spectroscopic confirmation of a new protocluster in the COSMOS field at z ∼ 2.2, COSMOS Cluster 2.2 (CC2.2), originally identified as an overdensity of narrowband selected Hα emitting candidates. With only two masks of Keck/MOSFIRE near-IR spectroscopy in both H (∼1.47–1.81 μm) and K (∼1.92–2.40 μm) bands (∼1.5 hr each), we confirm 35 unique protocluster members with at least two emission lines detected with S/N > 3. Combined with 12 extra members from the zCOSMOS-deep spectroscopic survey (47 in total), we estimate a mean redshift and a line-of-sight velocity dispersion of zmean = 2.23224 ± 0.00101 and σlos = 645 ± 69 km s−1 for this protocluster, respectively. Assuming virialization and spherical symmetry for the system, we estimate a total mass of Mvir ∼ (1–2) ×1014M⊙ for the structure. We evaluate a number density enhancement of δg ∼ 7 for this system and we argue that the structure is likely not fully virialized at z ∼ 2.2. However, in a spherical collapse model, δg is expected to grow to a linear matter enhancement of ∼1.9 by z = 0, exceeding the collapse threshold of 1.69, and leading to a fully collapsed and virialized Coma-type structure with a total mass of Mdyn(z = 0) ∼ 9.2 × 1014M⊙ by now. This observationally efficient confirmation suggests that large narrowband emission-line galaxy surveys, when combined with ancillary photometric data, can be used to effectively trace the large-scale structure and protoclusters at a time when they are mostly dominated by star-forming galaxies. acknowledgement: We are thankful to the anonymous referee for useful comments and suggestions that improved the quality of this paper. B.D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. B.D. is thankful to Andreas Faisst, Laura Danly, and Matthew Burlando for their companionship during the observing run. B.D. is grateful to the COSMOS team for their useful comments during the team meeting in New York City 2019 May 14–17. A.R. research was made possible by Friends of W. M. Keck Observatory who philanthropically support the Keck Science Collaborative (KSC) fund. The observations presented herein were obtained at the W. M. Keck Observatory (program C236, PI Scoville), which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors would like to recognize and acknowledge the very prominent cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawaiian community. We are fortunate to have the opportunity to perform observations from this mountain. article_number: '8' article_processing_charge: No article_type: original author: - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Nick Z. full_name: Scoville, Nick Z. last_name: Scoville - first_name: Christopher full_name: Martin, Christopher last_name: Martin - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher - first_name: Alessandro full_name: Rettura, Alessandro last_name: Rettura - 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: Peter full_name: Capak, Peter last_name: Capak - first_name: Nima full_name: Chartab, Nima last_name: Chartab - first_name: Shoubaneh full_name: Hemmati, Shoubaneh last_name: Hemmati - first_name: Daniel full_name: Masters, Daniel last_name: Masters - first_name: Hooshang full_name: Nayyeri, Hooshang last_name: Nayyeri - first_name: Donal full_name: O’Sullivan, Donal last_name: O’Sullivan - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Zahra full_name: Sattari, Zahra last_name: Sattari - first_name: Abtin full_name: Shahidi, Abtin last_name: Shahidi - first_name: Mara full_name: Salvato, Mara last_name: Salvato - first_name: Brian C. full_name: Lemaux, Brian C. last_name: Lemaux - first_name: Olivier Le full_name: Fèvre, Olivier Le last_name: Fèvre - first_name: Olga full_name: Cucciati, Olga last_name: Cucciati citation: ama: Darvish B, Scoville NZ, Martin C, et al. Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. 2020;892(1). doi:10.3847/1538-4357/ab75c3 apa: Darvish, B., Scoville, N. Z., Martin, C., Sobral, D., Mobasher, B., Rettura, A., … Cucciati, O. (2020). Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab75c3 chicago: Darvish, Behnam, Nick Z. Scoville, Christopher Martin, David Sobral, Bahram Mobasher, Alessandro Rettura, Jorryt J Matthee, et al. “Spectroscopic Confirmation of a Coma Cluster Progenitor at z ∼ 2.2.” The Astrophysical Journal. IOP Publishing, 2020. https://doi.org/10.3847/1538-4357/ab75c3. ieee: B. Darvish et al., “Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2,” The Astrophysical Journal, vol. 892, no. 1. IOP Publishing, 2020. ista: Darvish B, Scoville NZ, Martin C, Sobral D, Mobasher B, Rettura A, Matthee JJ, Capak P, Chartab N, Hemmati S, Masters D, Nayyeri H, O’Sullivan D, Paulino-Afonso A, Sattari Z, Shahidi A, Salvato M, Lemaux BC, Fèvre OL, Cucciati O. 2020. Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2. The Astrophysical Journal. 892(1), 8. mla: Darvish, Behnam, et al. “Spectroscopic Confirmation of a Coma Cluster Progenitor at z ∼ 2.2.” The Astrophysical Journal, vol. 892, no. 1, 8, IOP Publishing, 2020, doi:10.3847/1538-4357/ab75c3. short: B. Darvish, N.Z. Scoville, C. Martin, D. Sobral, B. Mobasher, A. Rettura, J.J. Matthee, P. Capak, N. Chartab, S. Hemmati, D. Masters, H. Nayyeri, D. O’Sullivan, A. Paulino-Afonso, Z. Sattari, A. Shahidi, M. Salvato, B.C. Lemaux, O.L. Fèvre, O. Cucciati, The Astrophysical Journal 892 (2020). date_created: 2022-07-06T13:10:51Z date_published: 2020-03-19T00:00:00Z date_updated: 2022-07-19T09:31:35Z day: '19' doi: 10.3847/1538-4357/ab75c3 extern: '1' external_id: arxiv: - '2002.06207' intvolume: ' 892' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.06207 month: '03' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 892 year: '2020' ... --- _id: '11528' abstract: - lang: eng text: Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ≈10−17 erg cm−2 s−1 (⁠≈1042 erg s−1⁠) and a median star formation rate (SFR) of ≈1.3 M⊙ yr−1 (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, Voffset∝SFR0.16±0.03⁠. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs. acknowledgement: 'We thank the anonymous referee for useful suggestions. This study is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme(s): 094.A-0131(B), 095.A 0200(A), 096.A0222(A), 097.A-0089(A), and 099.A-0159(A). SM acknowledges support from the Alexander von Humboldt Foundation, Germany. SM thanks Christian Herenz for useful discussion. SC gratefully acknowledges support from Swiss National Science Foundation grant PP00P2 163824. JB acknowledges support by FCT/MCTES through national funds by grant UID/FIS/04434/2019 and through Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. NB and JZ acknowledge support from ANR grant ANR-17-CE31- 0017 (3DGasFlows). AC and JR acknowledge support from the ERC starting grant 336736-CALENDS. MA acknowledges support from European Union’s H2020 Marie Skłodowska-Curie Actions grant 721463 to the SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness (MINECO) under grant number AYA2016-76219-P. MA also acknowledges support from the Fundacion BBVA under its 2017 programme of assistance to ´scientific research groups, for the project ‘Using machine-learning techniques to drag galaxies from the noise in deep imaging’. FL and AV acknowledge support from the ERC starting grant ERC757258-TRIPLE.' article_processing_charge: No article_type: original author: - first_name: Sowgat full_name: Muzahid, Sowgat last_name: Muzahid - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Raffaella Anna full_name: Marino, Raffaella Anna last_name: Marino - first_name: Sebastiano full_name: Cantalupo, Sebastiano last_name: Cantalupo - first_name: Jarle full_name: Brinchmann, Jarle last_name: Brinchmann - first_name: Thierry full_name: Contini, Thierry last_name: Contini - first_name: Martin full_name: Wendt, Martin last_name: Wendt - first_name: Lutz full_name: Wisotzki, Lutz last_name: Wisotzki - first_name: Johannes full_name: Zabl, Johannes last_name: Zabl - first_name: Nicolas full_name: Bouché, Nicolas last_name: Bouché - first_name: Mohammad full_name: Akhlaghi, Mohammad last_name: Akhlaghi - first_name: Hsiao-Wen full_name: Chen, Hsiao-Wen last_name: Chen - first_name: Adélaîde full_name: Claeyssens, Adélaîde last_name: Claeyssens - first_name: Sean full_name: Johnson, Sean last_name: Johnson - first_name: Floriane full_name: Leclercq, Floriane last_name: Leclercq - first_name: Michael full_name: Maseda, Michael last_name: Maseda - 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: Johan full_name: Richard, Johan last_name: Richard - first_name: Tanya full_name: Urrutia, Tanya last_name: Urrutia - first_name: Anne full_name: Verhamme, Anne last_name: Verhamme citation: ama: 'Muzahid S, Schaye J, Marino RA, et al. MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. 2020;496(2):1013-1022. doi:10.1093/mnras/staa1347' apa: 'Muzahid, S., Schaye, J., Marino, R. A., Cantalupo, S., Brinchmann, J., Contini, T., … Verhamme, A. (2020). MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa1347' chicago: 'Muzahid, Sowgat, Joop Schaye, Raffaella Anna Marino, Sebastiano Cantalupo, Jarle Brinchmann, Thierry Contini, Martin Wendt, et al. “MUSEQuBES: Calibrating the Redshifts of Lyα Emitters Using Stacked Circumgalactic Medium Absorption Profiles.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa1347.' ieee: 'S. Muzahid et al., “MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles,” Monthly Notices of the Royal Astronomical Society, vol. 496, no. 2. Oxford University Press, pp. 1013–1022, 2020.' ista: 'Muzahid S, Schaye J, Marino RA, Cantalupo S, Brinchmann J, Contini T, Wendt M, Wisotzki L, Zabl J, Bouché N, Akhlaghi M, Chen H-W, Claeyssens A, Johnson S, Leclercq F, Maseda M, Matthee JJ, Richard J, Urrutia T, Verhamme A. 2020. MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles. Monthly Notices of the Royal Astronomical Society. 496(2), 1013–1022.' mla: 'Muzahid, Sowgat, et al. “MUSEQuBES: Calibrating the Redshifts of Lyα Emitters Using Stacked Circumgalactic Medium Absorption Profiles.” Monthly Notices of the Royal Astronomical Society, vol. 496, no. 2, Oxford University Press, 2020, pp. 1013–22, doi:10.1093/mnras/staa1347.' short: S. Muzahid, J. Schaye, R.A. Marino, S. Cantalupo, J. Brinchmann, T. Contini, M. Wendt, L. Wisotzki, J. Zabl, N. Bouché, M. Akhlaghi, H.-W. Chen, A. Claeyssens, S. Johnson, F. Leclercq, M. Maseda, J.J. Matthee, J. Richard, T. Urrutia, A. Verhamme, Monthly Notices of the Royal Astronomical Society 496 (2020) 1013–1022. date_created: 2022-07-07T10:20:11Z date_published: 2020-08-01T00:00:00Z date_updated: 2022-08-18T11:00:24Z day: '01' doi: 10.1093/mnras/staa1347 extern: '1' external_id: arxiv: - '1910.03593' intvolume: ' 496' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: haloes' - 'galaxies: high-redshift' - 'quasars: absorption lines' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.03593 month: '08' oa: 1 oa_version: Preprint page: 1013-1022 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/mnras/staa2668 scopus_import: '1' status: public title: 'MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 496 year: '2020' ... --- _id: '11529' abstract: - lang: eng text: CR7 is among the most luminous Ly α emitters (LAEs) known at z = 6.6 and consists of at least three UV components that are surrounded by Ly α emission. Previous studies have suggested that it may host an extreme ionizing source. Here, we present deep integral field spectroscopy of CR7 with VLT/Multi Unit Spectroscopic Explorer (MUSE). We measure extended emission with a similar halo scale length as typical LAEs at z ≈ 5. CR7’s Ly α halo is clearly elongated along the direction connecting the multiple components, likely tracing the underlying gas distribution. The Ly α emission originates almost exclusively from the brightest UV component, but we also identify a faint kinematically distinct Ly α emitting region nearby a fainter component. Combined with new near-infrared data, the MUSE data show that the rest-frame Ly α equivalent width (EW) is ≈100 Å. This is a factor 4 higher than the EW measured in low-redshift analogues with carefully matched Ly α profiles (and thus arguably H I column density), but this EW can plausibly be explained by star formation. Alternative scenarios requiring active galactic nucleus (AGN) powering are also disfavoured by the narrower and steeper Ly α spectrum and much smaller IR to UV ratio compared to obscured AGN in other Ly α blobs. CR7’s Ly α emission, while extremely luminous, resembles the emission in more common LAEs at lower redshifts very well and is likely powered by a young metal-poor starburst. article_processing_charge: No article_type: original author: - 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: Gabriele full_name: Pezzulli, Gabriele last_name: Pezzulli - first_name: Ruari full_name: Mackenzie, Ruari last_name: Mackenzie - first_name: Sebastiano full_name: Cantalupo, Sebastiano last_name: Cantalupo - first_name: Haruka full_name: Kusakabe, Haruka last_name: Kusakabe - first_name: Floriane full_name: Leclercq, Floriane last_name: Leclercq - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Johan full_name: Richard, Johan last_name: Richard - first_name: Lutz full_name: Wisotzki, Lutz last_name: Wisotzki - first_name: Simon full_name: Lilly, Simon last_name: Lilly - first_name: Leindert full_name: Boogaard, Leindert last_name: Boogaard - first_name: Raffaella full_name: Marino, Raffaella last_name: Marino - first_name: Michael full_name: Maseda, Michael last_name: Maseda - first_name: Themiya full_name: Nanayakkara, Themiya last_name: Nanayakkara citation: ama: 'Matthee JJ, Pezzulli G, Mackenzie R, et al. The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. 