--- _id: '12119' abstract: - lang: eng text: Intravascular neutrophils and platelets collaborate in maintaining host integrity, but their interaction can also trigger thrombotic complications. We report here that cooperation between neutrophil and platelet lineages extends to the earliest stages of platelet formation by megakaryocytes in the bone marrow. Using intravital microscopy, we show that neutrophils “plucked” intravascular megakaryocyte extensions, termed proplatelets, to control platelet production. Following CXCR4-CXCL12-dependent migration towards perisinusoidal megakaryocytes, plucking neutrophils actively pulled on proplatelets and triggered myosin light chain and extracellular-signal-regulated kinase activation through reactive oxygen species. By these mechanisms, neutrophils accelerate proplatelet growth and facilitate continuous release of platelets in steady state. Following myocardial infarction, plucking neutrophils drove excessive release of young, reticulated platelets and boosted the risk of recurrent ischemia. Ablation of neutrophil plucking normalized thrombopoiesis and reduced recurrent thrombosis after myocardial infarction and thrombus burden in venous thrombosis. We establish neutrophil plucking as a target to reduce thromboischemic events. acknowledgement: "We thank Coung Kieu and Dominik van den Heuvel for excellent technical assistance. This work was supported by the German Research Foundation (PE2704/2-1, PE2704/3-1 to T.P., SFB 1123-project B06 to S.M., SFB1525 project A07 to D.S, TRR 332 project A7 to C.S., PO 2247/2-1 to A.P., SFB1116-project B11 to A.P. and B12 to M.K.), LMU Munich’s Institutional\r\nStrategy LMUexcellent within the framework of the German Excellence Initiative (No. 806 32 006 to T.P.), and by the German Centre for Cardiovascular Research (DZHK) to T.P. (Postdoc Start-up grant No. 100378833). 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. 833440 to S.M.). F.G. received funding from the European Union’s\r\nHorizon 2020 research and innovation program under the Marie Sk1odowska-Curie grant agreement no. 747687. A.H. was funded by RTI2018-095497-B-I00 from Ministerio de Ciencia e Innovacio´ n (MICINN), HR17_00527 from Fundacion La Caixa, and Transatlantic Network of Excellence (TNE-18CVD04) from the Leducq Foundation. The CNIC is supported by the MICINN and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (CEX2020-001041-S). A.P. was supported by the Forschungskommission of the Medical Faculty of the Heinrich-Heine-Universität Düsseldorf (No. 18-2019 to A.P.). C.G. was supported by the Helmholtz Alliance ‘Aging and Metabolic Programming, AMPro,’ by the German Federal\r\nMinistry of Education and Research to the German Center for Diabetes Research (DZD), and by the Bavarian State Ministry of Health and Care through the research project DigiMed Bayern." article_processing_charge: No article_type: original author: - first_name: Tobias full_name: Petzold, Tobias last_name: Petzold - first_name: Zhe full_name: Zhang, Zhe last_name: Zhang - first_name: Iván full_name: Ballesteros, Iván last_name: Ballesteros - first_name: Inas full_name: Saleh, Inas last_name: Saleh - first_name: Amin full_name: Polzin, Amin last_name: Polzin - first_name: Manuela full_name: Thienel, Manuela last_name: Thienel - first_name: Lulu full_name: Liu, Lulu last_name: Liu - first_name: Qurrat full_name: Ul Ain, Qurrat last_name: Ul Ain - first_name: Vincent full_name: Ehreiser, Vincent last_name: Ehreiser - first_name: Christian full_name: Weber, Christian last_name: Weber - first_name: Badr full_name: Kilani, Badr last_name: Kilani - first_name: Pontus full_name: Mertsch, Pontus last_name: Mertsch - first_name: Jeremias full_name: Götschke, Jeremias last_name: Götschke - first_name: Sophie full_name: Cremer, Sophie last_name: Cremer - first_name: Wenwen full_name: Fu, Wenwen last_name: Fu - first_name: Michael full_name: Lorenz, Michael last_name: Lorenz - first_name: Hellen full_name: Ishikawa-Ankerhold, Hellen last_name: Ishikawa-Ankerhold - first_name: Elisabeth full_name: Raatz, Elisabeth last_name: Raatz - first_name: Shaza full_name: El-Nemr, Shaza last_name: El-Nemr - first_name: Agnes full_name: Görlach, Agnes last_name: Görlach - first_name: Esther full_name: Marhuenda, Esther last_name: Marhuenda - first_name: Konstantin full_name: Stark, Konstantin last_name: Stark - first_name: Joachim full_name: Pircher, Joachim last_name: Pircher - first_name: David full_name: Stegner, David last_name: Stegner - first_name: Christian full_name: Gieger, Christian last_name: Gieger - first_name: Marc full_name: Schmidt-Supprian, Marc last_name: Schmidt-Supprian - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Isaac full_name: Almendros, Isaac last_name: Almendros - first_name: Malte full_name: Kelm, Malte last_name: Kelm - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Andrés full_name: Hidalgo, Andrés last_name: Hidalgo - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg citation: ama: Petzold T, Zhang Z, Ballesteros I, et al. Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. Immunity. 2022;55(12):2285-2299.e7. doi:10.1016/j.immuni.2022.10.001 apa: Petzold, T., Zhang, Z., Ballesteros, I., Saleh, I., Polzin, A., Thienel, M., … Massberg, S. (2022). Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2022.10.001 chicago: Petzold, Tobias, Zhe Zhang, Iván Ballesteros, Inas Saleh, Amin Polzin, Manuela Thienel, Lulu Liu, et al. “Neutrophil ‘Plucking’ on Megakaryocytes Drives Platelet Production and Boosts Cardiovascular Disease.” Immunity. Elsevier, 2022. https://doi.org/10.1016/j.immuni.2022.10.001. ieee: T. Petzold et al., “Neutrophil ‘plucking’ on megakaryocytes drives platelet production and boosts cardiovascular disease,” Immunity, vol. 55, no. 12. Elsevier, p. 2285–2299.e7, 2022. ista: Petzold T, Zhang Z, Ballesteros I, Saleh I, Polzin A, Thienel M, Liu L, Ul Ain Q, Ehreiser V, Weber C, Kilani B, Mertsch P, Götschke J, Cremer S, Fu W, Lorenz M, Ishikawa-Ankerhold H, Raatz E, El-Nemr S, Görlach A, Marhuenda E, Stark K, Pircher J, Stegner D, Gieger C, Schmidt-Supprian M, Gärtner FR, Almendros I, Kelm M, Schulz C, Hidalgo A, Massberg S. 2022. Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. Immunity. 55(12), 2285–2299.e7. mla: Petzold, Tobias, et al. “Neutrophil ‘Plucking’ on Megakaryocytes Drives Platelet Production and Boosts Cardiovascular Disease.” Immunity, vol. 55, no. 12, Elsevier, 2022, p. 2285–2299.e7, doi:10.1016/j.immuni.2022.10.001. short: T. Petzold, Z. Zhang, I. Ballesteros, I. Saleh, A. Polzin, M. Thienel, L. Liu, Q. Ul Ain, V. Ehreiser, C. Weber, B. Kilani, P. Mertsch, J. Götschke, S. Cremer, W. Fu, M. Lorenz, H. Ishikawa-Ankerhold, E. Raatz, S. El-Nemr, A. Görlach, E. Marhuenda, K. Stark, J. Pircher, D. Stegner, C. Gieger, M. Schmidt-Supprian, F.R. Gärtner, I. Almendros, M. Kelm, C. Schulz, A. Hidalgo, S. Massberg, Immunity 55 (2022) 2285–2299.e7. date_created: 2023-01-12T11:56:54Z date_published: 2022-12-13T00:00:00Z date_updated: 2025-04-14T07:43:16Z day: '13' ddc: - '570' department: - _id: MiSi doi: 10.1016/j.immuni.2022.10.001 ec_funded: 1 external_id: isi: - '000922019600003' pmid: - '36272416' file: - access_level: open_access checksum: 073267a9c0ad9f85a650053bc7b23777 content_type: application/pdf creator: dernst date_created: 2023-01-23T10:18:48Z date_updated: 2023-01-23T10:18:48Z file_id: '12341' file_name: 2022_Immunity_Petzold.pdf file_size: 5299475 relation: main_file success: 1 file_date_updated: 2023-01-23T10:18:48Z has_accepted_license: '1' intvolume: ' 55' isi: 1 issue: '12' keyword: - Infectious Diseases - Immunology - Immunology and Allergy language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 2285-2299.e7 pmid: 1 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Immunity publication_identifier: issn: - 1074-7613 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 55 year: '2022' ... --- OA_place: publisher OA_type: free access _id: '12120' abstract: - lang: eng text: Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth. acknowledgement: The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153). article_processing_charge: No article_type: original author: - first_name: Huixin full_name: Xiao, Huixin last_name: Xiao - first_name: Yumei full_name: Hu, Yumei last_name: Hu - first_name: Yaping full_name: Wang, Yaping last_name: Wang - first_name: Jinkui full_name: Cheng, Jinkui last_name: Cheng - first_name: Jinyi full_name: Wang, Jinyi last_name: Wang - first_name: Guojingwei full_name: Chen, Guojingwei last_name: Chen - first_name: Qian full_name: Li, Qian last_name: Li - first_name: Shuwei full_name: Wang, Shuwei last_name: Wang - first_name: Yalu full_name: Wang, Yalu last_name: Wang - first_name: Shao-Shuai full_name: Wang, Shao-Shuai last_name: Wang - first_name: Yi full_name: Wang, Yi last_name: Wang - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Zhen full_name: Li, Zhen last_name: Li - first_name: Yan full_name: Guo, Yan last_name: Guo - first_name: Zhizhong full_name: Gong, Zhizhong last_name: Gong - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jing full_name: Zhang, Jing last_name: Zhang citation: ama: Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 2022;57(23):2638-2651.e6. doi:10.1016/j.devcel.2022.11.006 apa: Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.11.006 chicago: Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.11.006. ieee: H. Xiao et al., “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” Developmental Cell, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022. ista: Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6. mla: Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:10.1016/j.devcel.2022.11.006. short: H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6. date_created: 2023-01-12T11:57:00Z date_published: 2022-12-05T00:00:00Z date_updated: 2025-06-25T07:29:52Z day: '05' department: - _id: JiFr doi: 10.1016/j.devcel.2022.11.006 external_id: isi: - '000919603800005' pmid: - '36473460' intvolume: ' 57' isi: 1 issue: '23' keyword: - Developmental Biology - Cell Biology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2022.11.006 month: '12' oa: 1 oa_version: Published Version page: 2638-2651.e6 pmid: 1 publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2022' ... --- _id: '12121' abstract: - lang: eng text: Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants. acknowledgement: "We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript." article_number: e202203139 article_processing_charge: No article_type: original author: - first_name: Jierui full_name: Zhao, Jierui last_name: Zhao - first_name: Mai Thu full_name: Bui, Mai Thu last_name: Bui - first_name: Juncai full_name: Ma, Juncai last_name: Ma - first_name: Fabian full_name: Künzl, Fabian last_name: Künzl - first_name: Lorenzo full_name: Picchianti, Lorenzo last_name: Picchianti - first_name: Juan Carlos full_name: De La Concepcion, Juan Carlos last_name: De La Concepcion - first_name: Yixuan full_name: Chen, Yixuan last_name: Chen - first_name: Sofia full_name: Petsangouraki, Sofia last_name: Petsangouraki - first_name: Azadeh full_name: Mohseni, Azadeh last_name: Mohseni - first_name: Marta full_name: García-Leon, Marta last_name: García-Leon - first_name: Marta Salas full_name: Gomez, Marta Salas last_name: Gomez - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Dubois full_name: Gwennogan, Dubois last_name: Gwennogan - first_name: Roksolana full_name: Kobylinska, Roksolana last_name: Kobylinska - first_name: Marion full_name: Clavel, Marion last_name: Clavel - first_name: Swen full_name: Schellmann, Swen last_name: Schellmann - first_name: Yvon full_name: Jaillais, Yvon last_name: Jaillais - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Byung-Ho full_name: Kang, Byung-Ho last_name: Kang - first_name: Yasin full_name: Dagdas, Yasin last_name: Dagdas citation: ama: Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 2022;221(12). doi:10.1083/jcb.202203139 apa: Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202203139 chicago: Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202203139. ieee: J. Zhao et al., “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” Journal of Cell Biology, vol. 221, no. 12. Rockefeller University Press, 2022. ista: Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139. mla: Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:10.1083/jcb.202203139. short: J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022). date_created: 2023-01-12T11:57:10Z date_published: 2022-12-01T00:00:00Z date_updated: 2023-08-03T14:20:15Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1083/jcb.202203139 external_id: isi: - '000932958800001' pmid: - '36260289' file: - access_level: open_access checksum: 050b5cc4b25e6b94fe3e3cbfe0f5c06b content_type: application/pdf creator: dernst date_created: 2023-01-23T10:30:11Z date_updated: 2023-01-23T10:30:11Z file_id: '12342' file_name: 2022_JCB_Zhao.pdf file_size: 10365777 relation: main_file success: 1 file_date_updated: 2023-01-23T10:30:11Z has_accepted_license: '1' intvolume: ' 221' isi: 1 issue: '12' keyword: - Cell Biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole 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: 221 year: '2022' ... --- _id: '12122' abstract: - lang: eng text: Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis. acknowledgement: "We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013." article_number: e202107134 article_processing_charge: No article_type: original author: - first_name: Ann-Kathrin full_name: Weier, Ann-Kathrin last_name: Weier - first_name: Mirka full_name: Homrich, Mirka last_name: Homrich - first_name: Stephanie full_name: Ebbinghaus, Stephanie last_name: Ebbinghaus - first_name: Pavel full_name: Juda, Pavel last_name: Juda - first_name: Eliška full_name: Miková, Eliška last_name: Miková - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Lili full_name: Zhang, Lili last_name: Zhang - first_name: Thomas full_name: Quast, Thomas last_name: Quast - first_name: Elvira full_name: Mass, Elvira last_name: Mass - first_name: Andreas full_name: Schlitzer, Andreas last_name: Schlitzer - first_name: Waldemar full_name: Kolanus, Waldemar last_name: Kolanus - first_name: Sven full_name: Burgdorf, Sven last_name: Burgdorf - first_name: Oliver J. full_name: Gruß, Oliver J. last_name: Gruß - first_name: Miroslav full_name: Hons, Miroslav last_name: Hons - first_name: Stefan full_name: Wieser, Stefan last_name: Wieser - first_name: Eva full_name: Kiermaier, Eva last_name: Kiermaier citation: ama: Weier A-K, Homrich M, Ebbinghaus S, et al. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 2022;221(12). doi:10.1083/jcb.202107134 apa: Weier, A.-K., Homrich, M., Ebbinghaus, S., Juda, P., Miková, E., Hauschild, R., … Kiermaier, E. (2022). Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202107134 chicago: Weier, Ann-Kathrin, Mirka Homrich, Stephanie Ebbinghaus, Pavel Juda, Eliška Miková, Robert Hauschild, Lili Zhang, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202107134. ieee: A.-K. Weier et al., “Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells,” Journal of Cell Biology, vol. 221, no. 12. Rockefeller University Press, 2022. ista: Weier A-K, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. 2022. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 221(12), e202107134. mla: Weier, Ann-Kathrin, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” Journal of Cell Biology, vol. 221, no. 12, e202107134, Rockefeller University Press, 2022, doi:10.1083/jcb.202107134. short: A.-K. Weier, M. Homrich, S. Ebbinghaus, P. Juda, E. Miková, R. Hauschild, L. Zhang, T. Quast, E. Mass, A. Schlitzer, W. Kolanus, S. Burgdorf, O.J. Gruß, M. Hons, S. Wieser, E. Kiermaier, Journal of Cell Biology 221 (2022). date_created: 2023-01-12T12:01:09Z date_published: 2022-12-05T00:00:00Z date_updated: 2025-04-15T08:37:41Z day: '05' ddc: - '570' department: - _id: Bio doi: 10.1083/jcb.202107134 external_id: isi: - '000932941400001' pmid: - '36214847 ' file: - access_level: open_access checksum: 0c9af38f82af30c6ce528f2caece4246 content_type: application/pdf creator: dernst date_created: 2023-08-16T11:24:53Z date_updated: 2023-08-16T11:24:53Z file_id: '14065' file_name: 2023_JCB_Weier.pdf file_size: 11090179 relation: main_file success: 1 file_date_updated: 2023-08-16T11:24:53Z has_accepted_license: '1' intvolume: ' 221' isi: 1 issue: '12' keyword: - Cell Biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473 grant_number: CZI01 name: Tools for automation and feedback microscopy publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 221 year: '2022' ... --- _id: '12128' abstract: - lang: eng text: We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness. acknowledgement: 'C P acknowledges funding from Astex through the Sustaining Innovation Program under the Milner Consortium. B C acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant EP/P020259/1. F A F acknowledges funding from the Swiss National Science Foundation (Grant No. P2BSP2_191736). ' article_number: '040501' article_processing_charge: No article_type: original author: - first_name: Carl full_name: Poelking, Carl last_name: Poelking - first_name: Felix A full_name: Faber, Felix A last_name: Faber - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: 'Poelking C, Faber FA, Cheng B. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. Machine Learning: Science and Technology. 2022;3(4). doi:10.1088/2632-2153/ac4d11' apa: 'Poelking, C., Faber, F. A., & Cheng, B. (2022). BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. Machine Learning: Science and Technology. IOP Publishing. https://doi.org/10.1088/2632-2153/ac4d11' chicago: 'Poelking, Carl, Felix A Faber, and Bingqing Cheng. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” Machine Learning: Science and Technology. IOP Publishing, 2022. https://doi.org/10.1088/2632-2153/ac4d11.' ieee: 'C. Poelking, F. A. Faber, and B. Cheng, “BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale,” Machine Learning: Science and Technology, vol. 3, no. 4. IOP Publishing, 2022.' ista: 'Poelking C, Faber FA, Cheng B. 2022. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. Machine Learning: Science and Technology. 3(4), 040501.' mla: 'Poelking, Carl, et al. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” Machine Learning: Science and Technology, vol. 3, no. 4, 040501, IOP Publishing, 2022, doi:10.1088/2632-2153/ac4d11.' short: 'C. Poelking, F.A. Faber, B. Cheng, Machine Learning: Science and Technology 3 (2022).' corr_author: '1' date_created: 2023-01-12T12:02:21Z date_published: 2022-11-17T00:00:00Z date_updated: 2024-10-09T21:03:32Z day: '17' ddc: - '000' department: - _id: BiCh doi: 10.1088/2632-2153/ac4d11 external_id: isi: - '000886534000001' file: - access_level: open_access checksum: 8930d4ad6ed9b47358c6f1a68666adb6 content_type: application/pdf creator: dernst date_created: 2023-01-23T10:42:04Z date_updated: 2023-01-23T10:42:04Z file_id: '12343' file_name: 2022_MachLearning_Poelking.pdf file_size: 13814559 relation: main_file success: 1 file_date_updated: 2023-01-23T10:42:04Z has_accepted_license: '1' intvolume: ' 3' isi: 1 issue: '4' keyword: - Artificial Intelligence - Human-Computer Interaction - Software language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: 'Machine Learning: Science and Technology' publication_identifier: issn: - 2632-2153 publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: link: - relation: software url: https://github.com/capoe/benchml scopus_import: '1' status: public title: 'BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale' 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: 3 year: '2022' ... --- _id: '12129' abstract: - lang: eng text: 'Given a finite point set P in general position in the plane, a full triangulation of P is a maximal straight-line embedded plane graph on P. A partial triangulation of P is a full triangulation