2020;498(2):3043-3059. doi:10.1093/mnras/staa2550' apa: 'Matthee, J. J., Pezzulli, G., Mackenzie, R., Cantalupo, S., Kusakabe, H., Leclercq, F., … Nanayakkara, T. (2020). The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa2550' chicago: 'Matthee, Jorryt J, Gabriele Pezzulli, Ruari Mackenzie, Sebastiano Cantalupo, Haruka Kusakabe, Floriane Leclercq, David Sobral, et al. “The Nature of CR7 Revealed with MUSE: A Young Starburst Powering Extended Ly α Emission at z = 6.6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa2550.' ieee: 'J. J. Matthee et al., “The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6,” Monthly Notices of the Royal Astronomical Society, vol. 498, no. 2. Oxford University Press, pp. 3043–3059, 2020.' ista: 'Matthee JJ, Pezzulli G, Mackenzie R, Cantalupo S, Kusakabe H, Leclercq F, Sobral D, Richard J, Wisotzki L, Lilly S, Boogaard L, Marino R, Maseda M, Nanayakkara T. 2020. The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6. Monthly Notices of the Royal Astronomical Society. 498(2), 3043–3059.' mla: 'Matthee, Jorryt J., et al. “The Nature of CR7 Revealed with MUSE: A Young Starburst Powering Extended Ly α Emission at z = 6.6.” Monthly Notices of the Royal Astronomical Society, vol. 498, no. 2, Oxford University Press, 2020, pp. 3043–59, doi:10.1093/mnras/staa2550.' short: J.J. Matthee, G. Pezzulli, R. Mackenzie, S. Cantalupo, H. Kusakabe, F. Leclercq, D. Sobral, J. Richard, L. Wisotzki, S. Lilly, L. Boogaard, R. Marino, M. Maseda, T. Nanayakkara, Monthly Notices of the Royal Astronomical Society 498 (2020) 3043–3059. date_created: 2022-07-07T10:36:01Z date_published: 2020-10-01T00:00:00Z date_updated: 2022-08-18T11:04:05Z day: '01' doi: 10.1093/mnras/staa2550 extern: '1' external_id: arxiv: - '2008.01731' intvolume: ' 498' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - dark ages - reionization - first stars - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.01731 month: '10' oa: 1 oa_version: Preprint page: 3043-3059 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 498 year: '2020' ... --- _id: '11533' abstract: - lang: eng text: We explore deep rest-frame UV to FIR data in the COSMOS field to measure the individual spectral energy distributions (SED) of the ∼4000 SC4K (Sobral et al.) Lyman α (Ly α) emitters (LAEs) at z ∼ 2–6. We find typical stellar masses of 109.3 ± 0.6 M⊙ and star formation rates (SFR) of SFRSED=4.4+10.5−2.4 M⊙ yr−1 and SFRLyα=5.9+6.3−2.6 M⊙ yr−1, combined with very blue UV slopes of β=−2.1+0.5−0.4⁠, but with significant variations within the population. MUV and β are correlated in a similar way to UV-selected sources, but LAEs are consistently bluer. This suggests that LAEs are the youngest and/or most dust-poor subset of the UV-selected population. We also study the Ly α rest-frame equivalent width (EW0) and find 45 ‘extreme’ LAEs with EW0 > 240 Å (3σ), implying a low number density of (7 ± 1) × 10−7 Mpc−3. Overall, we measure little to no evolution of the Ly α EW0 and scale length parameter (w0), which are consistently high (EW0=140+280−70 Å, w0=129+11−11 Å) from z ∼ 6 to z ∼ 2 and below. However, w0 is anticorrelated with MUV and stellar mass. Our results imply that sources selected as LAEs have a high Ly α escape fraction (fesc,Ly α) irrespective of cosmic time, but fesc,Ly α is still higher for UV-fainter and lower mass LAEs. The least massive LAEs (<109.5 M⊙) are typically located above the star formation ‘main sequence’ (MS), but the offset from the MS decreases towards z ∼ 6 and towards 1010 M⊙. Our results imply a lack of evolution in the properties of LAEs across time and reveals the increasing overlap in properties of LAEs and UV-continuum selected galaxies as typical star-forming galaxies at high redshift effectively become LAEs. acknowledgement: We thank the anonymous referee for the valuable feedback that significantly improved the quality and clarity of this paper. SS and JC acknowledge studentships from Lancaster University. APA acknowledges support from Fundação para a Ciência e a Tecnologia through the project PTDC/FISAST/31546/2017. The authors would like to thank Ali Khostovan, Sara Perez Sanchez, Alex Bennett and Tom Rose for contributions and discussions in the early stages of this work. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by CALET and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Finally, the authors acknowledge the unique value of the publicly available analysis software TOPCAT (Taylor 2005) and publicly available programming language Python, including the numpy, pyfits, matplotlib, scipy and astropy (Astropy Collaboration et al. 2013) packages. This work is based on the public SC4K sample of LAEs (Sobral et al. 2018a) and we release the full catalogue with all the photometry and properties derived in this paper, in electronic format, along with the relevant tables. article_processing_charge: No article_type: original author: - first_name: S full_name: Santos, S last_name: Santos - first_name: D full_name: Sobral, D last_name: Sobral - 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: J full_name: Calhau, J last_name: Calhau - first_name: E full_name: da Cunha, E last_name: da Cunha - first_name: B full_name: Ribeiro, B last_name: Ribeiro - first_name: A full_name: Paulino-Afonso, A last_name: Paulino-Afonso - first_name: P full_name: Arrabal Haro, P last_name: Arrabal Haro - first_name: J full_name: Butterworth, J last_name: Butterworth citation: ama: Santos S, Sobral D, Matthee JJ, et al. The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. 2020;493(1):141-160. doi:10.1093/mnras/staa093 apa: Santos, S., Sobral, D., Matthee, J. J., Calhau, J., da Cunha, E., Ribeiro, B., … Butterworth, J. (2020). The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa093 chicago: Santos, S, D Sobral, Jorryt J Matthee, J Calhau, E da Cunha, B Ribeiro, A Paulino-Afonso, P Arrabal Haro, and J Butterworth. “The Evolution of Rest-Frame UV Properties, Ly α EWs, and the SFR–Stellar Mass Relation at z ∼ 2–6 for SC4K LAEs.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa093. ieee: S. Santos et al., “The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 1. Oxford University Press, pp. 141–160, 2020. ista: Santos S, Sobral D, Matthee JJ, Calhau J, da Cunha E, Ribeiro B, Paulino-Afonso A, Arrabal Haro P, Butterworth J. 2020. The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs. Monthly Notices of the Royal Astronomical Society. 493(1), 141–160. mla: Santos, S., et al. “The Evolution of Rest-Frame UV Properties, Ly α EWs, and the SFR–Stellar Mass Relation at z ∼ 2–6 for SC4K LAEs.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 1, Oxford University Press, 2020, pp. 141–60, doi:10.1093/mnras/staa093. short: S. Santos, D. Sobral, J.J. Matthee, J. Calhau, E. da Cunha, B. Ribeiro, A. Paulino-Afonso, P. Arrabal Haro, J. Butterworth, Monthly Notices of the Royal Astronomical Society 493 (2020) 141–160. date_created: 2022-07-07T12:05:23Z date_published: 2020-03-01T00:00:00Z date_updated: 2022-08-18T11:27:43Z day: '01' doi: 10.1093/mnras/staa093 extern: '1' external_id: arxiv: - '1910.02959' intvolume: ' 493' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: high-redshift' - 'galaxies: star formation' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.02959 month: '03' oa: 1 oa_version: Preprint page: 141-160 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 493 year: '2020' ... --- _id: '11534' abstract: - lang: eng text: The observed properties of the Lyman-α (Ly α) emission line are a powerful probe of neutral gas in and around galaxies. We present spatially resolved Ly α spectroscopy with VLT/MUSE targeting VR7, a UV-luminous galaxy at z = 6.532 with moderate Ly α equivalent width (EW0 ≈ 38 Å). These data are combined with deep resolved [CII]158μm spectroscopy obtained with ALMA and UV imaging from HST and we also detect UV continuum with MUSE. Ly α emission is clearly detected with S/N ≈ 40 and FWHM of 374 km s−1. Ly α and [C II] are similarly extended beyond the UV, with effective radius reff = 2.1 ± 0.2 kpc for a single exponential model or reff,Lyα,halo=3.45+1.08−0.87 kpc when measured jointly with the UV continuum. The Ly α profile is broader and redshifted with respect to the [C II] line (by 213 km s−1), but there are spatial variations that are qualitatively similar in both lines and coincide with resolved UV components. This suggests that the emission originates from two components with plausibly different H I column densities. We place VR7 in the context of other galaxies at similar and lower redshift. The Ly α halo scale length is similar at different redshifts and velocity shifts with respect to the systemic are typically smaller. Overall, we find little indications of a more neutral vicinity at higher redshift. This means that the local (∼10 kpc) neutral gas conditions that determine the observed Ly α properties in VR7 resemble the conditions in post-reionization galaxies. acknowledgement: 'We thank the referee for their suggestions and constructive comments that helped to improve the presentation of our results. Based on observations obtained with the Very Large Telescope, program 99.A-0462. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program #14699. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2017.1.01451.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan) and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. MG acknowledges support from NASA grant NNX17AK58G. GP and SC gratefully acknowledge support from Swiss National Science Foundation grant PP00P2 163824. BD acknowledges financial support from the National Science Foundation, grant number 1716907. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, SCIPY (Jones et al. 2001; Hunter 2007; van der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration 2013) packages, the astronomical imaging tools SEXTRACTOR, SWARP, and SCAMP (Bertin & Arnouts 1996; Bertin 2006, 2010) and the TOPCAT analysis tool (Taylor 2013).' article_processing_charge: No article_type: original author: - 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: David full_name: Sobral, David last_name: Sobral - first_name: Max full_name: Gronke, Max last_name: Gronke - first_name: Gabriele full_name: Pezzulli, Gabriele last_name: Pezzulli - first_name: Sebastiano full_name: Cantalupo, Sebastiano last_name: Cantalupo - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos citation: ama: Matthee JJ, Sobral D, Gronke M, et al. Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. 2020;492(2):1778-1790. doi:10.1093/mnras/stz3554 apa: Matthee, J. J., Sobral, D., Gronke, M., Pezzulli, G., Cantalupo, S., Röttgering, H., … Santos, S. (2020). Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz3554 chicago: Matthee, Jorryt J, David Sobral, Max Gronke, Gabriele Pezzulli, Sebastiano Cantalupo, Huub Röttgering, Behnam Darvish, and Sérgio Santos. “Resolved Lyman-α Properties of a Luminous Lyman-Break Galaxy in a Large Ionized Bubble at z = 6.53 .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/stz3554. ieee: J. J. Matthee et al., “Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 ,” Monthly Notices of the Royal Astronomical Society, vol. 492, no. 2. Oxford University Press, pp. 1778–1790, 2020. ista: Matthee JJ, Sobral D, Gronke M, Pezzulli G, Cantalupo S, Röttgering H, Darvish B, Santos S. 2020. Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 . Monthly Notices of the Royal Astronomical Society. 