of some subset P′ of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge (called edge flip), removes a non-extreme point of degree 3, or adds a point in P∖P′ as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The edge flip graph is defined with full triangulations as vertices, and edge flips determining the adjacencies. Lawson showed in the early seventies that these graphs are connected. The goal of this paper is to investigate the structure of these graphs, with emphasis on their vertex connectivity. For sets P of n points in the plane in general position, we show that the edge flip graph is ⌈n/2−2⌉-vertex connected, and the bistellar flip graph is (n−3)-vertex connected; both results are tight. The latter bound matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points to 3-space and projecting back the lower convex hull), where (n−3)-vertex connectivity has been known since the late eighties through the secondary polytope due to Gelfand, Kapranov, & Zelevinsky and Balinski’s Theorem. For the edge flip-graph, we additionally show that the vertex connectivity is at least as large as (and hence equal to) the minimum degree (i.e., the minimum number of flippable edges in any full triangulation), provided that n is large enough. Our methods also yield several other results: (i) The edge flip graph can be covered by graphs of polytopes of dimension ⌈n/2−2⌉ (products of associahedra) and the bistellar flip graph can be covered by graphs of polytopes of dimension n−3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n−3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations of a point set are regular iff the partial order of partial subdivisions has height n−3. (iv) There are arbitrarily large sets P with non-regular partial triangulations and such that every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular triangulations.' acknowledgement: "This is a full and revised version of [38] (on partial triangulations) in Proceedings of the 36th Annual International Symposium on Computational Geometry (SoCG‘20) and of some of the results in [37] (on full triangulations) in Proceedings of the 31st Annual ACM-SIAM Symposium on Discrete Algorithms (SODA‘20).\r\nThis research started at the 11th Gremo’s Workshop on Open Problems (GWOP), Alp Sellamatt, Switzerland, June 24–28, 2013, motivated by a question posed by Filip Mori´c on full triangulations. Research was supported by the Swiss National Science Foundation within the collaborative DACH project Arrangements and Drawings as SNSF Project 200021E-171681, and by IST Austria and Berlin Free University during a sabbatical stay of the second author. We thank Michael Joswig, Jesús De Loera, and Francisco Santos for helpful discussions on the topics of this paper, and Daniel Bertschinger and Valentin Stoppiello for carefully reading earlier versions and for many helpful comments.\r\nOpen access funding provided by the Swiss Federal Institute of Technology Zürich" article_processing_charge: No article_type: original author: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Emo full_name: Welzl, Emo last_name: Welzl citation: ama: Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane. Discrete & Computational Geometry. 2022;68(4):1227-1284. doi:10.1007/s00454-022-00436-2 apa: Wagner, U., & Welzl, E. (2022). Connectivity of triangulation flip graphs in the plane. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00436-2 chicago: Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” Discrete & Computational Geometry. Springer Nature, 2022. https://doi.org/10.1007/s00454-022-00436-2. ieee: U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane,” Discrete & Computational Geometry, vol. 68, no. 4. Springer Nature, pp. 1227–1284, 2022. ista: Wagner U, Welzl E. 2022. Connectivity of triangulation flip graphs in the plane. Discrete & Computational Geometry. 68(4), 1227–1284. mla: Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” Discrete & Computational Geometry, vol. 68, no. 4, Springer Nature, 2022, pp. 1227–84, doi:10.1007/s00454-022-00436-2. short: U. Wagner, E. Welzl, Discrete & Computational Geometry 68 (2022) 1227–1284. corr_author: '1' date_created: 2023-01-12T12:02:28Z date_published: 2022-11-14T00:00:00Z date_updated: 2025-07-10T11:54:56Z day: '14' ddc: - '510' department: - _id: UlWa doi: 10.1007/s00454-022-00436-2 external_id: isi: - '000883222200003' file: - access_level: open_access checksum: 307e879d09e52eddf5b225d0aaa9213a content_type: application/pdf creator: dernst date_created: 2023-01-23T11:10:03Z date_updated: 2023-01-23T11:10:03Z file_id: '12345' file_name: 2022_DiscreteCompGeometry_Wagner.pdf file_size: 1747581 relation: main_file success: 1 file_date_updated: 2023-01-23T11:10:03Z has_accepted_license: '1' intvolume: ' 68' isi: 1 issue: '4' keyword: - Computational Theory and Mathematics - Discrete Mathematics and Combinatorics - Geometry and Topology - Theoretical Computer Science language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1227-1284 publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '7807' relation: earlier_version status: public - id: '7990' relation: earlier_version status: public scopus_import: '1' status: public title: Connectivity of triangulation flip graphs in the plane 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: 68 year: '2022' ... --- _id: '12130' abstract: - lang: eng text: Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants. acknowledgement: "We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs." article_number: '6960' article_processing_charge: No article_type: original author: - first_name: Jian full_name: Huang, Jian last_name: Huang - first_name: Lei full_name: Zhao, Lei last_name: Zhao - first_name: Shikha full_name: Malik, Shikha last_name: Malik - first_name: Benjamin R. full_name: Gentile, Benjamin R. last_name: Gentile - first_name: Va full_name: Xiong, Va last_name: Xiong - first_name: Tzahi full_name: Arazi, Tzahi last_name: Arazi - first_name: Heather A. full_name: Owen, Heather A. last_name: Owen - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dazhong full_name: Zhao, Dazhong last_name: Zhao citation: ama: Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 2022;13. doi:10.1038/s41467-022-34723-6 apa: Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-34723-6 chicago: Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-34723-6. ieee: J. Huang et al., “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960. mla: Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications, vol. 13, 6960, Springer Nature, 2022, doi:10.1038/s41467-022-34723-6. short: J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022). date_created: 2023-01-12T12:02:41Z date_published: 2022-11-15T00:00:00Z date_updated: 2025-07-08T09:01:02Z day: '15' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-022-34723-6 external_id: isi: - '000884426700001' pmid: - '36379956' file: - access_level: open_access checksum: 233922a7b9507d9d48591e6799e4526e content_type: application/pdf creator: dernst date_created: 2023-01-23T11:17:33Z date_updated: 2023-01-23T11:17:33Z file_id: '12346' file_name: 2022_NatureCommunications_Huang.pdf file_size: 3375249 relation: main_file success: 1 file_date_updated: 2023-01-23T11:17:33Z has_accepted_license: '1' intvolume: ' 13' isi: 1 keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry - Multidisciplinary language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis 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: 13 year: '2022' ... --- _id: '12131' abstract: - lang: eng text: Replication-incompetent adenoviral vectors have been extensively used as a platform for vaccine design, with at least four anti-COVID-19 vaccines authorized to date. These vaccines elicit neutralizing antibody responses directed against SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2 infection. Immunization with adenovirus-vectored vaccines is known to be accompanied by the production of anti-vector antibodies, which may translate into reduced efficacy of booster or repeated rounds of revaccination. Here, we used blood samples from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address the question of whether anti-vector antibodies may influence the magnitude of SARS-CoV-2-specific humoral response after booster vaccination. We observed that rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing antibodies, which persisted in circulation for at least 9 months. Our analysis further indicates that high pre-boost Ad26 neutralizing antibody titers do not appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron, were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus, our results support the development of repeated immunization schedule with adenovirus-based COVID-19 vaccines. acknowledgement: We thank Sergey Kulemzin, Grigory Efimov, Yuri Lebedin, Alexander Taranin and Rudolf Valenta for providing reagents. Figures were created with the help of BioRender.com. This work was supported by the Russian Science Foundation (Project 21-15-00286). Byazrova M.G. was supported by the RUDN University Strategic Academic Leadership Program. article_number: '145' article_processing_charge: No article_type: original author: - first_name: Maria G. full_name: Byazrova, Maria G. last_name: Byazrova - first_name: Ekaterina A. full_name: Astakhova, Ekaterina A. last_name: Astakhova - first_name: Aygul full_name: Minnegalieva, Aygul id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E last_name: Minnegalieva - first_name: Maria M. full_name: Sukhova, Maria M. last_name: Sukhova - first_name: Artem A. full_name: Mikhailov, Artem A. last_name: Mikhailov - first_name: Alexey G. full_name: Prilipov, Alexey G. last_name: Prilipov - first_name: Andrey A. full_name: Gorchakov, Andrey A. last_name: Gorchakov - first_name: Alexander V. full_name: Filatov, Alexander V. last_name: Filatov citation: ama: Byazrova MG, Astakhova EA, Minnegalieva A, et al. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 2022;7. doi:10.1038/s41541-022-00566-x apa: Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov, A. A., Prilipov, A. G., … Filatov, A. V. (2022). Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. Npj Vaccines. Springer Nature. https://doi.org/10.1038/s41541-022-00566-x chicago: Byazrova, Maria G., Ekaterina A. Astakhova, Aygul Minnegalieva, Maria M. Sukhova, Artem A. Mikhailov, Alexey G. Prilipov, Andrey A. Gorchakov, and Alexander V. Filatov. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” Npj Vaccines. Springer Nature, 2022. https://doi.org/10.1038/s41541-022-00566-x. ieee: M. G. Byazrova et al., “Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination,” npj Vaccines, vol. 7. Springer Nature, 2022. ista: Byazrova MG, Astakhova EA, Minnegalieva A, Sukhova MM, Mikhailov AA, Prilipov AG, Gorchakov AA, Filatov AV. 2022. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 7, 145. mla: Byazrova, Maria G., et al. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” Npj Vaccines, vol. 7, 145, Springer Nature, 2022, doi:10.1038/s41541-022-00566-x. short: M.G. Byazrova, E.A. Astakhova, A. Minnegalieva, M.M. Sukhova, A.A. Mikhailov, A.G. Prilipov, A.A. Gorchakov, A.V. Filatov, Npj Vaccines 7 (2022). date_created: 2023-01-12T12:02:54Z date_published: 2022-11-15T00:00:00Z date_updated: 2023-08-04T08:52:40Z day: '15' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41541-022-00566-x external_id: isi: - '000884278600004' pmid: - '36379998' file: - access_level: open_access checksum: ddaac096381565b2b4b7dcc34cdbc4ee content_type: application/pdf creator: dernst date_created: 2023-01-23T11:22:09Z date_updated: 2023-01-23T11:22:09Z file_id: '12347' file_name: 2022_njpVaccines_Byazrova.pdf file_size: 1856046 relation: main_file success: 1 file_date_updated: 2023-01-23T11:22:09Z has_accepted_license: '1' intvolume: ' 7' isi: 1 keyword: - Pharmacology (medical) - Infectious Diseases - Pharmacology - Immunology - SARS-COV-2 - COVID language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: npj Vaccines publication_identifier: issn: - 2059-0105 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination 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: 7 year: '2022' ... --- _id: '12133' abstract: - lang: eng text: Social distancing is an effective way to prevent the spread of disease in societies, whereas infection elimination is a key element of organismal immunity. Here, we discuss how the study of social insects such as ants — which form a superorganism of unconditionally cooperative individuals and thus represent a level of organization that is intermediate between a classical society of individuals and an organism of cells — can help to determine common principles of disease defence across levels of organization. article_processing_charge: No article_type: letter_note author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Cremer S, Sixt MK. Principles of disease defence in organisms, superorganisms and societies. Nature Reviews Immunology. 2022;22(12):713-714. doi:10.1038/s41577-022-00797-y apa: Cremer, S., & Sixt, M. K. (2022). Principles of disease defence in organisms, superorganisms and societies. Nature Reviews Immunology. Springer Nature. https://doi.org/10.1038/s41577-022-00797-y chicago: Cremer, Sylvia, and Michael K Sixt. “Principles of Disease Defence in Organisms, Superorganisms and Societies.” Nature Reviews Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41577-022-00797-y. ieee: S. Cremer and M. K. Sixt, “Principles of disease defence in organisms, superorganisms and societies,” Nature Reviews Immunology, vol. 22, no. 12. Springer Nature, pp. 713–714, 2022. ista: Cremer S, Sixt MK. 2022. Principles of disease defence in organisms, superorganisms and societies. Nature Reviews Immunology. 22(12), 713–714. mla: Cremer, Sylvia, and Michael K. Sixt. “Principles of Disease Defence in Organisms, Superorganisms and Societies.” Nature Reviews Immunology, vol. 22, no. 12, Springer Nature, 2022, pp. 713–14, doi:10.1038/s41577-022-00797-y. short: S. Cremer, M.K. Sixt, Nature Reviews Immunology 22 (2022) 713–714. corr_author: '1' date_created: 2023-01-12T12:03:14Z date_published: 2022-12-01T00:00:00Z date_updated: 2024-10-09T21:03:33Z day: '01' department: - _id: SyCr - _id: MiSi doi: 10.1038/s41577-022-00797-y external_id: isi: - '000871836300001' pmid: - '36284178' intvolume: ' 22' isi: 1 issue: '12' keyword: - Energy Engineering and Power Technology - Fuel Technology language: - iso: eng month: '12' oa_version: None page: 713-714 pmid: 1 publication: Nature Reviews Immunology publication_identifier: eissn: - 1474-1741 issn: - 1474-1733 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Principles of disease defence in organisms, superorganisms and societies type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2022' ... --- _id: '12134' abstract: - lang: eng text: Standard epidemic models exhibit one continuous, second order phase transition to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally alter epidemic dynamics. Here we reveal how such interventions modify the type of phase transition. In particular, we uncover three distinct types of explosive phase transitions for epidemic dynamics with capacity-limited interventions. Depending on the capacity limit, interventions may (i) leave the standard second order phase transition unchanged but exponentially suppress the probability of large outbreaks, (ii) induce a first-order discontinuous transition to macroscopic outbreaks, or (iii) cause a secondary explosive yet continuous third-order transition. These insights highlight inherent limitations in predicting and containing epidemic outbreaks. More generally our study offers a cornerstone example of a third-order explosive phase transition in complex systems. acknowledgement: We acknowledge support from the Volkswagen Foundation under Grant No. 99720 and the German Federal Ministry for Education and Research (BMBF) under Grant No. 16ICR01. This research was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2068—390729961—Cluster of Excellence Physics of Life of TU Dresden. article_number: 04LT02 article_processing_charge: No article_type: original author: - first_name: Georg full_name: Börner, Georg last_name: Börner - first_name: Malte full_name: Schröder, Malte last_name: Schröder - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Marc full_name: Timme, Marc last_name: Timme citation: ama: 'Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. Explosive transitions in epidemic dynamics. Journal of Physics: Complexity. 2022;3(4). doi:10.1088/2632-072x/ac99cd' apa: 'Börner, G., Schröder, M., Scarselli, D., Budanur, N. B., Hof, B., & Timme, M. (2022). Explosive transitions in epidemic dynamics. Journal of Physics: Complexity. IOP Publishing. https://doi.org/10.1088/2632-072x/ac99cd' chicago: 'Börner, Georg, Malte Schröder, Davide Scarselli, Nazmi B Budanur, Björn Hof, and Marc Timme. “Explosive Transitions in Epidemic Dynamics.” Journal of Physics: Complexity. IOP Publishing, 2022. https://doi.org/10.1088/2632-072x/ac99cd.' ieee: 'G. Börner, M. Schröder, D. Scarselli, N. B. Budanur, B. Hof, and M. Timme, “Explosive transitions in epidemic dynamics,” Journal of Physics: Complexity, vol. 3, no. 4. IOP Publishing, 2022.' ista: 'Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. 2022. Explosive transitions in epidemic dynamics. Journal of Physics: Complexity. 3(4), 04LT02.' mla: 'Börner, Georg, et al. “Explosive Transitions in Epidemic Dynamics.” Journal of Physics: Complexity, vol. 3, no. 4, 04LT02, IOP Publishing, 2022, doi:10.1088/2632-072x/ac99cd.' short: 'G. Börner, M. Schröder, D. Scarselli, N.B. Budanur, B. Hof, M. Timme, Journal of Physics: Complexity 3 (2022).' date_created: 2023-01-12T12:03:43Z date_published: 2022-10-25T00:00:00Z date_updated: 2023-02-13T09:15:13Z day: '25' ddc: - '530' department: - _id: BjHo doi: 10.1088/2632-072x/ac99cd file: - access_level: open_access checksum: 35c5c5cb0eb17ea1b5184755daab9fc9 content_type: application/pdf creator: dernst date_created: 2023-01-24T07:24:37Z date_updated: 2023-01-24T07:24:37Z file_id: '12350' file_name: 2022_JourPhysics_Boerner.pdf file_size: 1006106 relation: main_file success: 1 file_date_updated: 2023-01-24T07:24:37Z has_accepted_license: '1' intvolume: ' 3' issue: '4' keyword: - Artificial Intelligence - Computer Networks and Communications - Computer Science Applications - Information Systems language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: 'Journal of Physics: Complexity' publication_identifier: issn: - 2632-072X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Explosive transitions in epidemic dynamics 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: 3 year: '2022' ... --- _id: '12135' abstract: - lang: eng text: A good match of material appearance between real-world objects and their digital on-screen representations is critical for many applications such as fabrication, design, and e-commerce. However, faithful appearance reproduction is challenging, especially for complex phenomena, such as gloss. In most cases, the view-dependent nature of gloss and the range of luminance values required for reproducing glossy materials exceeds the current capabilities of display devices. As a result, appearance reproduction poses significant problems even with accurately rendered images. This paper studies the gap between the gloss perceived from real-world objects and their digital counterparts. Based on our psychophysical experiments on a wide range of 3D printed samples and their corresponding photographs, we derive insights on the influence of geometry, illumination, and the display’s brightness and measure the change in gloss appearance due to the display limitations. Our evaluation experiments demonstrate that using the prediction to correct material parameters in a rendering system improves the match of gloss appearance between real objects and their visualization on a display device. acknowledgement: This work is supported by FWF Lise Meitner (Grant M 3319), European Research Council (project CHAMELEON, Grant no. 682080), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta. article_number: '35' article_processing_charge: No author: - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Hans-Peter full_name: Seidel, Hans-Peter last_name: Seidel - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Ana full_name: Serrano, Ana last_name: Serrano citation: ama: 'Chen B, Piovarci M, Wang C, et al. Gloss management for consistent reproduction of real and virtual objects. In: SIGGRAPH Asia 2022 Conference Papers. Vol 2022. Association for Computing Machinery; 2022. doi:10.1145/3550469.3555406' apa: 'Chen, B., Piovarci, M., Wang, C., Seidel, H.