492(2), 1778–1790. mla: Matthee, Jorryt J., et al. “Resolved Lyman-α Properties of a Luminous Lyman-Break Galaxy in a Large Ionized Bubble at z = 6.53 .” Monthly Notices of the Royal Astronomical Society, vol. 492, no. 2, Oxford University Press, 2020, pp. 1778–90, doi:10.1093/mnras/stz3554. short: J.J. Matthee, D. Sobral, M. Gronke, G. Pezzulli, S. Cantalupo, H. Röttgering, B. Darvish, S. Santos, Monthly Notices of the Royal Astronomical Society 492 (2020) 1778–1790. date_created: 2022-07-07T12:21:36Z date_published: 2020-02-01T00:00:00Z date_updated: 2022-08-18T11:29:53Z day: '01' doi: 10.1093/mnras/stz3554 extern: '1' external_id: arxiv: - '1909.06376' intvolume: ' 492' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - dark ages - reionization - first stars - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.06376 month: '02' oa: 1 oa_version: Preprint page: 1778-1790 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 492 year: '2020' ... --- _id: '11531' abstract: - lang: eng text: While low-luminosity galaxies dominate number counts at all redshifts, their contribution to cosmic reionization is poorly understood due to a lack of knowledge of their physical properties. We isolate a sample of 35 z ≈ 4–5 continuum-faint Lyman-α emitters from deep VLT/MUSE spectroscopy and directly measure their H α emission using stacked Spitzer/IRAC Ch. 1 photometry. Based on Hubble Space Telescope imaging, we determine that the average UV continuum magnitude is fainter than −16 (≈ 0.01 L⋆), implying a median Lyman-α equivalent width of 259 Å. By combining the H α measurement with the UV magnitude, we determine the ionizing photon production efficiency, ξion, a first for such faint galaxies. The measurement of log10 (ξion [Hz erg−1]) = 26.28 (⁠+0.28−0.40⁠) is in excess of literature measurements of both continuum- and emission line-selected samples, implying a more efficient production of ionizing photons in these lower luminosity, Lyman-α-selected systems. We conclude that this elevated efficiency can be explained by stellar populations with metallicities between 4 × 10−4 and 0.008, with light-weighted ages less than 3 Myr. acknowledgement: 'We would like to thank the anonymous referee for a thoughtful report and suggestions that have improved this manuscript. We are also grateful to everyone involved in the Spitzer Space Telescope mission and everyone at the Spitzer Science Center: we are truly fortunate to have been able to use data from this facility. J. B. acknowledges support by FCT/MCTES through national funds by this grant UID/FIS/04434/2019 and through the Investigador FCT contract no. IF/01654/2014/CP1215/CT0003. S. C. gratefully acknowledges support from Swiss National Science Foundation grant PP00P2 163824. We would also like to thank Mauro Stefanon for his assistance with de-blending the IRAC photometry, Pieter van Dokkum for a number of useful suggestions, and Daniel Schaerer for information regarding the stellar population models. This study is based on observations made with ESO telescopes at the La Silla Paranal Observatory under programs IDs 094.A-2089(B), 095.A0010(A), 096.A-0045(A), and 096.A-0045(B).' article_processing_charge: No article_type: original author: - first_name: Michael V full_name: Maseda, Michael V last_name: Maseda - first_name: Roland full_name: Bacon, Roland last_name: Bacon - first_name: Daniel full_name: Lam, Daniel last_name: Lam - 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: Jarle full_name: Brinchmann, Jarle last_name: Brinchmann - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Ivo full_name: Labbe, Ivo last_name: Labbe - first_name: Kasper B full_name: Schmidt, Kasper B last_name: Schmidt - first_name: Leindert full_name: Boogaard, Leindert last_name: Boogaard - first_name: Rychard full_name: Bouwens, Rychard last_name: Bouwens - first_name: Sebastiano full_name: Cantalupo, Sebastiano last_name: Cantalupo - first_name: Marijn full_name: Franx, Marijn last_name: Franx - first_name: Takuya full_name: Hashimoto, Takuya last_name: Hashimoto - first_name: Hanae full_name: Inami, Hanae last_name: Inami - first_name: Haruka full_name: Kusakabe, Haruka last_name: Kusakabe - first_name: Guillaume full_name: Mahler, Guillaume last_name: Mahler - first_name: Themiya full_name: Nanayakkara, Themiya last_name: Nanayakkara - first_name: Johan full_name: Richard, Johan last_name: Richard - first_name: Lutz full_name: Wisotzki, Lutz last_name: Wisotzki citation: ama: Maseda MV, Bacon R, Lam D, et al. Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. 2020;493(4):5120-5130. doi:10.1093/mnras/staa622 apa: Maseda, M. V., Bacon, R., Lam, D., Matthee, J. J., Brinchmann, J., Schaye, J., … Wisotzki, L. (2020). Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa622 chicago: Maseda, Michael V, Roland Bacon, Daniel Lam, Jorryt J Matthee, Jarle Brinchmann, Joop Schaye, Ivo Labbe, et al. “Elevated Ionizing Photon Production Efficiency in Faint High-Equivalent-Width Lyman-α Emitters.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa622. ieee: M. V. Maseda et al., “Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 4. Oxford University Press, pp. 5120–5130, 2020. ista: Maseda MV, Bacon R, Lam D, Matthee JJ, Brinchmann J, Schaye J, Labbe I, Schmidt KB, Boogaard L, Bouwens R, Cantalupo S, Franx M, Hashimoto T, Inami H, Kusakabe H, Mahler G, Nanayakkara T, Richard J, Wisotzki L. 2020. Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters. Monthly Notices of the Royal Astronomical Society. 493(4), 5120–5130. mla: Maseda, Michael V., et al. “Elevated Ionizing Photon Production Efficiency in Faint High-Equivalent-Width Lyman-α Emitters.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 4, Oxford University Press, 2020, pp. 5120–30, doi:10.1093/mnras/staa622. short: M.V. Maseda, R. Bacon, D. Lam, J.J. Matthee, J. Brinchmann, J. Schaye, I. Labbe, K.B. Schmidt, L. Boogaard, R. Bouwens, S. Cantalupo, M. Franx, T. Hashimoto, H. Inami, H. Kusakabe, G. Mahler, T. Nanayakkara, J. Richard, L. Wisotzki, Monthly Notices of the Royal Astronomical Society 493 (2020) 5120–5130. date_created: 2022-07-07T10:46:41Z date_published: 2020-04-01T00:00:00Z date_updated: 2022-08-18T11:23:27Z day: '01' doi: 10.1093/mnras/staa622 extern: '1' external_id: arxiv: - '2002.11117' intvolume: ' 493' issue: '4' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'Galaxies: evolution' - 'Galaxies: high-redshift' - 'Galaxies: ISM' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/staa622 month: '04' oa: 1 oa_version: Published Version page: 5120-5130 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 493 year: '2020' ... --- _id: '11530' abstract: - lang: eng text: A prediction of the classic active galactic nucleus (AGN) unification model is the presence of ionization cones with different orientations depending on the AGN type. Confirmations of this model exist for present times, but it is less clear in the early Universe. Here, we use the morphology of giant Ly α nebulae around AGNs at redshift z ∼ 3 to probe AGN emission and therefore the validity of the AGN unification model at this redshift. We compare the spatial morphology of 19 nebulae previously found around type I AGNs with a new sample of four Ly α nebulae detected around type II AGNs. Using two independent techniques, we find that nebulae around type II AGNs are more asymmetric than around type I, at least at radial distances r > 30 physical kpc (pkpc) from the ionizing source. We conclude that the type I and type II AGNs in our sample show evidence of different surrounding ionizing geometries. This suggests that the classical AGN unification model is also valid for high-redshift sources. Finally, we discuss how the lack of asymmetry in the inner parts (r ≲ 30 pkpc) and the associated high values of the He II to Ly α ratios in these regions could indicate additional sources of (hard) ionizing radiation originating within or in proximity of the AGN host galaxies. This work demonstrates that the morphologies of giant Ly α nebulae can be used to understand and study the geometry of high-redshift AGNs on circumnuclear scales and it lays the foundation for future studies using much larger statistical samples. acknowledgement: SC and GP gratefully acknowledge support from Swiss National Science Foundation grant PP00P2 163824. MK acknowledges support by DLR500R1904. article_processing_charge: No article_type: original author: - first_name: J S full_name: den Brok, J S last_name: den Brok - first_name: S full_name: Cantalupo, S last_name: Cantalupo - first_name: R full_name: Mackenzie, R last_name: Mackenzie - first_name: R A full_name: Marino, R A last_name: Marino - first_name: G full_name: Pezzulli, G last_name: Pezzulli - 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: S D full_name: Johnson, S D last_name: Johnson - first_name: M full_name: Krumpe, M last_name: Krumpe - first_name: T full_name: Urrutia, T last_name: Urrutia - first_name: W full_name: Kollatschny, W last_name: Kollatschny citation: ama: den Brok JS, Cantalupo S, Mackenzie R, et al. Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. 2020;495(2):1874-1887. doi:10.1093/mnras/staa1269 apa: den Brok, J. S., Cantalupo, S., Mackenzie, R., Marino, R. A., Pezzulli, G., Matthee, J. J., … Kollatschny, W. (2020). Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa1269 chicago: den Brok, J S, S Cantalupo, R Mackenzie, R A Marino, G Pezzulli, Jorryt J Matthee, S D Johnson, M Krumpe, T Urrutia, and W Kollatschny. “Probing the AGN Unification Model at Redshift z ∼ 3 with MUSE Observations of Giant Lyα Nebulae.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa1269. ieee: J. S. den Brok et al., “Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae,” Monthly Notices of the Royal Astronomical Society, vol. 495, no. 2. Oxford University Press, pp. 1874–1887, 2020. ista: den Brok JS, Cantalupo S, Mackenzie R, Marino RA, Pezzulli G, Matthee JJ, Johnson SD, Krumpe M, Urrutia T, Kollatschny W. 2020. Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae. Monthly Notices of the Royal Astronomical Society. 495(2), 1874–1887. mla: den Brok, J. S., et al. “Probing the AGN Unification Model at Redshift z ∼ 3 with MUSE Observations of Giant Lyα Nebulae.” Monthly Notices of the Royal Astronomical Society, vol. 495, no. 2, Oxford University Press, 2020, pp. 1874–87, doi:10.1093/mnras/staa1269. short: J.S. den Brok, S. Cantalupo, R. Mackenzie, R.A. Marino, G. Pezzulli, J.J. Matthee, S.D. Johnson, M. Krumpe, T. Urrutia, W. Kollatschny, Monthly Notices of the Royal Astronomical Society 495 (2020) 1874–1887. date_created: 2022-07-07T10:40:17Z date_published: 2020-06-01T00:00:00Z date_updated: 2022-08-18T11:17:47Z day: '01' doi: 10.1093/mnras/staa1269 extern: '1' external_id: arxiv: - '2005.01732' intvolume: ' 495' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: high-redshift' - intergalactic medium - 'quasars: emission lines' - 'quasars: general' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2005.01732 month: '06' oa: 1 oa_version: Preprint page: 1874-1887 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 495 year: '2020' ... --- _id: '11539' abstract: - lang: eng text: 'Despite recent progress in understanding Ly α emitters (LAEs), relatively little is known regarding their typical black hole activity across cosmic time. Here, we study the X-ray and radio properties of ∼4000 LAEs at 2.2 < z < 6 from the SC4K survey in the COSMOS field. We detect 254 (⁠6.8per cent±0.4per cent⁠) LAEs individually in the X-rays (S/N > 3) with an average luminosity of 1044.31±0.01ergs−1 and average black hole accretion rate (BHAR) of 0.72±0.01 M⊙ yr−1, consistent with moderate to high accreting active galactic neuclei (AGNs). We detect 120 sources in deep radio data (radio AGN fraction of 3.2per cent±0.3per cent⁠). The global AGN fraction (⁠8.6per cent±0.4per cent⁠) rises with Ly α luminosity and declines with increasing redshift. For X-ray-detected LAEs, Ly α luminosities correlate with the BHARs, suggesting that Ly α luminosity becomes a BHAR indicator. Most LAEs (⁠93.1per cent±0.6per cent⁠) at 2 < z < 6 have no detectable X-ray emission (BHARs < 0.017 M⊙ yr−1). The median star formation rate (SFR) of star-forming LAEs from Ly α and radio luminosities is 7.6+6.6−2.8 M⊙ yr−1. The black hole to galaxy growth ratio (BHAR/SFR) for LAEs is <0.0022, consistent with typical star-forming galaxies and the local BHAR/SFR relation. We conclude that LAEs at 2 < z < 6 include two different populations: an AGN population, where Ly α luminosity traces BHAR, and another with low SFRs which remain undetected in even the deepest X-ray stacks but is detected in the radio stacks.' acknowledgement: JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Camila Correa for help analysing snipshot merger trees. We thank the anonymous referee for constructive comments. We also thank Jarle Brinchmann, Rob Crain, Antonios Katsianis, Paola Popesso, and David Sobral for discussions and suggestions. We also thank the participants of the Lorentz Center workshop ‘A Decade of the Star-Forming Main Sequence’ held on 2017 September 4–8, for discussions and ideas. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, and SCIPY (Hunter 2007) packages and the TOPCAT analysis tool (Taylor 2013). article_processing_charge: No article_type: original author: - first_name: João full_name: Calhau, João last_name: Calhau - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - 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: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: Brooke full_name: Simmons, Brooke last_name: Simmons - first_name: Cassandra full_name: Barlow-Hall, Cassandra last_name: Barlow-Hall - first_name: Benjamin full_name: Adams, Benjamin last_name: Adams citation: ama: 'Calhau J, Sobral D, Santos S, et al. The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. 2020;493(3):3341-3362. doi:10.1093/mnras/staa476' apa: 'Calhau, J., Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Stroe, A., … Adams, B. (2020). The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staa476' chicago: 'Calhau, João, David Sobral, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Andra Stroe, Brooke Simmons, Cassandra Barlow-Hall, and Benjamin Adams. “The X-Ray and Radio Activity of Typical and Luminous Ly α Emitters from z ∼ 2 to z ∼ 6: Evidence for a Diverse, Evolving Population.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa476.' ieee: 'J. Calhau et al., “The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population,” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 3. Oxford University Press, pp. 3341–3362, 2020.' ista: 'Calhau J, Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Stroe A, Simmons B, Barlow-Hall C, Adams B. 2020. The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population. Monthly Notices of the Royal Astronomical Society. 493(3), 3341–3362.' mla: 'Calhau, João, et al. “The X-Ray and Radio Activity of Typical and Luminous Ly α Emitters from z ∼ 2 to z ∼ 6: Evidence for a Diverse, Evolving Population.” Monthly Notices of the Royal Astronomical Society, vol. 493, no. 3, Oxford University Press, 2020, pp. 3341–62, doi:10.1093/mnras/staa476.' short: J. Calhau, D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, A. Stroe, B. Simmons, C. Barlow-Hall, B. Adams, Monthly Notices of the Royal Astronomical Society 493 (2020) 3341–3362. date_created: 2022-07-08T07:34:10Z date_published: 2020-04-01T00:00:00Z date_updated: 2022-08-18T11:25:31Z day: '01' doi: 10.1093/mnras/staa476 extern: '1' external_id: arxiv: - '1909.11672' intvolume: ' 493' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: evolution' - 'galaxies: high-redshift' - 'quasars: supermassive black holes' - 'galaxies: star formation' - 'cosmology: observations' - 'X-rays: galaxies' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.11672 month: '04' oa: 1 oa_version: Preprint page: 3341-3362 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 493 year: '2020' ... --- _id: '11586' abstract: - lang: eng text: Distant luminous Lyman-α emitters are excellent targets for detailed observations of galaxies in the epoch of reionisation. Spatially resolved observations of these galaxies allow us to simultaneously probe the emission from young stars, partially ionised gas in the interstellar medium and to constrain the properties of the surrounding hydrogen in the circumgalactic medium. We review recent results from (spectroscopic) follow-up studies of the rest-frame UV, Lyman-α and [CII] emission in luminous galaxies observed ∼500 Myr after the Big Bang with ALMA, HST/WFC3 and VLT/X-SHOOTER. These galaxies likely reside in early ionised bubbles and are complex systems, consisting of multiple well separated and resolved components where traces of metals are already present. article_processing_charge: No author: - 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: David full_name: Sobral, David last_name: Sobral citation: ama: 'Matthee JJ, Sobral D. Unveiling the most luminous Lyman-α emitters in the epoch of reionisation. In: Proceedings of the International Astronomical Union. Vol 15. Cambridge University Press; 2020:21-25. doi:10.1017/s1743921319009451' apa: Matthee, J. J., & Sobral, D. (2020). Unveiling the most luminous Lyman-α emitters in the epoch of reionisation. In Proceedings of the International Astronomical Union (Vol. 15, pp. 21–25). Cambridge University Press. https://doi.org/10.1017/s1743921319009451 chicago: Matthee, Jorryt J, and David Sobral. “Unveiling the Most Luminous Lyman-α Emitters in the Epoch of Reionisation.” In Proceedings of the International Astronomical Union, 15:21–25. Cambridge University Press, 2020. https://doi.org/10.1017/s1743921319009451. ieee: J. J. Matthee and D. Sobral, “Unveiling the most luminous Lyman-α emitters in the epoch of reionisation,” in Proceedings of the International Astronomical Union, 2020, vol. 15, no. S352, pp. 21–25. ista: Matthee JJ, Sobral D. 2020. Unveiling the most luminous Lyman-α emitters in the epoch of reionisation. Proceedings of the International Astronomical Union. vol. 15, 21–25. mla: Matthee, Jorryt J., and David Sobral. “Unveiling the Most Luminous Lyman-α Emitters in the Epoch of Reionisation.” Proceedings of the International Astronomical Union, vol. 15, no. S352, Cambridge University Press, 2020, pp. 21–25, doi:10.1017/s1743921319009451. short: J.J. Matthee, D. Sobral, in:, Proceedings of the International Astronomical Union, Cambridge University Press, 2020, pp. 21–25. date_created: 2022-07-14T14:08:41Z date_published: 2020-06-04T00:00:00Z date_updated: 2022-08-19T08:41:12Z day: '04' doi: 10.1017/s1743921319009451 extern: '1' external_id: arxiv: - '1911.04774' intvolume: ' 15' issue: S352 keyword: - Astronomy and Astrophysics - Space and Planetary Science - 'galaxies: formation' - 'galaxies: evolution' - 'galaxies: high-redshift' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1911.04774 month: '06' oa: 1 oa_version: Preprint page: 21-25 publication: Proceedings of the International Astronomical Union publication_identifier: eissn: - 1743-9221 issn: - 1743-9213 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Unveiling the most luminous Lyman-α emitters in the epoch of reionisation type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2020' ... --- _id: '11610' abstract: - lang: eng text: Studies of Galactic structure and evolution have benefited enormously from Gaia kinematic information, though additional, intrinsic stellar parameters like age are required to best constrain Galactic models. Asteroseismology is the most precise method of providing such information for field star populations en masse, but existing samples for the most part have been limited to a few narrow fields of view by the CoRoT and Kepler missions. In an effort to provide well-characterized stellar parameters across a wide range in Galactic position, we present the second data release of red giant asteroseismic parameters for the K2 Galactic Archaeology Program (GAP). We provide ${\nu }_{\max }$ and ${\rm{\Delta }}\nu $ based on six independent pipeline analyses; first-ascent red giant branch (RGB) and red clump (RC) evolutionary state classifications from machine learning; and ready-to-use radius and mass coefficients, κR and κM, which, when appropriately multiplied by a solar-scaled effective temperature factor, yield physical stellar radii and masses. In total, we report 4395 radius and mass coefficients, with typical uncertainties of 3.3% (stat.) ± 1% (syst.) for κR and 7.7% (stat.) ± 2% (syst.) for κM among RGB stars, and 5.0% (stat.) ± 1% (syst.) for κR and 10.5% (stat.) ± 2% (syst.) for κM among RC stars. We verify that the sample is nearly complete—except for a dearth of stars with ${\nu }_{\max }\lesssim 10\mbox{--}20\,\mu \mathrm{Hz}$—by comparing to Galactic models and visual inspection. Our asteroseismic radii agree with radii derived from Gaia Data Release 2 parallaxes to within 2.2% ± 0.3% for RGB stars and 2.0% ± 0.6% for RC stars. acknowledgement: "We thank the referee for comments that strengthened the manuscript. J. C. Z. and M. H. P. acknowledge support from NASA grants 80NSSC18K0391 and NNX17AJ40G. Y. E. and C. J. acknowledge the support of the UK Science and Technology Facilities Council (STFC). S. M. would like to acknowledge support from the Spanish Ministry with the Ramon y Cajal fellowship number RYC-2015-17697. R. A. G. acknowledges funding received from the PLATO CNES grant. R. S. acknowledges funding via a Royal Society University Research Fellowship. D.H. acknowledges support from the Alfred P. Sloan Foundation and the National Aeronautics and Space Administration (80NSSC19K0108). V.S.A. acknowledges support from the Independent Research Fund Denmark (Research grant 7027-00096B), and the Carlsberg foundation (grant agreement CF19-0649). This research was supported in part by the National Science Foundation under grant No. NSF PHY-1748958.\r\n\r\nFunding for the Stellar Astrophysics Centre (SAC) is provided by The Danish National Research Foundation (grant agreement No. DNRF106).\r\n\r\nThe K2 Galactic Archaeology Program is supported by the National Aeronautics and Space Administration under grant NNX16AJ17G issued through the K2 Guest Observer Program.\r\n\r\nThis publication makes use of data products from the Two Micron All Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation.\r\n\r\nThis work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement.\r\n\r\nFunding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High Performance Computing at the University of Utah. The SDSS website is www.sdss.org.\r\n\r\nSDSS-IV is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS Collaboration, including the Brazilian Participation Group, the Carnegie Institution for Science, Carnegie Mellon University, the Chilean Participation Group, the French Participation Group, the Harvard–Smithsonian Center for Astrophysics, Instituto de Astrofísica de Canarias, The Johns Hopkins University, Kavli Institute for the Physics and Mathematics of the Universe (IPMU)/University of Tokyo, the Korean Participation Group, Lawrence Berkeley National Laboratory, Leibniz Institut für Astrophysik Potsdam (AIP), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Max-Planck-Institut für Astrophysik (MPA Garching), Max-Planck-Institut für Extraterrestrische Physik (MPE), National Astronomical Observatories of China, New Mexico State University, New York University, University of Notre Dame, Observatário Nacional/MCTI, The Ohio State University, Pennsylvania State University, Shanghai Astronomical Observatory, United Kingdom Participation Group, Universidad Nacional Autónoma de México, University of Arizona, University of Colorado Boulder, University of Oxford, University of Portsmouth, University of Utah, University of Virginia, University of Washington, University of Wisconsin, Vanderbilt University, and Yale University.\r\n\r\nSoftware: asfgrid (Sharma & Stello 2016), emcee (Foreman-Mackey et al. 2013), NumPy (Walt 2011), pandas (McKinney 2010; Reback et al. 2020), Matplotlib (Hunter 2007), IPython (Pérez & Granger 2007), SciPy (Virtanen et al. 2020)." article_number: '23' article_processing_charge: No article_type: original author: - first_name: Joel C. full_name: Zinn, Joel C. last_name: Zinn - first_name: Dennis full_name: Stello, Dennis last_name: Stello - first_name: Yvonne full_name: Elsworth, Yvonne last_name: Elsworth - first_name: Rafael A. full_name: García, Rafael A. last_name: García - first_name: Thomas full_name: Kallinger, Thomas last_name: Kallinger - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Benoît full_name: Mosser, Benoît last_name: Mosser - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Caitlin full_name: Jones, Caitlin last_name: Jones - first_name: Marc full_name: Hon, Marc last_name: Hon - first_name: Sanjib full_name: Sharma, Sanjib last_name: Sharma - first_name: Ralph full_name: Schönrich, Ralph last_name: Schönrich - first_name: Jack T. full_name: Warfield, Jack T. last_name: Warfield - first_name: Rodrigo full_name: Luger, Rodrigo last_name: Luger - first_name: Marc H. full_name: Pinsonneault, Marc H. last_name: Pinsonneault - first_name: Jennifer A. full_name: Johnson, Jennifer A. last_name: Johnson - first_name: Daniel full_name: Huber, Daniel last_name: Huber - first_name: Victor Silva full_name: Aguirre, Victor Silva last_name: Aguirre - first_name: William J. full_name: Chaplin, William J. last_name: Chaplin - first_name: Guy R. full_name: Davies, Guy R. last_name: Davies - first_name: Andrea full_name: Miglio, Andrea last_name: Miglio citation: ama: 'Zinn JC, Stello D, Elsworth Y, et al. The K2 galactic archaeology program data release 2: Asteroseismic results from campaigns 4, 6, and 7. The Astrophysical Journal Supplement Series. 2020;251(2). doi:10.3847/1538-4365/abbee3' apa: 'Zinn, J. C., Stello, D., Elsworth, Y., García, R. A., Kallinger, T., Mathur, S., … Miglio, A. (2020). The K2 galactic archaeology program data release 2: Asteroseismic results from campaigns 4, 6, and 7. The Astrophysical Journal Supplement Series. IOP Publishing. https://doi.org/10.3847/1538-4365/abbee3' chicago: 'Zinn, Joel C., Dennis Stello, Yvonne Elsworth, Rafael A. García, Thomas Kallinger, Savita Mathur, Benoît Mosser, et al. “The K2 Galactic Archaeology Program Data Release 2: Asteroseismic Results from Campaigns 4, 6, and 7.” The Astrophysical Journal Supplement Series. IOP Publishing, 2020. https://doi.org/10.3847/1538-4365/abbee3.' ieee: 'J. C. Zinn et al., “The K2 galactic archaeology program data release 2: Asteroseismic results from campaigns 4, 6, and 7,” The Astrophysical Journal Supplement Series, vol. 251, no. 2. IOP Publishing, 2020.' ista: 'Zinn JC, Stello D, Elsworth Y, García RA, Kallinger T, Mathur S, Mosser B, Bugnet LA, Jones C, Hon M, Sharma S, Schönrich R, Warfield JT, Luger R, Pinsonneault MH, Johnson JA, Huber D, Aguirre VS, Chaplin WJ, Davies GR, Miglio A. 2020. The K2 galactic archaeology program data release 2: Asteroseismic results from campaigns 4, 6, and 7. The Astrophysical Journal Supplement Series. 