-P., Didyk, P., Myszkowski, K., & Serrano, A. (2022). Gloss management for consistent reproduction of real and virtual objects. In SIGGRAPH Asia 2022 Conference Papers (Vol. 2022). Daegu, South Korea: Association for Computing Machinery. https://doi.org/10.1145/3550469.3555406' chicago: Chen, Bin, Michael Piovarci, Chao Wang, Hans-Peter Seidel, Piotr Didyk, Karol Myszkowski, and Ana Serrano. “Gloss Management for Consistent Reproduction of Real and Virtual Objects.” In SIGGRAPH Asia 2022 Conference Papers, Vol. 2022. Association for Computing Machinery, 2022. https://doi.org/10.1145/3550469.3555406. ieee: B. Chen et al., “Gloss management for consistent reproduction of real and virtual objects,” in SIGGRAPH Asia 2022 Conference Papers, Daegu, South Korea, 2022, vol. 2022. ista: 'Chen B, Piovarci M, Wang C, Seidel H-P, Didyk P, Myszkowski K, Serrano A. 2022. Gloss management for consistent reproduction of real and virtual objects. SIGGRAPH Asia 2022 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference vol. 2022, 35.' mla: Chen, Bin, et al. “Gloss Management for Consistent Reproduction of Real and Virtual Objects.” SIGGRAPH Asia 2022 Conference Papers, vol. 2022, 35, Association for Computing Machinery, 2022, doi:10.1145/3550469.3555406. short: B. Chen, M. Piovarci, C. Wang, H.-P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, in:, SIGGRAPH Asia 2022 Conference Papers, Association for Computing Machinery, 2022. conference: end_date: 2022-12-09 location: Daegu, South Korea name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2022-12-06 date_created: 2023-01-12T12:03:56Z date_published: 2022-11-01T00:00:00Z date_updated: 2025-09-10T09:47:32Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1145/3550469.3555406 external_id: isi: - '001074614400031' file: - access_level: open_access checksum: f47f3215ab8bb919e3546b3438c34c21 content_type: application/pdf creator: dernst date_created: 2023-01-24T07:35:21Z date_updated: 2023-01-24T07:35:21Z file_id: '12351' file_name: 2022_ACM_SIGGRAPH_Chen.pdf file_size: 28826826 relation: main_file success: 1 file_date_updated: 2023-01-24T07:35:21Z has_accepted_license: '1' intvolume: ' 2022' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: SIGGRAPH Asia 2022 Conference Papers publication_identifier: isbn: - '9781450394703' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Gloss management for consistent reproduction of real and virtual objects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 2022 year: '2022' ... --- _id: '12137' abstract: - lang: eng text: We investigate the local self-sustained process underlying spiral turbulence in counter-rotating Taylor–Couette flow using a periodic annular domain, shaped as a parallelogram, two of whose sides are aligned with the cylindrical helix described by the spiral pattern. The primary focus of the study is placed on the emergence of drifting–rotating waves (DRW) that capture, in a relatively small domain, the main features of coherent structures typically observed in developed turbulence. The transitional dynamics of the subcritical region, far below the first instability of the laminar circular Couette flow, is determined by the upper and lower branches of DRW solutions originated at saddle-node bifurcations. The mechanism whereby these solutions self-sustain, and the chaotic dynamics they induce, are conspicuously reminiscent of other subcritical shear flows. Remarkably, the flow properties of DRW persist even as the Reynolds number is increased beyond the linear stability threshold of the base flow. Simulations in a narrow parallelogram domain stretched in the azimuthal direction to revolve around the apparatus a full turn confirm that self-sustained vortices eventually concentrate into a localised pattern. The resulting statistical steady state satisfactorily reproduces qualitatively, and to a certain degree also quantitatively, the topology and properties of spiral turbulence as calculated in a large periodic domain of sufficient aspect ratio that is representative of the real system. acknowledgement: "K.D.’s research was supported by an Australian Research Council Discovery Early Career\r\nResearcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitivdad (grant numbers FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant number PID2020-114043GB-I00) and the Generalitat de Catalunya (grant 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152)." article_number: A21 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: B. full_name: Wang, B. last_name: Wang - first_name: Roger full_name: Ayats López, Roger id: ab77522d-073b-11ed-8aff-e71b39258362 last_name: Ayats López orcid: 0000-0001-6572-0621 - first_name: K. full_name: Deguchi, K. last_name: Deguchi - first_name: F. full_name: Mellibovsky, F. last_name: Mellibovsky - first_name: A. full_name: Meseguer, A. last_name: Meseguer citation: ama: Wang B, Ayats López R, Deguchi K, Mellibovsky F, Meseguer A. Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow. Journal of Fluid Mechanics. 2022;951. doi:10.1017/jfm.2022.828 apa: Wang, B., Ayats López, R., Deguchi, K., Mellibovsky, F., & Meseguer, A. (2022). Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.828 chicago: Wang, B., Roger Ayats López, K. Deguchi, F. Mellibovsky, and A. Meseguer. “Self-Sustainment of Coherent Structures in Counter-Rotating Taylor–Couette Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2022. https://doi.org/10.1017/jfm.2022.828. ieee: B. Wang, R. Ayats López, K. Deguchi, F. Mellibovsky, and A. Meseguer, “Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow,” Journal of Fluid Mechanics, vol. 951. Cambridge University Press, 2022. ista: Wang B, Ayats López R, Deguchi K, Mellibovsky F, Meseguer A. 2022. Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow. Journal of Fluid Mechanics. 951, A21. mla: Wang, B., et al. “Self-Sustainment of Coherent Structures in Counter-Rotating Taylor–Couette Flow.” Journal of Fluid Mechanics, vol. 951, A21, Cambridge University Press, 2022, doi:10.1017/jfm.2022.828. short: B. Wang, R. Ayats López, K. Deguchi, F. Mellibovsky, A. Meseguer, Journal of Fluid Mechanics 951 (2022). date_created: 2023-01-12T12:04:17Z date_published: 2022-11-07T00:00:00Z date_updated: 2023-08-04T08:54:16Z day: '07' department: - _id: BjHo doi: 10.1017/jfm.2022.828 external_id: arxiv: - '2207.12990' isi: - '000879446900001' intvolume: ' 951' isi: 1 keyword: - Mechanical Engineering - Mechanics of Materials - Condensed Matter Physics - Applied Mathematics language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2207.12990' month: '11' oa: 1 oa_version: Preprint publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 951 year: '2022' ... --- _id: '12139' abstract: - lang: eng text: We demonstrate the formation of robust zero-energy modes close to magnetic impurities in the iron-based superconductor FeSe1-z Tez. We find that the Zeeman field generated by the impurity favors a spin-triplet interorbital pairing as opposed to the spin-singlet intraorbital pairing prevalent in the bulk. The preferred spin-triplet pairing preserves time-reversal symmetry and is topological, as robust, topologically protected zero modes emerge at the boundary between regions with different pairing states. Moreover, the zero modes form Kramers doublets that are insensitive to the direction of the spin polarization or to the separation between impurities. We argue that our theoretical results are consistent with recent experimental measurements on FeSe1-z Tez. acknowledgement: "We thank Armin Rahmani, Andrey V. Chubukov, Jay D. Sau and Ruixing Zhang for fruitful discussions. AK and PG are supported by NSF-DMR2037996. PG also acknowledges support from NSF-DMR1824265. RMF was supported by the U. S. Department of Energy, Office\r\nof Science, Basic Energy Sciences, Materials Sciences and Engineering Division, under Award No. DE-SC0020045. Part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation grant PHY-1607611. " article_number: L201107 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Ammar full_name: Kirmani, Ammar last_name: Kirmani - first_name: Rafael M. full_name: Fernandes, Rafael M. last_name: Fernandes - first_name: Pouyan full_name: Ghaemi, Pouyan last_name: Ghaemi citation: ama: Ghazaryan A, Kirmani A, Fernandes RM, Ghaemi P. Anomalous Shiba states in topological iron-based superconductors. Physical Review B. 2022;106(20). doi:10.1103/physrevb.106.l201107 apa: Ghazaryan, A., Kirmani, A., Fernandes, R. M., & Ghaemi, P. (2022). Anomalous Shiba states in topological iron-based superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.106.l201107 chicago: Ghazaryan, Areg, Ammar Kirmani, Rafael M. Fernandes, and Pouyan Ghaemi. “Anomalous Shiba States in Topological Iron-Based Superconductors.” Physical Review B. American Physical Society, 2022. https://doi.org/10.1103/physrevb.106.l201107. ieee: A. Ghazaryan, A. Kirmani, R. M. Fernandes, and P. Ghaemi, “Anomalous Shiba states in topological iron-based superconductors,” Physical Review B, vol. 106, no. 20. American Physical Society, 2022. ista: Ghazaryan A, Kirmani A, Fernandes RM, Ghaemi P. 2022. Anomalous Shiba states in topological iron-based superconductors. Physical Review B. 