251(2), 23.' mla: 'Zinn, Joel C., et al. “The K2 Galactic Archaeology Program Data Release 2: Asteroseismic Results from Campaigns 4, 6, and 7.” The Astrophysical Journal Supplement Series, vol. 251, no. 2, 23, IOP Publishing, 2020, doi:10.3847/1538-4365/abbee3.' short: J.C. Zinn, D. Stello, Y. Elsworth, R.A. García, T. Kallinger, S. Mathur, B. Mosser, L.A. Bugnet, C. Jones, M. Hon, S. Sharma, R. Schönrich, J.T. Warfield, R. Luger, M.H. Pinsonneault, J.A. Johnson, D. Huber, V.S. Aguirre, W.J. Chaplin, G.R. Davies, A. Miglio, The Astrophysical Journal Supplement Series 251 (2020). date_created: 2022-07-18T13:27:26Z date_published: 2020-12-01T00:00:00Z date_updated: 2022-08-22T07:04:45Z day: '01' doi: 10.3847/1538-4365/abbee3 extern: '1' external_id: arxiv: - '2012.04051' intvolume: ' 251' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.04051 month: '12' oa: 1 oa_version: Preprint publication: The Astrophysical Journal Supplement Series publication_identifier: eissn: - 1538-4365 issn: - 0067-0049 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'The K2 galactic archaeology program data release 2: Asteroseismic results from campaigns 4, 6, and 7' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 251 year: '2020' ... --- _id: '11611' abstract: - lang: eng text: Over the course of its history, the Milky Way has ingested multiple smaller satellite galaxies1. Although these accreted stellar populations can be forensically identified as kinematically distinct structures within the Galaxy, it is difficult in general to date precisely the age at which any one merger occurred. Recent results have revealed a population of stars that were accreted via the collision of a dwarf galaxy, called Gaia–Enceladus1, leading to substantial pollution of the chemical and dynamical properties of the Milky Way. Here we identify the very bright, naked-eye star ν Indi as an indicator of the age of the early in situ population of the Galaxy. We combine asteroseismic, spectroscopic, astrometric and kinematic observations to show that this metal-poor, alpha-element-rich star was an indigenous member of the halo, and we measure its age to be 11.0±0.7 (stat) ±0.8 (sys) billion years. The star bears hallmarks consistent with having been kinematically heated by the Gaia–Enceladus collision. Its age implies that the earliest the merger could have begun was 11.6 and 13.2 billion years ago, at 68% and 95% confidence, respectively. Computations based on hierarchical cosmological models slightly reduce the above limits. acknowledgement: This paper includes data collected by the TESS mission, which are publicly available from the Mikulski Archive for Space Telescopes (MAST). Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at Ames Research Center for the production of the SPOC data products. W.J.C. acknowledges support from the UK Science and Technology Facilities Council (STFC) and UK Space Agency. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (grant agreement number DNRF106). This research was partially conducted during the Exostar19 programme at the Kavli Institute for Theoretical Physics at UC Santa Barbara, which was supported in part by the National Science Foundation under grant number NSF PHY-1748958. A.M., J.T.M., F.V. and J.M. acknowledge support from the ERC Consolidator Grant funding scheme (project ASTEROCHRONOMETRY, grant agreement number 772293). F.V. acknowledges the support of a Fellowship from the Center for Cosmology and AstroParticle Physics at The Ohio State University. W.H.B. and M.B.N. acknowledge support from the UK Space Agency. K.J.B. is supported by the National Science Foundation under award AST-1903828. M.B.N. acknowledges partial support from the NYU Abu Dhabi Center for Space Science under grant number G1502. A.M.S. is partially supported by the Spanish Government (ESP2017-82674-R) and Generalitat de Catalunya (2017-SGR-1131). T.M. acknowledges financial support from Belspo for contract PRODEX PLATO. H.K. acknowledges support from the European Social Fund via the Lithuanian Science Council grant number 09.3.3-LMT-K-712-01-0103. S.B. acknowledges support from NSF grant AST-1514676 and NASA grant 80NSSC19K0374. V.S.A. acknowledges support from the Independent Research Fund Denmark (research grant 7027-00096B). D.H. acknowledges support by the National Aeronautics and Space Administration (80NSSC18K1585, 80NSSC19K0379) awarded through the TESS Guest Investigator Program and by the National Science Foundation (AST-1717000). T.S.M. acknowledges support from a visiting fellowship at the Max Planck Institute for Solar System Research. Computational resources were provided through XSEDE allocation TG-AST090107. D.L.B. acknowledges support from NASA under grant NNX16AB76G. T.L.C. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 792848 (PULSATION). This work was supported by FCT/MCTES through national funds (PIDDAC) by means of grant UID/FIS/04434/2019. K.J.B., S.H., J.S.K. and N.T. are supported by the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement number 338251 (StellarAges). E.C. is funded by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement number 664931. L.G.-C. acknowledges support from the MINECO FPI-SO doctoral research project SEV-2015-0548-17-2 and predoctoral contract BES-2017-082610. P.G. is supported by the German space agency (Deutsches Zentrum für Luft- und Raumfahrt) under PLATO data grant 50OO1501. R.K. acknowledges support from the UK Science and Technology Facilities Council (STFC), under consolidated grant ST/L000733/1. M.S.L. is supported by the Carlsberg Foundation (grant agreement number CF17-076). Z.C.O., S.O. and M.Y. acknowledge support from the Scientific and Technological Research Council of Turkey (TÜBİTAK:118F352). S.M. acknowledges support from the Spanish ministry through the Ramon y Cajal fellowship number RYC-2015-17697. T.S.R. acknowledges financial support from Premiale 2015 MITiC (PI B. Garilli). R.Sz. acknowledges the support from NKFIH grant project No. K-115709, and the Lendület program of the Hungarian Academy of Science (project number 2018-7/2019). J.T. acknowledges support was provided by NASA through the NASA Hubble Fellowship grant number 51424 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. This work was supported by FEDER through COMPETE2020 (POCI-01-0145-FEDER-030389. A.M.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 749962 (project THOT). A.M. and P.R. acknowledge the support of the Government of India, Department of Atomic Energy, under Project No. 12-R&D-TFR-6.04-0600. K.J.B. is an NSF Astronomy and Astrophysics Postdoctoral Fellow and DIRAC Fellow. article_processing_charge: No article_type: letter_note author: - first_name: William J. full_name: Chaplin, William J. last_name: Chaplin - first_name: Aldo M. full_name: Serenelli, Aldo M. last_name: Serenelli - first_name: Andrea full_name: Miglio, Andrea last_name: Miglio - first_name: Thierry full_name: Morel, Thierry last_name: Morel - first_name: J. Ted full_name: Mackereth, J. Ted last_name: Mackereth - first_name: Fiorenzo full_name: Vincenzo, Fiorenzo last_name: Vincenzo - first_name: Hans full_name: Kjeldsen, Hans last_name: Kjeldsen - first_name: Sarbani full_name: Basu, Sarbani last_name: Basu - first_name: Warrick H. full_name: Ball, Warrick H. last_name: Ball - first_name: Amalie full_name: Stokholm, Amalie last_name: Stokholm - first_name: Kuldeep full_name: Verma, Kuldeep last_name: Verma - first_name: Jakob Rørsted full_name: Mosumgaard, Jakob Rørsted last_name: Mosumgaard - first_name: Victor full_name: Silva Aguirre, Victor last_name: Silva Aguirre - first_name: Anwesh full_name: Mazumdar, Anwesh last_name: Mazumdar - first_name: Pritesh full_name: Ranadive, Pritesh last_name: Ranadive - first_name: H. M. full_name: Antia, H. M. last_name: Antia - first_name: Yveline full_name: Lebreton, Yveline last_name: Lebreton - first_name: Joel full_name: Ong, Joel last_name: Ong - first_name: Thierry full_name: Appourchaux, Thierry last_name: Appourchaux - first_name: Timothy R. full_name: Bedding, Timothy R. last_name: Bedding - first_name: Jørgen full_name: Christensen-Dalsgaard, Jørgen last_name: Christensen-Dalsgaard - first_name: Orlagh full_name: Creevey, Orlagh last_name: Creevey - first_name: Rafael A. full_name: García, Rafael A. last_name: García - first_name: Rasmus full_name: Handberg, Rasmus last_name: Handberg - first_name: Daniel full_name: Huber, Daniel last_name: Huber - first_name: Steven D. full_name: Kawaler, Steven D. last_name: Kawaler - first_name: Mikkel N. full_name: Lund, Mikkel N. last_name: Lund - first_name: Travis S. full_name: Metcalfe, Travis S. last_name: Metcalfe - first_name: Keivan G. full_name: Stassun, Keivan G. last_name: Stassun - first_name: Michäel full_name: Bazot, Michäel last_name: Bazot - first_name: Paul G. full_name: Beck, Paul G. last_name: Beck - first_name: Keaton J. full_name: Bell, Keaton J. last_name: Bell - first_name: Maria full_name: Bergemann, Maria last_name: Bergemann - first_name: Derek L. full_name: Buzasi, Derek L. last_name: Buzasi - first_name: Othman full_name: Benomar, Othman last_name: Benomar - first_name: Diego full_name: Bossini, Diego last_name: Bossini - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Tiago L. full_name: Campante, Tiago L. last_name: Campante - first_name: Zeynep Çelik full_name: Orhan, Zeynep Çelik last_name: Orhan - first_name: Enrico full_name: Corsaro, Enrico last_name: Corsaro - first_name: Lucía full_name: González-Cuesta, Lucía last_name: González-Cuesta - first_name: Guy R. full_name: Davies, Guy R. last_name: Davies - first_name: Maria Pia full_name: Di Mauro, Maria Pia last_name: Di Mauro - first_name: Ricky full_name: Egeland, Ricky last_name: Egeland - first_name: Yvonne P. full_name: Elsworth, Yvonne P. last_name: Elsworth - first_name: Patrick full_name: Gaulme, Patrick last_name: Gaulme - first_name: Hamed full_name: Ghasemi, Hamed last_name: Ghasemi - first_name: Zhao full_name: Guo, Zhao last_name: Guo - first_name: Oliver J. full_name: Hall, Oliver J. last_name: Hall - first_name: Amir full_name: Hasanzadeh, Amir last_name: Hasanzadeh - first_name: Saskia full_name: Hekker, Saskia last_name: Hekker - first_name: Rachel full_name: Howe, Rachel last_name: Howe - first_name: Jon M. full_name: Jenkins, Jon M. last_name: Jenkins - first_name: Antonio full_name: Jiménez, Antonio last_name: Jiménez - first_name: René full_name: Kiefer, René last_name: Kiefer - first_name: James S. full_name: Kuszlewicz, James S. last_name: Kuszlewicz - first_name: Thomas full_name: Kallinger, Thomas last_name: Kallinger - first_name: David W. full_name: Latham, David W. last_name: Latham - first_name: Mia S. full_name: Lundkvist, Mia S. last_name: Lundkvist - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Josefina full_name: Montalbán, Josefina last_name: Montalbán - first_name: Benoit full_name: Mosser, Benoit last_name: Mosser - first_name: Andres Moya full_name: Bedón, Andres Moya last_name: Bedón - first_name: Martin Bo full_name: Nielsen, Martin Bo last_name: Nielsen - first_name: Sibel full_name: Örtel, Sibel last_name: Örtel - first_name: Ben M. full_name: Rendle, Ben M. last_name: Rendle - first_name: George R. full_name: Ricker, George R. last_name: Ricker - first_name: Thaíse S. full_name: Rodrigues, Thaíse S. last_name: Rodrigues - first_name: Ian W. full_name: Roxburgh, Ian W. last_name: Roxburgh - first_name: Hossein full_name: Safari, Hossein last_name: Safari - first_name: Mathew full_name: Schofield, Mathew last_name: Schofield - first_name: Sara full_name: Seager, Sara last_name: Seager - first_name: Barry full_name: Smalley, Barry last_name: Smalley - first_name: Dennis full_name: Stello, Dennis last_name: Stello - first_name: Róbert full_name: Szabó, Róbert last_name: Szabó - first_name: Jamie full_name: Tayar, Jamie last_name: Tayar - first_name: Nathalie full_name: Themeßl, Nathalie last_name: Themeßl - first_name: Alexandra E. L. full_name: Thomas, Alexandra E. L. last_name: Thomas - first_name: Roland K. full_name: Vanderspek, Roland K. last_name: Vanderspek - first_name: Walter E. full_name: van Rossem, Walter E. last_name: van Rossem - first_name: Mathieu full_name: Vrard, Mathieu last_name: Vrard - first_name: Achim full_name: Weiss, Achim last_name: Weiss - first_name: Timothy R. full_name: White, Timothy R. last_name: White - first_name: Joshua N. full_name: Winn, Joshua N. last_name: Winn - first_name: Mutlu full_name: Yıldız, Mutlu last_name: Yıldız citation: ama: Chaplin WJ, Serenelli AM, Miglio A, et al. Age dating of an early Milky Way merger via asteroseismology of the naked-eye star ν Indi. Nature Astronomy. 2020;4(4):382-389. doi:10.1038/s41550-019-0975-9 apa: Chaplin, W. J., Serenelli, A. M., Miglio, A., Morel, T., Mackereth, J. T., Vincenzo, F., … Yıldız, M. (2020). Age dating of an early Milky Way merger via asteroseismology of the naked-eye star ν Indi. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-019-0975-9 chicago: Chaplin, William J., Aldo M. Serenelli, Andrea Miglio, Thierry Morel, J. Ted Mackereth, Fiorenzo Vincenzo, Hans Kjeldsen, et al. “Age Dating of an Early Milky Way Merger via Asteroseismology of the Naked-Eye Star ν Indi.” Nature Astronomy. Springer Nature, 2020. https://doi.org/10.1038/s41550-019-0975-9. ieee: W. J. Chaplin et al., “Age dating of an early Milky Way merger via asteroseismology of the naked-eye star ν Indi,” Nature Astronomy, vol. 4, no. 4. Springer Nature, pp. 382–389, 2020. ista: Chaplin WJ, Serenelli AM, Miglio A, Morel T, Mackereth JT, Vincenzo F, Kjeldsen H, Basu S, Ball WH, Stokholm A, Verma K, Mosumgaard JR, Silva Aguirre V, Mazumdar A, Ranadive P, Antia HM, Lebreton Y, Ong J, Appourchaux T, Bedding TR, Christensen-Dalsgaard J, Creevey O, García RA, Handberg R, Huber D, Kawaler SD, Lund MN, Metcalfe TS, Stassun KG, Bazot M, Beck PG, Bell KJ, Bergemann M, Buzasi DL, Benomar O, Bossini D, Bugnet LA, Campante TL, Orhan ZÇ, Corsaro E, González-Cuesta L, Davies GR, Di Mauro MP, Egeland R, Elsworth YP, Gaulme P, Ghasemi H, Guo Z, Hall OJ, Hasanzadeh A, Hekker S, Howe R, Jenkins JM, Jiménez A, Kiefer R, Kuszlewicz JS, Kallinger T, Latham DW, Lundkvist MS, Mathur S, Montalbán J, Mosser B, Bedón AM, Nielsen MB, Örtel S, Rendle BM, Ricker GR, Rodrigues TS, Roxburgh IW, Safari H, Schofield M, Seager S, Smalley B, Stello D, Szabó R, Tayar J, Themeßl N, Thomas AEL, Vanderspek RK, van Rossem WE, Vrard M, Weiss A, White TR, Winn JN, Yıldız M. 2020. Age dating of an early Milky Way merger via asteroseismology of the naked-eye star ν Indi. Nature Astronomy. 4(4), 382–389. mla: Chaplin, William J., et al. “Age Dating of an Early Milky Way Merger via Asteroseismology of the Naked-Eye Star ν Indi.” Nature Astronomy, vol. 4, no. 4, Springer Nature, 2020, pp. 382–89, doi:10.1038/s41550-019-0975-9. short: W.J. Chaplin, A.M. Serenelli, A. Miglio, T. Morel, J.T. Mackereth, F. Vincenzo, H. Kjeldsen, S. Basu, W.H. Ball, A. Stokholm, K. Verma, J.R. Mosumgaard, V. Silva Aguirre, A. Mazumdar, P. Ranadive, H.M. Antia, Y. Lebreton, J. Ong, T. Appourchaux, T.R. Bedding, J. Christensen-Dalsgaard, O. Creevey, R.A. García, R. Handberg, D. Huber, S.D. Kawaler, M.N. Lund, T.S. Metcalfe, K.G. Stassun, M. Bazot, P.G. Beck, K.J. Bell, M. Bergemann, D.L. Buzasi, O. Benomar, D. Bossini, L.A. Bugnet, T.L. Campante, Z.Ç. Orhan, E. Corsaro, L. González-Cuesta, G.R. Davies, M.P. Di Mauro, R. Egeland, Y.P. Elsworth, P. Gaulme, H. Ghasemi, Z. Guo, O.J. Hall, A. Hasanzadeh, S. Hekker, R. Howe, J.M. Jenkins, A. Jiménez, R. Kiefer, J.S. Kuszlewicz, T. Kallinger, D.W. Latham, M.S. Lundkvist, S. Mathur, J. Montalbán, B. Mosser, A.M. Bedón, M.B. Nielsen, S. Örtel, B.M. Rendle, G.R. Ricker, T.S. Rodrigues, I.W. Roxburgh, H. Safari, M. Schofield, S. Seager, B. Smalley, D. Stello, R. Szabó, J. Tayar, N. Themeßl, A.E.L. Thomas, R.K. Vanderspek, W.E. van Rossem, M. Vrard, A. Weiss, T.R. White, J.N. Winn, M. Yıldız, Nature Astronomy 4 (2020) 382–389. date_created: 2022-07-18T13:36:19Z date_published: 2020-04-01T00:00:00Z date_updated: 2022-08-22T07:08:29Z day: '01' doi: 10.1038/s41550-019-0975-9 extern: '1' external_id: arxiv: - '2001.04653' intvolume: ' 4' issue: '4' keyword: - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2001.04653 month: '04' oa: 1 oa_version: Preprint page: 382-389 publication: Nature Astronomy publication_identifier: eissn: - 2397-3366 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Age dating of an early Milky Way merger via asteroseismology of the naked-eye star ν Indi type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2020' ... --- _id: '11612' abstract: - lang: eng text: Since the onset of the "space revolution" of high-precision high-cadence photometry, asteroseismology has been demonstrated as a powerful tool for informing Galactic archeology investigations. The launch of the NASA Transiting Exoplanet Survey Satellite (TESS) mission has enabled seismic-based inferences to go full sky—providing a clear advantage for large ensemble studies of the different Milky Way components. Here we demonstrate its potential for investigating the Galaxy by carrying out the first asteroseismic ensemble study of red giant stars observed by TESS. We use a sample of 25 stars for which we measure their global asteroseimic observables and estimate their fundamental stellar properties, such as radius, mass, and age. Significant improvements are seen in the uncertainties of our estimates when combining seismic observables from TESS with astrometric measurements from the Gaia mission compared to when the seismology and astrometry are applied separately. Specifically, when combined we show that stellar radii can be determined to a precision of a few percent, masses to 5%–10%, and ages to the 20% level. This is comparable to the precision typically obtained using end-of-mission Kepler data. acknowledgement: 'This Letter includes data collected by the TESS mission, which are publicly available from the Mikulski Archive for Space Telescopes (MAST). Funding for the TESS mission is provided by NASA''s Science Mission directorate. Funding for the TESS Asteroseismic Science Operations Centre is provided by the Danish National Research Foundation (grant agreement No. DNRF106), ESA PRODEX (PEA 4000119301), and Stellar Astrophysics Centre (SAC) at Aarhus University. V.S.A. acknowledges support from the Independent Research Fund Denmark (Research grant 7027-00096B). D.B. is supported in the form of work contract FCT/MCTES through national funds and by FEDER through COMPETE2020 in connection to these grants: UID/FIS/04434/2019; PTDC/FIS-AST/30389/2017 & POCI-01-0145-FEDER-030389. L.B., R.A.G., and B.M. acknowledge the support from the CNES/PLATO grant. D.B. acknowledges NASA grant NNX16AB76G. T.L.C. acknowledges support from the European Union''s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 792848 (PULSATION). This work was supported by FCT/MCTES through national funds (UID/FIS/04434/2019). E.C. is funded by the European Union''s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 664931. R.H. and M.N.L. acknowledge the support of the ESA PRODEX programme. T.S.R. acknowledges financial support from Premiale 2015 MITiC (PI B. Garilli). K.J.B. is supported by the National Science Foundation under Award AST-1903828. M.S.L. is supported by the Carlsberg Foundation (grant agreement No. CF17-0760). M.C. is funded by FCT//MCTES through national funds and by FEDER through COMPETE2020 through these grants: UID/FIS/04434/2019, PTDC/FIS-AST/30389/2017 & POCI-01-0145-FEDER-030389, CEECIND/02619/2017. The research leading to the presented results has received funding from the European Research Council under the European Community''s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 338251 (StellarAges). A.M. acknowledges support from the European Research Council Consolidator Grant funding scheme (project ASTEROCHRONOMETRY, grant agreement No. 772293, http://www.asterochronometry.eu). A.M.S. is partially supported by MINECO grant ESP2017-82674-R. J.C.S. acknowledges funding support from Spanish public funds for research under projects ESP2017-87676-2-2, and from project RYC-2012-09913 under the ''Ramón y Cajal'' program of the Spanish Ministry of Science and Education. Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at Ames Research Center for the production of the SPOC data products.' article_number: L34 article_processing_charge: No article_type: original author: - first_name: Víctor Silva full_name: Aguirre, Víctor Silva last_name: Aguirre - first_name: Dennis full_name: Stello, Dennis last_name: Stello - first_name: Amalie full_name: Stokholm, Amalie last_name: Stokholm - first_name: Jakob R. full_name: Mosumgaard, Jakob R. last_name: Mosumgaard - first_name: Warrick H. full_name: Ball, Warrick H. last_name: Ball - first_name: Sarbani full_name: Basu, Sarbani last_name: Basu - first_name: Diego full_name: Bossini, Diego last_name: Bossini - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Derek full_name: Buzasi, Derek last_name: Buzasi - first_name: Tiago L. full_name: Campante, Tiago L. last_name: Campante - first_name: Lindsey full_name: Carboneau, Lindsey last_name: Carboneau - first_name: William J. full_name: Chaplin, William J. last_name: Chaplin - first_name: Enrico full_name: Corsaro, Enrico last_name: Corsaro - first_name: Guy R. full_name: Davies, Guy R. last_name: Davies - first_name: Yvonne full_name: Elsworth, Yvonne last_name: Elsworth - first_name: Rafael A. full_name: García, Rafael A. last_name: García - first_name: Patrick full_name: Gaulme, Patrick last_name: Gaulme - first_name: Oliver J. full_name: Hall, Oliver J. last_name: Hall - first_name: Rasmus full_name: Handberg, Rasmus last_name: Handberg - first_name: Marc full_name: Hon, Marc last_name: Hon - first_name: Thomas full_name: Kallinger, Thomas last_name: Kallinger - first_name: Liu full_name: Kang, Liu last_name: Kang - first_name: Mikkel N. full_name: Lund, Mikkel N. last_name: Lund - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Alexey full_name: Mints, Alexey last_name: Mints - first_name: Benoit full_name: Mosser, Benoit last_name: Mosser - first_name: Zeynep full_name: Çelik Orhan, Zeynep last_name: Çelik Orhan - first_name: Thaíse S. full_name: Rodrigues, Thaíse S. last_name: Rodrigues - first_name: Mathieu full_name: Vrard, Mathieu last_name: Vrard - first_name: Mutlu full_name: Yıldız, Mutlu last_name: Yıldız - first_name: Joel C. full_name: Zinn, Joel C. last_name: Zinn - first_name: Sibel full_name: Örtel, Sibel last_name: Örtel - first_name: Paul G. full_name: Beck, Paul G. last_name: Beck - first_name: Keaton J. full_name: Bell, Keaton J. last_name: Bell - first_name: Zhao full_name: Guo, Zhao last_name: Guo - first_name: Chen full_name: Jiang, Chen last_name: Jiang - first_name: James S. full_name: Kuszlewicz, James S. last_name: Kuszlewicz - first_name: Charles A. full_name: Kuehn, Charles A. last_name: Kuehn - first_name: Tanda full_name: Li, Tanda last_name: Li - first_name: Mia S. full_name: Lundkvist, Mia S. last_name: Lundkvist - first_name: Marc full_name: Pinsonneault, Marc last_name: Pinsonneault - first_name: Jamie full_name: Tayar, Jamie last_name: Tayar - first_name: Margarida S. full_name: Cunha, Margarida S. last_name: Cunha - first_name: Saskia full_name: Hekker, Saskia last_name: Hekker - first_name: Daniel full_name: Huber, Daniel last_name: Huber - first_name: Andrea full_name: Miglio, Andrea last_name: Miglio - first_name: Mario J. P. full_name: F. G. Monteiro, Mario J. P. last_name: F. G. Monteiro - first_name: Ditte full_name: Slumstrup, Ditte last_name: Slumstrup - first_name: Mark L. full_name: Winther, Mark L. last_name: Winther - first_name: George full_name: Angelou, George last_name: Angelou - first_name: Othman full_name: Benomar, Othman last_name: Benomar - first_name: Attila full_name: Bódi, Attila last_name: Bódi - first_name: Bruno L. full_name: De Moura, Bruno L. last_name: De Moura - first_name: Sébastien full_name: Deheuvels, Sébastien last_name: Deheuvels - first_name: Aliz full_name: Derekas, Aliz last_name: Derekas - first_name: Maria Pia full_name: Di Mauro, Maria Pia last_name: Di Mauro - first_name: Marc-Antoine full_name: Dupret, Marc-Antoine last_name: Dupret - first_name: Antonio full_name: Jiménez, Antonio last_name: Jiménez - first_name: Yveline full_name: Lebreton, Yveline last_name: Lebreton - first_name: Jaymie full_name: Matthews, Jaymie last_name: Matthews - first_name: Nicolas full_name: Nardetto, Nicolas last_name: Nardetto - first_name: Jose D. full_name: do Nascimento, Jose D. last_name: do Nascimento - first_name: Filipe full_name: Pereira, Filipe last_name: Pereira - first_name: Luisa F. full_name: Rodríguez Díaz, Luisa F. last_name: Rodríguez Díaz - first_name: Aldo M. full_name: Serenelli, Aldo M. last_name: Serenelli - first_name: Emanuele full_name: Spitoni, Emanuele last_name: Spitoni - first_name: Edita full_name: Stonkutė, Edita last_name: Stonkutė - first_name: Juan Carlos full_name: Suárez, Juan Carlos last_name: Suárez - first_name: Robert full_name: Szabó, Robert last_name: Szabó - first_name: Vincent full_name: Van Eylen, Vincent last_name: Van Eylen - first_name: Rita full_name: Ventura, Rita last_name: Ventura - first_name: Kuldeep full_name: Verma, Kuldeep last_name: Verma - first_name: Achim full_name: Weiss, Achim last_name: Weiss - first_name: Tao full_name: Wu, Tao last_name: Wu - first_name: Thomas full_name: Barclay, Thomas last_name: Barclay - first_name: Jørgen full_name: Christensen-Dalsgaard, Jørgen last_name: Christensen-Dalsgaard - first_name: Jon M. full_name: Jenkins, Jon M. last_name: Jenkins - first_name: Hans full_name: Kjeldsen, Hans last_name: Kjeldsen - first_name: George R. full_name: Ricker, George R. last_name: Ricker - first_name: Sara full_name: Seager, Sara last_name: Seager - first_name: Roland full_name: Vanderspek, Roland last_name: Vanderspek citation: ama: 'Aguirre VS, Stello D, Stokholm A, et al. Detection and characterization of oscillating red giants: First results from the TESS satellite. The Astrophysical Journal Letters. 