106(20), L201107. mla: Ghazaryan, Areg, et al. “Anomalous Shiba States in Topological Iron-Based Superconductors.” Physical Review B, vol. 106, no. 20, L201107, American Physical Society, 2022, doi:10.1103/physrevb.106.l201107. short: A. Ghazaryan, A. Kirmani, R.M. Fernandes, P. Ghaemi, Physical Review B 106 (2022). date_created: 2023-01-12T12:04:43Z date_published: 2022-11-15T00:00:00Z date_updated: 2023-08-04T08:55:31Z day: '15' department: - _id: MiLe doi: 10.1103/physrevb.106.l201107 external_id: arxiv: - '2207.12425' isi: - '000893171800001' intvolume: ' 106' isi: 1 issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2207.12425' month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Anomalous Shiba states in topological iron-based superconductors type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 106 year: '2022' ... --- _id: '12140' abstract: - lang: eng text: Microglia are dynamic cells, constantly surveying their surroundings and interacting with neurons and synapses. Indeed, a wealth of knowledge has revealed a critical role of microglia in modulating synaptic transmission and plasticity in the developing brain. In the past decade, novel pharmacological and genetic strategies have allowed the acute removal of microglia, opening the possibility to explore and understand the role of microglia also in the adult brain. In this review, we summarized and discussed the contribution of microglia depletion strategies to the current understanding of the role of microglia on synaptic function, learning and memory, and behavior both in physiological and pathological conditions. We first described the available microglia depletion methods highlighting their main strengths and weaknesses. We then reviewed the impact of microglia depletion on structural and functional synaptic plasticity. Next, we focused our analysis on the effects of microglia depletion on behavior, including general locomotor activity, sensory perception, motor function, sociability, learning and memory both in healthy animals and animal models of disease. Finally, we integrated the findings from the reviewed studies and discussed the emerging roles of microglia on the maintenance of synaptic function, learning, memory strength and forgetfulness, and the implications of microglia depletion in models of brain disease. acknowledgement: "The write-up of the review was supported by Sapienza University of Rome (Fondi di Ateneo, grant numbers #MA32117A7B698029 and #PH12017270934C3C to SD), Regione Lazio (POR FSE 2014/20, grant number #19036AP000000019 to SD), Fulbright 2019 (grant number\r\n#FSP-P005556 to SD), Institute Pasteur Italia (Fondi Cenci Bolognetti #363 to DR), and Network of European Funding for Neuroscience Research (ERA-NET NEURON Transnational\r\nResearch Projects on Neurodevelopmental Disorders 2021, grant acronym #JTC2021-SHANKAstro to DR)." article_number: '1022431' article_processing_charge: No article_type: original author: - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Laura full_name: Ferrucci, Laura last_name: Ferrucci - first_name: Azka full_name: Khan, Azka last_name: Khan - first_name: Silvia full_name: Di Angelantonio, Silvia last_name: Di Angelantonio - first_name: Davide full_name: Ragozzino, Davide last_name: Ragozzino - first_name: Ingrid full_name: Reverte, Ingrid last_name: Reverte citation: ama: Basilico B, Ferrucci L, Khan A, Di Angelantonio S, Ragozzino D, Reverte I. What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior. Frontiers in Cellular Neuroscience. 2022;16. doi:10.3389/fncel.2022.1022431 apa: Basilico, B., Ferrucci, L., Khan, A., Di Angelantonio, S., Ragozzino, D., & Reverte, I. (2022). What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2022.1022431 chicago: Basilico, Bernadette, Laura Ferrucci, Azka Khan, Silvia Di Angelantonio, Davide Ragozzino, and Ingrid Reverte. “What Microglia Depletion Approaches Tell Us about the Role of Microglia on Synaptic Function and Behavior.” Frontiers in Cellular Neuroscience. Frontiers Media, 2022. https://doi.org/10.3389/fncel.2022.1022431. ieee: B. Basilico, L. Ferrucci, A. Khan, S. Di Angelantonio, D. Ragozzino, and I. Reverte, “What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior,” Frontiers in Cellular Neuroscience, vol. 16. Frontiers Media, 2022. ista: Basilico B, Ferrucci L, Khan A, Di Angelantonio S, Ragozzino D, Reverte I. 2022. What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior. Frontiers in Cellular Neuroscience. 16, 1022431. mla: Basilico, Bernadette, et al. “What Microglia Depletion Approaches Tell Us about the Role of Microglia on Synaptic Function and Behavior.” Frontiers in Cellular Neuroscience, vol. 16, 1022431, Frontiers Media, 2022, doi:10.3389/fncel.2022.1022431. short: B. Basilico, L. Ferrucci, A. Khan, S. Di Angelantonio, D. Ragozzino, I. Reverte, Frontiers in Cellular Neuroscience 16 (2022). date_created: 2023-01-12T12:04:50Z date_published: 2022-11-04T00:00:00Z date_updated: 2023-08-04T08:56:10Z day: '04' ddc: - '570' department: - _id: GaNo doi: 10.3389/fncel.2022.1022431 external_id: isi: - '000886526600001' pmid: - '36406752' file: - access_level: open_access checksum: 84696213ecf99182c58a9f34b9ff2e23 content_type: application/pdf creator: dernst date_created: 2023-01-24T09:16:29Z date_updated: 2023-01-24T09:16:29Z file_id: '12352' file_name: 2022_FrontiersNeuroscience_Basilico.pdf file_size: 6399987 relation: main_file success: 1 file_date_updated: 2023-01-24T09:16:29Z has_accepted_license: '1' intvolume: ' 16' isi: 1 keyword: - Cellular and Molecular Neuroscience language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Cellular Neuroscience publication_identifier: issn: - 1662-5102 publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior 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: 16 year: '2022' ... --- _id: '12142' abstract: - lang: eng text: Theory for liability-scale models of the underlying genetic basis of complex disease provides an important way to interpret, compare, and understand results generated from biological studies. In particular, through estimation of the liability-scale heritability (LSH), liability models facilitate an understanding and comparison of the relative importance of genetic and environmental risk factors that shape different clinically important disease outcomes. Increasingly, large-scale biobank studies that link genetic information to electronic health records, containing hundreds of disease diagnosis indicators that mostly occur infrequently within the sample, are becoming available. Here, we propose an extension of the existing liability-scale model theory suitable for estimating LSH in biobank studies of low-prevalence disease. In a simulation study, we find that our derived expression yields lower mean square error (MSE) and is less sensitive to prevalence misspecification as compared to previous transformations for diseases with =< 2% population prevalence and LSH of =< 0.45, especially if the biobank sample prevalence is less than that of the wider population. Applying our expression to 13 diagnostic outcomes of =< 3% prevalence in the UK Biobank study revealed important differences in LSH obtained from the different theoretical expressions that impact the conclusions made when comparing LSH across disease outcomes. This demonstrates the importance of careful consideration for estimation and prediction of low-prevalence disease outcomes and facilitates improved inference of the underlying genetic basis of =< 2% population prevalence diseases, especially where biobank sample ascertainment results in a healthier sample population. acknowledged_ssus: - _id: ScienComp acknowledgement: This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181), core funding from the Institute of Science and Technology Austria, and core funding from the Department of Computational Biology of the University of Lausanne. Z.K. was funded by the Swiss National Science Foundation (310030-189147). This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp). We would like to thank the participants of the UK Biobank. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sven E. full_name: Ojavee, Sven E. last_name: Ojavee - first_name: Zoltan full_name: Kutalik, Zoltan last_name: Kutalik - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Ojavee SE, Kutalik Z, Robinson MR. Liability-scale heritability estimation for biobank studies of low-prevalence disease. The American Journal of Human Genetics. 2022;109(11):2009-2017. doi:10.1016/j.ajhg.2022.09.011 apa: Ojavee, S. E., Kutalik, Z., & Robinson, M. R. (2022). Liability-scale heritability estimation for biobank studies of low-prevalence disease. The American Journal of Human Genetics. Elsevier. https://doi.org/10.1016/j.ajhg.2022.09.011 chicago: Ojavee, Sven E., Zoltan Kutalik, and Matthew Richard Robinson. “Liability-Scale Heritability Estimation for Biobank Studies of Low-Prevalence Disease.” The American Journal of Human Genetics. Elsevier, 2022. https://doi.org/10.1016/j.ajhg.2022.09.011. ieee: S. E. Ojavee, Z. Kutalik, and M. R. Robinson, “Liability-scale heritability estimation for biobank studies of low-prevalence disease,” The American Journal of Human Genetics, vol. 109, no. 11. Elsevier, pp. 2009–2017, 2022. ista: Ojavee SE, Kutalik Z, Robinson MR. 2022. Liability-scale heritability estimation for biobank studies of low-prevalence disease. The American Journal of Human Genetics. 