2020;889(2). doi:10.3847/2041-8213/ab6443' apa: 'Aguirre, V. S., Stello, D., Stokholm, A., Mosumgaard, J. R., Ball, W. H., Basu, S., … Vanderspek, R. (2020). Detection and characterization of oscillating red giants: First results from the TESS satellite. The Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ab6443' chicago: 'Aguirre, Víctor Silva, Dennis Stello, Amalie Stokholm, Jakob R. Mosumgaard, Warrick H. Ball, Sarbani Basu, Diego Bossini, et al. “Detection and Characterization of Oscillating Red Giants: First Results from the TESS Satellite.” The Astrophysical Journal Letters. IOP Publishing, 2020. https://doi.org/10.3847/2041-8213/ab6443.' ieee: 'V. S. Aguirre et al., “Detection and characterization of oscillating red giants: First results from the TESS satellite,” The Astrophysical Journal Letters, vol. 889, no. 2. IOP Publishing, 2020.' ista: 'Aguirre VS, Stello D, Stokholm A, Mosumgaard JR, Ball WH, Basu S, Bossini D, Bugnet LA, Buzasi D, Campante TL, Carboneau L, Chaplin WJ, Corsaro E, Davies GR, Elsworth Y, García RA, Gaulme P, Hall OJ, Handberg R, Hon M, Kallinger T, Kang L, Lund MN, Mathur S, Mints A, Mosser B, Çelik Orhan Z, Rodrigues TS, Vrard M, Yıldız M, Zinn JC, Örtel S, Beck PG, Bell KJ, Guo Z, Jiang C, Kuszlewicz JS, Kuehn CA, Li T, Lundkvist MS, Pinsonneault M, Tayar J, Cunha MS, Hekker S, Huber D, Miglio A, F. G. Monteiro MJP, Slumstrup D, Winther ML, Angelou G, Benomar O, Bódi A, De Moura BL, Deheuvels S, Derekas A, Di Mauro MP, Dupret M-A, Jiménez A, Lebreton Y, Matthews J, Nardetto N, do Nascimento JD, Pereira F, Rodríguez Díaz LF, Serenelli AM, Spitoni E, Stonkutė E, Suárez JC, Szabó R, Van Eylen V, Ventura R, Verma K, Weiss A, Wu T, Barclay T, Christensen-Dalsgaard J, Jenkins JM, Kjeldsen H, Ricker GR, Seager S, Vanderspek R. 2020. Detection and characterization of oscillating red giants: First results from the TESS satellite. The Astrophysical Journal Letters. 889(2), L34.' mla: 'Aguirre, Víctor Silva, et al. “Detection and Characterization of Oscillating Red Giants: First Results from the TESS Satellite.” The Astrophysical Journal Letters, vol. 889, no. 2, L34, IOP Publishing, 2020, doi:10.3847/2041-8213/ab6443.' short: V.S. Aguirre, D. Stello, A. Stokholm, J.R. Mosumgaard, W.H. Ball, S. Basu, D. Bossini, L.A. Bugnet, D. Buzasi, T.L. Campante, L. Carboneau, W.J. Chaplin, E. Corsaro, G.R. Davies, Y. Elsworth, R.A. García, P. Gaulme, O.J. Hall, R. Handberg, M. Hon, T. Kallinger, L. Kang, M.N. Lund, S. Mathur, A. Mints, B. Mosser, Z. Çelik Orhan, T.S. Rodrigues, M. Vrard, M. Yıldız, J.C. Zinn, S. Örtel, P.G. Beck, K.J. Bell, Z. Guo, C. Jiang, J.S. Kuszlewicz, C.A. Kuehn, T. Li, M.S. Lundkvist, M. Pinsonneault, J. Tayar, M.S. Cunha, S. Hekker, D. Huber, A. Miglio, M.J.P. F. G. Monteiro, D. Slumstrup, M.L. Winther, G. Angelou, O. Benomar, A. Bódi, B.L. De Moura, S. Deheuvels, A. Derekas, M.P. Di Mauro, M.-A. Dupret, A. Jiménez, Y. Lebreton, J. Matthews, N. Nardetto, J.D. do Nascimento, F. Pereira, L.F. Rodríguez Díaz, A.M. Serenelli, E. Spitoni, E. Stonkutė, J.C. Suárez, R. Szabó, V. Van Eylen, R. Ventura, K. Verma, A. Weiss, T. Wu, T. Barclay, J. Christensen-Dalsgaard, J.M. Jenkins, H. Kjeldsen, G.R. Ricker, S. Seager, R. Vanderspek, The Astrophysical Journal Letters 889 (2020). date_created: 2022-07-18T13:52:54Z date_published: 2020-02-01T00:00:00Z date_updated: 2022-08-22T07:25:51Z day: '01' doi: 10.3847/2041-8213/ab6443 extern: '1' external_id: arxiv: - '1912.07604' intvolume: ' 889' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.07604 month: '02' oa: 1 oa_version: Preprint publication: The Astrophysical Journal Letters publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Detection and characterization of oscillating red giants: First results from the TESS satellite' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 889 year: '2020' ... --- _id: '11622' abstract: - lang: eng text: 'The recent discovery of low-amplitude dipolar oscillation mixed modes in massive red giants indicates the presence of a missing physical process inside their cores. Stars more massive than ∼ 1.3 M⊙ are known to develop a convective core during the main-sequence: the dynamo process triggered by this convection could be the origin of a strong magnetic field inside the core of the star, trapped when it becomes stably stratified and for the rest of its evolution. The presence of highly magnetized white dwarfs strengthens the hypothesis of buried fossil magnetic fields inside the core of evolved low-mass stars. If such a fossil field exists, it should affect the mixed modes of red giants as they are sensitive to processes affecting the deepest layers of these stars. The impact of a magnetic field on dipolar oscillations modes was one of Pr. Michael J. Thompson’s research topics during the 90s when preparing the helioseismic SoHO space mission. As the detection of gravity modes in the Sun is still controversial, the investigation of the solar oscillation modes did not provide any hint of the existence of a magnetic field in the solar radiative core. Today we have access to the core of evolved stars thanks to the asteroseismic observation of mixed modes from CoRoT, Kepler, K2 and TESS missions. The idea of applying and generalizing the work done for the Sun came from discussions with Pr. Michael Thompson in early 2018 before we lost him. Following the path we drew together, we theoretically investigate the effect of a stable axisymmetric mixed poloidal and toroidal magnetic field, aligned with the rotation axis of the star, on the mixed modes frequencies of a typical evolved low-mass star. This enables us to estimate the magnetic perturbations to the eigenfrequencies of mixed dipolar modes, depending on the magnetic field strength and the evolutionary state of the star. We conclude that strong magnetic fields of ∼ 1MG should perturb the mixed-mode frequency pattern enough for its effects to be detectable inside current asteroseismic data.' acknowledgement: The authors of this work acknowledge the support received from the PLATO CNES grant, the National Aeronautics and Space Administration under Grant NNX15AF13G, by the National Science Foundation grant AST-1411685, the Ramon y Cajal fellowship number RYC-2015-17697, the ERC SPIRE grant (647383), and the Fundation L’Oréal-Unesco-Académie des sciences. alternative_title: - Astrophysics and Space Science Proceedings article_processing_charge: No author: - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: V. full_name: Prat, V. last_name: Prat - first_name: S. full_name: Mathis, S. last_name: Mathis - first_name: R. A. full_name: García, R. A. last_name: García - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: K. full_name: Augustson, K. last_name: Augustson - first_name: C. full_name: Neiner, C. last_name: Neiner - first_name: M. J. full_name: Thompson, M. J. last_name: Thompson citation: ama: 'Bugnet LA, Prat V, Mathis S, et al. The impact of a fossil magnetic field on dipolar mixed-mode frequencies in sub- and red-giant stars. In: Monteiro M, Garcia RA, Christensen-Dalsgaard J, McIntosh SW, eds. Dynamics of the Sun and Stars. Vol 57. 1st ed. ASSSP. Cham: Springer Nature; 2020:251-257. doi:10.1007/978-3-030-55336-4_33' apa: 'Bugnet, L. A., Prat, V., Mathis, S., García, R. A., Mathur, S., Augustson, K., … Thompson, M. J. (2020). The impact of a fossil magnetic field on dipolar mixed-mode frequencies in sub- and red-giant stars. In M. Monteiro, R. A. Garcia, J. Christensen-Dalsgaard, & S. W. McIntosh (Eds.), Dynamics of the Sun and Stars (1st ed., Vol. 57, pp. 251–257). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-55336-4_33' chicago: 'Bugnet, Lisa Annabelle, V. Prat, S. Mathis, R. A. García, S. Mathur, K. Augustson, C. Neiner, and M. J. Thompson. “The Impact of a Fossil Magnetic Field on Dipolar Mixed-Mode Frequencies in Sub- and Red-Giant Stars.” In Dynamics of the Sun and Stars, edited by Mario Monteiro, Rafael A Garcia, Jorgen Christensen-Dalsgaard, and Scott W McIntosh, 1st ed., 57:251–57. ASSSP. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-55336-4_33.' ieee: 'L. A. Bugnet et al., “The impact of a fossil magnetic field on dipolar mixed-mode frequencies in sub- and red-giant stars,” in Dynamics of the Sun and Stars, 1st ed., vol. 57, M. Monteiro, R. A. Garcia, J. Christensen-Dalsgaard, and S. W. McIntosh, Eds. Cham: Springer Nature, 2020, pp. 251–257.' ista: 'Bugnet LA, Prat V, Mathis S, García RA, Mathur S, Augustson K, Neiner C, Thompson MJ. 2020.The impact of a fossil magnetic field on dipolar mixed-mode frequencies in sub- and red-giant stars. In: Dynamics of the Sun and Stars. Astrophysics and Space Science Proceedings, vol. 57, 251–257.' mla: Bugnet, Lisa Annabelle, et al. “The Impact of a Fossil Magnetic Field on Dipolar Mixed-Mode Frequencies in Sub- and Red-Giant Stars.” Dynamics of the Sun and Stars, edited by Mario Monteiro et al., 1st ed., vol. 57, Springer Nature, 2020, pp. 251–57, doi:10.1007/978-3-030-55336-4_33. short: L.A. Bugnet, V. Prat, S. Mathis, R.A. García, S. Mathur, K. Augustson, C. Neiner, M.J. Thompson, in:, M. Monteiro, R.A. Garcia, J. Christensen-Dalsgaard, S.W. McIntosh (Eds.), Dynamics of the Sun and Stars, 1st ed., Springer Nature, Cham, 2020, pp. 251–257. date_created: 2022-07-19T08:25:41Z date_published: 2020-12-19T00:00:00Z date_updated: 2022-08-22T08:07:42Z day: '19' doi: 10.1007/978-3-030-55336-4_33 edition: '1' editor: - first_name: Mario full_name: Monteiro, Mario last_name: Monteiro - first_name: Rafael A full_name: Garcia, Rafael A last_name: Garcia - first_name: Jorgen full_name: Christensen-Dalsgaard, Jorgen last_name: Christensen-Dalsgaard - first_name: Scott W full_name: McIntosh, Scott W last_name: McIntosh extern: '1' external_id: arxiv: - '2012.08684' intvolume: ' 57' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.08684 month: '12' oa: 1 oa_version: Preprint page: 251-257 place: Cham publication: Dynamics of the Sun and Stars publication_identifier: eisbn: - 978-3-030-55336-4 eissn: - 1570-6605 isbn: - 978-3-030-55335-7 issn: - 1570-6591 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: ASSSP status: public title: The impact of a fossil magnetic field on dipolar mixed-mode frequencies in sub- and red-giant stars type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2020' ... --- _id: '11675' abstract: - lang: eng text: 'We consider the problems of maintaining an approximate maximum matching and an approximate minimum vertex cover in a dynamic graph undergoing a sequence of edge insertions/deletions. Starting with the seminal work of Onak and Rubinfeld (in: Proceedings of the ACM symposium on theory of computing (STOC), 2010), this problem has received significant attention in recent years. Very recently, extending the framework of Baswana et al. (in: Proceedings of the IEEE symposium on foundations of computer science (FOCS), 2011) , Solomon (in: Proceedings of the IEEE symposium on foundations of computer science (FOCS), 2016) gave a randomized dynamic algorithm for this problem that has an approximation ratio of 2 and an amortized update time of O(1) with high probability. This algorithm requires the assumption of an oblivious adversary, meaning that the future sequence of edge insertions/deletions in the graph cannot depend in any way on the algorithm’s past output. A natural way to remove the assumption on oblivious adversary is to give a deterministic dynamic algorithm for the same problem in O(1) update time. In this paper, we resolve this question. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya et al. (in: Proceedings of the ACM-SIAM symposium on discrete algorithms (SODA), 2015); it had an approximation ratio of (2+ε) and an amortized update time of O(logn/ε2). Our result can be generalized to give a fully dynamic O(f3)-approximate algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional hypergraph matching problem, where every hyperedge has at most f vertices.' article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Deeparnab full_name: Chakrabarty, Deeparnab last_name: Chakrabarty - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: Bhattacharya S, Chakrabarty D, Henzinger MH. Deterministic dynamic matching in O(1) update time. Algorithmica. 2020;82(4):1057-1080. doi:10.1007/s00453-019-00630-4 apa: Bhattacharya, S., Chakrabarty, D., & Henzinger, M. H. (2020). Deterministic dynamic matching in O(1) update time. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-019-00630-4 chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, and Monika H Henzinger. “Deterministic Dynamic Matching in O(1) Update Time.” Algorithmica. Springer Nature, 2020. https://doi.org/10.1007/s00453-019-00630-4. ieee: S. Bhattacharya, D. Chakrabarty, and M. H. Henzinger, “Deterministic dynamic matching in O(1) update time,” Algorithmica, vol. 82, no. 4. Springer Nature, pp. 1057–1080, 2020. ista: Bhattacharya S, Chakrabarty D, Henzinger MH. 2020. Deterministic dynamic matching in O(1) update time. Algorithmica. 