109(11), 2009–2017. mla: Ojavee, Sven E., et al. “Liability-Scale Heritability Estimation for Biobank Studies of Low-Prevalence Disease.” The American Journal of Human Genetics, vol. 109, no. 11, Elsevier, 2022, pp. 2009–17, doi:10.1016/j.ajhg.2022.09.011. short: S.E. Ojavee, Z. Kutalik, M.R. Robinson, The American Journal of Human Genetics 109 (2022) 2009–2017. corr_author: '1' date_created: 2023-01-12T12:05:28Z date_published: 2022-11-03T00:00:00Z date_updated: 2025-06-11T13:55:19Z day: '03' ddc: - '570' department: - _id: MaRo doi: 10.1016/j.ajhg.2022.09.011 external_id: isi: - '000898683500006' pmid: - '36265482' file: - access_level: open_access checksum: 4cd7f12bfe21a8237bb095eedfa26361 content_type: application/pdf creator: dernst date_created: 2023-01-24T09:23:01Z date_updated: 2023-01-24T09:23:01Z file_id: '12353' file_name: 2022_AJHG_Ojavee.pdf file_size: 705195 relation: main_file success: 1 file_date_updated: 2023-01-24T09:23:01Z has_accepted_license: '1' intvolume: ' 109' isi: 1 issue: '11' keyword: - Genetics (clinical) - Genetics language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 2009-2017 pmid: 1 project: - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication: The American Journal of Human Genetics publication_identifier: issn: - 0002-9297 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Liability-scale heritability estimation for biobank studies of low-prevalence 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2022' ... --- _id: '12143' abstract: - lang: eng text: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways. acknowledged_ssus: - _id: EM-Fac acknowledgement: We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants. article_processing_charge: No article_type: original author: - first_name: David full_name: Zapletal, David last_name: Zapletal - first_name: Eliska full_name: Taborska, Eliska last_name: Taborska - first_name: Josef full_name: Pasulka, Josef last_name: Pasulka - first_name: Radek full_name: Malik, Radek last_name: Malik - first_name: Karel full_name: Kubicek, Karel last_name: Kubicek - first_name: Martina full_name: Zanova, Martina last_name: Zanova - first_name: Christian full_name: Much, Christian last_name: Much - first_name: Marek full_name: Sebesta, Marek last_name: Sebesta - first_name: Valeria full_name: Buccheri, Valeria last_name: Buccheri - first_name: Filip full_name: Horvat, Filip last_name: Horvat - first_name: Irena full_name: Jenickova, Irena last_name: Jenickova - first_name: Michaela full_name: Prochazkova, Michaela last_name: Prochazkova - first_name: Jan full_name: Prochazka, Jan last_name: Prochazka - first_name: Matyas full_name: Pinkas, Matyas last_name: Pinkas - first_name: Jiri full_name: Novacek, Jiri last_name: Novacek - first_name: Diego F. full_name: Joseph, Diego F. last_name: Joseph - first_name: Radislav full_name: Sedlacek, Radislav last_name: Sedlacek - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Dónal full_name: O’Carroll, Dónal last_name: O’Carroll - first_name: Richard full_name: Stefl, Richard last_name: Stefl - first_name: Petr full_name: Svoboda, Petr last_name: Svoboda citation: ama: Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 2022;82(21):4064-4079.e13. doi:10.1016/j.molcel.2022.10.010 apa: Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2022.10.010 chicago: Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” Molecular Cell. Elsevier, 2022. https://doi.org/10.1016/j.molcel.2022.10.010. ieee: D. Zapletal et al., “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” Molecular Cell, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022. ista: Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13. mla: Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” Molecular Cell, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:10.1016/j.molcel.2022.10.010. short: D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13. date_created: 2023-01-12T12:05:36Z date_published: 2022-11-03T00:00:00Z date_updated: 2023-08-04T08:57:17Z day: '03' ddc: - '570' department: - _id: CaBe doi: 10.1016/j.molcel.2022.10.010 external_id: isi: - '000898565300011' pmid: - '36332606' file: - access_level: open_access checksum: 999e443b54e4fdaa2542ca5a97619731 content_type: application/pdf creator: dernst date_created: 2023-01-24T09:29:02Z date_updated: 2023-01-24T09:29:02Z file_id: '12354' file_name: 2022_MolecularCell_Zapletal.pdf file_size: 7368534 relation: main_file success: 1 file_date_updated: 2023-01-24T09:29:02Z has_accepted_license: '1' intvolume: ' 82' isi: 1 issue: '21' keyword: - Cell Biology - Molecular Biology language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 4064-4079.e13 pmid: 1 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Structural and functional basis of mammalian microRNA biogenesis by Dicer 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: 82 year: '2022' ... --- _id: '12144' abstract: - lang: eng text: The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1. article_processing_charge: No article_type: original author: - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Mateusz full_name: Kwiatkowski, Mateusz last_name: Kwiatkowski - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Scott A full_name: Sinclair, Scott A id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87 last_name: Sinclair orcid: 0000-0002-4566-0593 - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Charo I. full_name: del Genio, Charo I. last_name: del Genio - first_name: Martin F. full_name: Kubeš, Martin F. last_name: Kubeš - first_name: Richard full_name: Napier, Richard last_name: Napier - first_name: Krzysztof full_name: Jaworski, Krzysztof last_name: Jaworski - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 2022;611(7934):133-138. doi:10.1038/s41586-022-05369-7 apa: Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05369-7 chicago: Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05369-7. ieee: L. Qi et al., “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” Nature, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022. ista: Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138. mla: Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:10.1038/s41586-022-05369-7. short: L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138. corr_author: '1' date_created: 2023-01-12T12:06:05Z date_published: 2022-11-03T00:00:00Z date_updated: 2025-04-14T07:45:02Z day: '03' department: - _id: JiFr doi: 10.1038/s41586-022-05369-7 ec_funded: 1 external_id: isi: - '000875061600013' pmid: - '36289340' intvolume: ' 611' isi: 1 issue: '7934' language: - iso: eng main_file_link: - open_access: '1' url: http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf month: '11' oa: 1 oa_version: Submitted Version page: 133-138 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 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: Adenylate cyclase activity of TIR1/AFB auxin receptors in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 611 year: '2022' ... --- _id: '12145' abstract: - lang: eng text: In the class of strictly convex smooth boundaries each of which has no strip around its boundary foliated by invariant curves, we prove that the Taylor coefficients of the “normalized” Mather’s β-function are invariant under C∞-conjugacies. In contrast, we prove that any two elliptic billiard maps are C0-conjugate near their respective boundaries, and C∞-conjugate, near the boundary and away from a line passing through the center of the underlying ellipse. We also prove that, if the billiard maps corresponding to two ellipses are topologically conjugate, then the two ellipses are similar. acknowledgement: "We are grateful to the anonymous referees for their careful reading and valuable remarks and\r\ncomments which helped to improve the paper significantly. We gratefully acknowledge support from the European Research Council (ERC) through the Advanced Grant “SPERIG” (#885707)." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Edmond full_name: Koudjinan, Edmond id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E last_name: Koudjinan orcid: 0000-0003-2640-4049 - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Koudjinan E, Kaloshin V. On some invariants of Birkhoff billiards under conjugacy. Regular and Chaotic Dynamics. 2022;27(6):525-537. doi:10.1134/S1560354722050021 apa: Koudjinan, E., & Kaloshin, V. (2022). On some invariants of Birkhoff billiards under conjugacy. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/S1560354722050021 chicago: Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff Billiards under Conjugacy.” Regular and Chaotic Dynamics. Springer Nature, 2022. https://doi.org/10.1134/S1560354722050021. ieee: E. Koudjinan and V. Kaloshin, “On some invariants of Birkhoff billiards under conjugacy,” Regular and Chaotic Dynamics, vol. 27, no. 6. Springer Nature, pp. 525–537, 2022. ista: Koudjinan E, Kaloshin V. 2022. On some invariants of Birkhoff billiards under conjugacy. Regular and Chaotic Dynamics. 27(6), 525–537. mla: Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff Billiards under Conjugacy.” Regular and Chaotic Dynamics, vol. 27, no. 6, Springer Nature, 2022, pp. 525–37, doi:10.1134/S1560354722050021. short: E. Koudjinan, V. Kaloshin, Regular and Chaotic Dynamics 27 (2022) 525–537. corr_author: '1' date_created: 2023-01-12T12:06:49Z date_published: 2022-10-03T00:00:00Z date_updated: 2025-04-14T07:53:45Z day: '03' department: - _id: VaKa doi: 10.1134/S1560354722050021 ec_funded: 1 external_id: arxiv: - '2105.14640' isi: - '000865267300002' intvolume: ' 27' isi: 1 issue: '6' keyword: - Mechanical Engineering - Applied Mathematics - Mathematical Physics - Modeling and Simulation - Statistical and Nonlinear Physics - Mathematics (miscellaneous) language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2105.14640 month: '10' oa: 1 oa_version: Preprint page: 525-537 project: - _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '885707' name: Spectral rigidity and integrability for billiards and geodesic flows publication: Regular and Chaotic Dynamics publication_identifier: eissn: - 1468-4845 issn: - 1560-3547 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1134/s1560354722060107 scopus_import: '1' status: public title: On some invariants of Birkhoff billiards under conjugacy type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2022' ... --- _id: '12146' abstract: - lang: eng text: 'In this paper, we explore the stability and dynamical relevance of a wide variety of steady, time-periodic, quasiperiodic, and