82(4), 1057–1080. mla: Bhattacharya, Sayan, et al. “Deterministic Dynamic Matching in O(1) Update Time.” Algorithmica, vol. 82, no. 4, Springer Nature, 2020, pp. 1057–80, doi:10.1007/s00453-019-00630-4. short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, Algorithmica 82 (2020) 1057–1080. date_created: 2022-07-27T14:31:06Z date_published: 2020-04-01T00:00:00Z date_updated: 2022-09-12T08:55:46Z day: '01' doi: 10.1007/s00453-019-00630-4 extern: '1' intvolume: ' 82' issue: '4' keyword: - Dynamic algorithms - Data structures - Graph algorithms - Matching - Vertex cover language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00453-019-00630-4 month: '04' oa: 1 oa_version: Published Version page: 1057-1080 publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Deterministic dynamic matching in O(1) update time type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2020' ... --- _id: '11674' abstract: - lang: eng text: In this paper, we study the problem of opening centers to cluster a set of clients in a metric space so as to minimize the sum of the costs of the centers and of the cluster radii, in a dynamic environment where clients arrive and depart, and the solution must be updated efficiently while remaining competitive with respect to the current optimal solution. We call this dynamic sum-of-radii clustering problem. We present a data structure that maintains a solution whose cost is within a constant factor of the cost of an optimal solution in metric spaces with bounded doubling dimension and whose worst-case update time is logarithmic in the parameters of the problem. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Dariusz full_name: Leniowski, Dariusz last_name: Leniowski - first_name: Claire full_name: Mathieu, Claire last_name: Mathieu citation: ama: Henzinger MH, Leniowski D, Mathieu C. Dynamic clustering to minimize the sum of radii. Algorithmica. 2020;82(11):3183-3194. doi:10.1007/s00453-020-00721-7 apa: Henzinger, M. H., Leniowski, D., & Mathieu, C. (2020). Dynamic clustering to minimize the sum of radii. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-020-00721-7 chicago: Henzinger, Monika H, Dariusz Leniowski, and Claire Mathieu. “Dynamic Clustering to Minimize the Sum of Radii.” Algorithmica. Springer Nature, 2020. https://doi.org/10.1007/s00453-020-00721-7. ieee: M. H. Henzinger, D. Leniowski, and C. Mathieu, “Dynamic clustering to minimize the sum of radii,” Algorithmica, vol. 82, no. 11. Springer Nature, pp. 3183–3194, 2020. ista: Henzinger MH, Leniowski D, Mathieu C. 2020. Dynamic clustering to minimize the sum of radii. Algorithmica. 82(11), 3183–3194. mla: Henzinger, Monika H., et al. “Dynamic Clustering to Minimize the Sum of Radii.” Algorithmica, vol. 82, no. 11, Springer Nature, 2020, pp. 3183–94, doi:10.1007/s00453-020-00721-7. short: M.H. Henzinger, D. Leniowski, C. Mathieu, Algorithmica 82 (2020) 3183–3194. date_created: 2022-07-27T13:58:58Z date_published: 2020-11-01T00:00:00Z date_updated: 2022-09-12T08:50:14Z day: '01' doi: 10.1007/s00453-020-00721-7 extern: '1' external_id: arxiv: - '1707.02577' intvolume: ' 82' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1707.02577 month: '11' oa: 1 oa_version: Preprint page: 3183-3194 publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering to minimize the sum of radii type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2020' ... --- _id: '11818' abstract: - lang: eng text: "With input sizes becoming massive, coresets - small yet representative summary of the input - are relevant more than ever. A weighted set C_w that is a subset of the input is an ε-coreset if the cost of any feasible solution S with respect to C_w is within [1±ε] of the cost of S with respect to the original input. We give a very general technique to compute coresets in the fully-dynamic setting where input points can be added or deleted. Given a static (i.e., not dynamic) ε-coreset-construction algorithm that runs in time t(n, ε, λ) and computes a coreset of size s(n, ε, λ), where n is the number of input points and 1-λ is the success probability, we give a fully-dynamic algorithm that computes an ε-coreset with worst-case update time O((log n) ⋅ t(s(n, ε/log n, λ/n), ε/log n, λ/n)) (this bound is stated informally), where the success probability is 1-λ. Our technique is a fully-dynamic analog of the merge-and-reduce technique, which is due to Har-Peled and Mazumdar [Har-Peled and Mazumdar, 2004] and is based on a technique of Bentley and Saxe [Jon Louis Bentley and James B. Saxe, 1980], that applies to the insertion-only setting where points can only be added. Although, our space usage is O(n), our technique works in the presence of an adaptive adversary, and we show that Ω(n) space is required when adversary is adaptive.\r\nAs a concrete implication of our technique, using the result of Braverman et al. [{Braverman} et al., 2016], we get fully-dynamic ε-coreset-construction algorithms for k-median and k-means with worst-case update time O(ε^{-2} k² log⁵ n log³ k) and coreset size O(ε^{-2} k log n log² k) ignoring log log n and log(1/ε) factors and assuming that ε = Ω(1/poly(n)) and λ = Ω(1/poly(n)) (which are very weak assumptions made only to make these bounds easy to parse). This results in the first fully-dynamic constant-approximation algorithms for k-median and k-means with update times O(poly(k, log n, ε^{-1})). Specifically, the dependence on k is only quadratic, and the bounds are worst-case. The best previous bound for both problems was amortized O(nlog n) by Cohen-Addad et al. [Cohen-Addad et al., 2019] via randomized O(1)-coresets in O(n) space.\r\nWe also show that under the OMv conjecture [Monika Henzinger et al., 2015], a fully-dynamic (4 - δ)-approximation algorithm for k-means must either have an amortized update time of Ω(k^{1-γ}) or amortized query time of Ω(k^{2 - γ}), where γ > 0 is a constant." alternative_title: - LIPIcs article_number: '57' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sagar full_name: Kale, Sagar last_name: Kale citation: ama: 'Henzinger MH, Kale S. Fully-dynamic coresets. In: 28th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.57' apa: 'Henzinger, M. H., & Kale, S. (2020). Fully-dynamic coresets. In 28th Annual European Symposium on Algorithms (Vol. 173). Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.57' chicago: Henzinger, Monika H, and Sagar Kale. “Fully-Dynamic Coresets.” In 28th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.57. ieee: M. H. Henzinger and S. Kale, “Fully-dynamic coresets,” in 28th Annual European Symposium on Algorithms, Pisa, Italy, 2020, vol. 173. ista: 'Henzinger MH, Kale S. 2020. Fully-dynamic coresets. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 57.' mla: Henzinger, Monika H., and Sagar Kale. “Fully-Dynamic Coresets.” 28th Annual European Symposium on Algorithms, vol. 173, 57, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.57. short: M.H. Henzinger, S. Kale, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-09-09 location: Pisa, Italy name: 'ESA: Annual European Symposium on Algorithms' start_date: 2020-09-07 date_created: 2022-08-12T07:22:55Z date_published: 2020-08-26T00:00:00Z date_updated: 2023-02-14T09:29:51Z day: '26' doi: 10.4230/LIPIcs.ESA.2020.57 extern: '1' external_id: arxiv: - '2004.14891' intvolume: ' 173' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2020.57 month: '08' oa: 1 oa_version: Published Version publication: 28th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959771627' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Fully-dynamic coresets type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 173 year: '2020' ... --- _id: '11816' abstract: - lang: eng text: In recent years, significant advances have been made in the design and analysis of fully dynamic maximal matching algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. In this paper, we attempt to bridge the gap between theory and practice that is currently observed for the fully dynamic maximal matching problem. We engineer several algorithms and empirically study those algorithms on an extensive set of dynamic instances. alternative_title: - LIPIcs article_number: '58' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Khan full_name: Shahbaz, Khan last_name: Shahbaz - first_name: Richard full_name: Paul, Richard last_name: Paul - first_name: Christian full_name: Schulz, Christian last_name: Schulz citation: ama: 'Henzinger MH, Shahbaz K, Paul R, Schulz C. Dynamic matching algorithms in practice. In: 8th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.58' apa: 'Henzinger, M. H., Shahbaz, K., Paul, R., & Schulz, C. (2020). Dynamic matching algorithms in practice. In 8th Annual European Symposium on Algorithms (Vol. 173). Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.58' chicago: Henzinger, Monika H, Khan Shahbaz, Richard Paul, and Christian Schulz. “Dynamic Matching Algorithms in Practice.” In 8th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.58. ieee: M. H. Henzinger, K. Shahbaz, R. Paul, and C. Schulz, “Dynamic matching algorithms in practice,” in 8th Annual European Symposium on Algorithms, Pisa, Italy, 2020, vol. 173. ista: 'Henzinger MH, Shahbaz K, Paul R, Schulz C. 2020. Dynamic matching algorithms in practice. 8th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 58.' mla: Henzinger, Monika H., et al. “Dynamic Matching Algorithms in Practice.” 8th Annual European Symposium on Algorithms, vol. 173, 58, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.58. short: M.H. Henzinger, K. Shahbaz, R. Paul, C. Schulz, in:, 8th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-09-09 location: Pisa, Italy name: 'ESA: Annual European Symposium on Algorithms' start_date: 2020-09-07 date_created: 2022-08-12T07:13:25Z date_published: 2020-08-26T00:00:00Z date_updated: 2023-02-14T08:57:55Z day: '26' doi: 10.4230/LIPIcs.ESA.2020.58 extern: '1' external_id: arxiv: - '2004.09099' intvolume: ' 173' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2020.58 month: '08' oa: 1 oa_version: Published Version publication: 8th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959771627' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Dynamic matching algorithms in practice type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 173 year: '2020' ... --- _id: '11824' abstract: - lang: eng text: "Independent set is a fundamental problem in combinatorial optimization. While in general graphs the problem is essentially inapproximable, for many important graph classes there are approximation algorithms known in the offline setting. These graph classes include interval graphs and geometric intersection graphs, where vertices correspond to intervals/geometric objects and an edge indicates that the two corresponding objects intersect.\r\nWe present dynamic approximation algorithms for independent set of intervals, hypercubes and hyperrectangles in d dimensions. They work in the fully dynamic model where each update inserts or deletes a geometric object. All our algorithms are deterministic and have worst-case update times that are polylogarithmic for constant d and ε>0, assuming that the coordinates of all input objects are in [0, N]^d and each of their edges has length at least 1. We obtain the following results:\r\n- For weighted intervals, we maintain a (1+ε)-approximate solution.\r\n- For d-dimensional hypercubes we maintain a (1+ε)2^d-approximate solution in the unweighted case and a O(2^d)-approximate solution in the weighted case. Also, we show that for maintaining an unweighted (1+ε)-approximate solution one needs polynomial update time for d ≥ 2 if the ETH holds.\r\n- For weighted d-dimensional hyperrectangles we present a dynamic algorithm with approximation ratio (1+ε)log^{d-1}N." alternative_title: - LIPIcs article_number: '51' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Stefan full_name: Neumann, Stefan last_name: Neumann - first_name: Andreas full_name: Wiese, Andreas last_name: Wiese citation: ama: 'Henzinger MH, Neumann S, Wiese A. Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles. In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.51' apa: 'Henzinger, M. H., Neumann, S., & Wiese, A. (2020). Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles. In 36th International Symposium on Computational Geometry (Vol. 164). Zurich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.51' chicago: Henzinger, Monika H, Stefan Neumann, and Andreas Wiese. “Dynamic Approximate Maximum Independent Set of Intervals, Hypercubes and Hyperrectangles.” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.51. ieee: M. H. Henzinger, S. Neumann, and A. Wiese, “Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles,” in 36th International Symposium on Computational Geometry, Zurich, Switzerland, 2020, vol. 164. ista: 'Henzinger MH, Neumann S, Wiese A. 2020. Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles. 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 51.' mla: Henzinger, Monika H., et al. “Dynamic Approximate Maximum Independent Set of Intervals, Hypercubes and Hyperrectangles.” 36th International Symposium on Computational Geometry, vol. 164, 51, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.51. short: M.H. Henzinger, S. Neumann, A. Wiese, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-06-26 location: Zurich, Switzerland name: 'SoCG: Symposium on Computational Geometry' start_date: 2020-06-23 date_created: 2022-08-12T07:46:44Z date_published: 2020-06-08T00:00:00Z date_updated: 2023-02-14T10:00:58Z day: '08' doi: 10.4230/LIPIcs.SoCG.2020.51 extern: '1' external_id: arxiv: - '2003.02605' intvolume: ' 164' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.SoCG.2020.51 month: '06' oa: 1 oa_version: Published Version publication: 36th International Symposium on Computational Geometry publication_identifier: isbn: - '9783959771436' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 164 year: '2020' ...