chaotic flows arising between orthogonally stretching parallel plates. We first explore the stability of all the steady flow solution families formerly identified by Ayats et al. [“Flows between orthogonally stretching parallel plates,” Phys. Fluids 33, 024103 (2021)], concluding that only the one that originates from the Stokesian approximation is actually stable. When both plates are shrinking at identical or nearly the same deceleration rates, this Stokesian flow exhibits a Hopf bifurcation that leads to stable time-periodic regimes. The resulting time-periodic orbits or flows are tracked for different Reynolds numbers and stretching rates while monitoring their Floquet exponents to identify secondary instabilities. It is found that these time-periodic flows also exhibit Neimark–Sacker bifurcations, generating stable quasiperiodic flows (tori) that may sometimes give rise to chaotic dynamics through a Ruelle–Takens–Newhouse scenario. However, chaotic dynamics is unusually observed, as the quasiperiodic flows generally become phase-locked through a resonance mechanism before a strange attractor may arise, thus restoring the time-periodicity of the flow. In this work, we have identified and tracked four different resonance regions, also known as Arnold tongues or horns. In particular, the 1 : 4 strong resonance region is explored in great detail, where the identified scenarios are in very good agreement with normal form theory. ' acknowledgement: "This work was supported by the Spanish MINECO under Grant Nos. FIS2017-85794-P and PRX18/00179, the Spanish MICINN through Grant No. PID2020-114043GB-I00, and the\r\nGeneralitat de Catalunya under Grant No. 2017-SGR-785. B.W.’s research was also supported by the Chinese Scholarship Council through Grant CSC No. 201806440152." article_number: '114111' article_processing_charge: No article_type: original author: - first_name: B. full_name: Wang, B. last_name: Wang - first_name: Roger full_name: Ayats López, Roger id: ab77522d-073b-11ed-8aff-e71b39258362 last_name: Ayats López orcid: 0000-0001-6572-0621 - first_name: A. full_name: Meseguer, A. last_name: Meseguer - first_name: F. full_name: Marques, F. last_name: Marques citation: ama: Wang B, Ayats López R, Meseguer A, Marques F. Phase-locking flows between orthogonally stretching parallel plates. Physics of Fluids. 2022;34(11). doi:10.1063/5.0124152 apa: Wang, B., Ayats López, R., Meseguer, A., & Marques, F. (2022). Phase-locking flows between orthogonally stretching parallel plates. Physics of Fluids. AIP Publishing. https://doi.org/10.1063/5.0124152 chicago: Wang, B., Roger Ayats López, A. Meseguer, and F. Marques. “Phase-Locking Flows between Orthogonally Stretching Parallel Plates.” Physics of Fluids. AIP Publishing, 2022. https://doi.org/10.1063/5.0124152. ieee: B. Wang, R. Ayats López, A. Meseguer, and F. Marques, “Phase-locking flows between orthogonally stretching parallel plates,” Physics of Fluids, vol. 34, no. 11. AIP Publishing, 2022. ista: Wang B, Ayats López R, Meseguer A, Marques F. 2022. Phase-locking flows between orthogonally stretching parallel plates. Physics of Fluids. 34(11), 114111. mla: Wang, B., et al. “Phase-Locking Flows between Orthogonally Stretching Parallel Plates.” Physics of Fluids, vol. 34, no. 11, 114111, AIP Publishing, 2022, doi:10.1063/5.0124152. short: B. Wang, R. Ayats López, A. Meseguer, F. Marques, Physics of Fluids 34 (2022). date_created: 2023-01-12T12:06:58Z date_published: 2022-11-04T00:00:00Z date_updated: 2023-10-03T11:07:58Z day: '04' department: - _id: BjHo doi: 10.1063/5.0124152 external_id: isi: - '000880665300024' intvolume: ' 34' isi: 1 issue: '11' keyword: - Condensed Matter Physics - Fluid Flow and Transfer Processes - Mechanics of Materials - Computational Mechanics - Mechanical Engineering language: - iso: eng main_file_link: - open_access: '1' url: https://upcommons.upc.edu/handle/2117/385635 month: '11' oa: 1 oa_version: Submitted Version publication: Physics of Fluids publication_identifier: eissn: - 1089-7666 issn: - 1070-6631 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Phase-locking flows between orthogonally stretching parallel plates type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2022' ... --- _id: '12147' abstract: - lang: eng text: Continuous-time neural networks are a class of machine learning systems that can tackle representation learning on spatiotemporal decision-making tasks. These models are typically represented by continuous differential equations. However, their expressive power when they are deployed on computers is bottlenecked by numerical differential equation solvers. This limitation has notably slowed down the scaling and understanding of numerous natural physical phenomena such as the dynamics of nervous systems. Ideally, we would circumvent this bottleneck by solving the given dynamical system in closed form. This is known to be intractable in general. Here, we show that it is possible to closely approximate the interaction between neurons and synapses—the building blocks of natural and artificial neural networks—constructed by liquid time-constant networks efficiently in closed form. To this end, we compute a tightly bounded approximation of the solution of an integral appearing in liquid time-constant dynamics that has had no known closed-form solution so far. This closed-form solution impacts the design of continuous-time and continuous-depth neural models. For instance, since time appears explicitly in closed form, the formulation relaxes the need for complex numerical solvers. Consequently, we obtain models that are between one and five orders of magnitude faster in training and inference compared with differential equation-based counterparts. More importantly, in contrast to ordinary differential equation-based continuous networks, closed-form networks can scale remarkably well compared with other deep learning instances. Lastly, as these models are derived from liquid networks, they show good performance in time-series modelling compared with advanced recurrent neural network models. acknowledgement: This research was supported in part by the AI2050 program at Schmidt Futures (grant G-22-63172), the Boeing Company, and the United States Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under cooperative agreement number FA8750-19-2-1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes, notwithstanding any copyright notation herein. This work was further supported by The Boeing Company and Office of Naval Research grant N00014-18-1-2830. M.T. is supported by the Poul Due Jensen Foundation, grant 883901. M.L. was supported in part by the Austrian Science Fund under grant Z211-N23 (Wittgenstein Award). A.A. was supported by the National Science Foundation Graduate Research Fellowship Program. We thank T.-H. Wang, P. Kao, M. Chahine, W. Xiao, X. Li, L. Yin and Y. Ben for useful suggestions and for testing of CfC models to confirm the results across other domains. article_processing_charge: No article_type: original arxiv: 1 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: Lucas full_name: Liebenwein, Lucas last_name: Liebenwein - first_name: Aaron full_name: Ray, Aaron last_name: Ray - first_name: Max full_name: Tschaikowski, Max last_name: Tschaikowski - first_name: Gerald full_name: Teschl, Gerald last_name: Teschl - first_name: Daniela full_name: Rus, Daniela last_name: Rus citation: ama: Hasani R, Lechner M, Amini A, et al. Closed-form continuous-time neural networks. Nature Machine Intelligence. 2022;4(11):992-1003. doi:10.1038/s42256-022-00556-7 apa: Hasani, R., Lechner, M., Amini, A., Liebenwein, L., Ray, A., Tschaikowski, M., … Rus, D. (2022). Closed-form continuous-time neural networks. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-022-00556-7 chicago: Hasani, Ramin, Mathias Lechner, Alexander Amini, Lucas Liebenwein, Aaron Ray, Max Tschaikowski, Gerald Teschl, and Daniela Rus. “Closed-Form Continuous-Time Neural Networks.” Nature Machine Intelligence. Springer Nature, 2022. https://doi.org/10.1038/s42256-022-00556-7. ieee: R. Hasani et al., “Closed-form continuous-time neural networks,” Nature Machine Intelligence, vol. 4, no. 11. Springer Nature, pp. 992–1003, 2022. ista: Hasani R, Lechner M, Amini A, Liebenwein L, Ray A, Tschaikowski M, Teschl G, Rus D. 2022. Closed-form continuous-time neural networks. Nature Machine Intelligence. 4(11), 992–1003. mla: Hasani, Ramin, et al. “Closed-Form Continuous-Time Neural Networks.” Nature Machine Intelligence, vol. 4, no. 11, Springer Nature, 2022, pp. 992–1003, doi:10.1038/s42256-022-00556-7. short: R. Hasani, M. Lechner, A. Amini, L. Liebenwein, A. Ray, M. Tschaikowski, G. Teschl, D. Rus, Nature Machine Intelligence 4 (2022) 992–1003. date_created: 2023-01-12T12:07:21Z date_published: 2022-11-15T00:00:00Z date_updated: 2025-04-15T06:26:02Z day: '15' ddc: - '000' department: - _id: ToHe doi: 10.1038/s42256-022-00556-7 external_id: arxiv: - '2106.13898' isi: - '000884215600003' file: - access_level: open_access checksum: b4789122ce04bfb4ac042390f59aaa8b content_type: application/pdf creator: dernst date_created: 2023-01-24T09:49:44Z date_updated: 2023-01-24T09:49:44Z file_id: '12355' file_name: 2022_NatureMachineIntelligence_Hasani.pdf file_size: 3259553 relation: main_file success: 1 file_date_updated: 2023-01-24T09:49:44Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '11' keyword: - Artificial Intelligence - Computer Networks and Communications - Computer Vision and Pattern Recognition - Human-Computer Interaction - Software language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 992-1003 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems publication: Nature Machine Intelligence publication_identifier: issn: - 2522-5839 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s42256-022-00597-y scopus_import: '1' status: public title: Closed-form continuous-time neural networks 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: 4 year: '2022' ...